scMuscle2_metadata_v1-0.csv

source.label,sample,description,tissue,subtissue,suspension_type,sex,genotype,sort.markers,comments,include,ambient.decon,species,GSE.accession,GSM.accession,chemistry,file.format,SRR.accession,file.link,experiment.accession,study.accession,sample.accession,SAMN.accession,file.checksum,other.accession,source,manuscript.doi,manuscript.pubmed,experiment.instrument,study.title,study.abstract
Yang J 2022,Single-cell sedentary standard (chow) diet rep1 [SC1.scWAT],NA,adipose,white adipose tissue,NA,NA,NA,NA,NA,FALSE,TRUE,Mus musculus,GSE183288,GSM5554964,3p_v3,fastq,SRR15702753;SRR15702754,NA,SRX11998640,NA,NA,SRX11998640,NA,NA,NA,NA,NA,NA,NA,NA
Yang J 2022,Single-cell sedentary standard (chow) diet rep2 [SC2.scWAT],NA,adipose,white adipose tissue,NA,NA,NA,NA,NA,FALSE,TRUE,Mus musculus,GSE183288,GSM5554965,3p_v3,fastq,SRR15702755;SRR15702756,NA,SRX11998641,NA,NA,SRX11998641,NA,NA,NA,NA,NA,NA,NA,NA
Yang J 2022,Single-cell sedentary standard (chow) diet rep3 [SC3.scWAT],NA,adipose,white adipose tissue,NA,NA,NA,NA,NA,FALSE,TRUE,Mus musculus,GSE183288,GSM5554966,3p_v3,fastq,SRR15702757;SRR15702758,NA,SRX11998642,NA,NA,SRX11998642,NA,NA,NA,NA,NA,NA,NA,NA
Yang J 2022,Single-cell training standard (chow) diet rep1 [TC1.scWAT],NA,adipose,white adipose tissue,NA,NA,NA,NA,NA,FALSE,TRUE,Mus musculus,GSE183288,GSM5554967,3p_v3,fastq,SRR15702759;SRR15702760,NA,SRX11998643,NA,NA,SRX11998643,NA,NA,NA,NA,NA,NA,NA,NA
Yang J 2022,Single-cell training standard (chow) diet rep2 [TC2.scWAT],NA,adipose,white adipose tissue,NA,NA,NA,NA,NA,FALSE,TRUE,Mus musculus,GSE183288,GSM5554968,3p_v3,fastq,SRR15702761;SRR15702762,NA,SRX11998644,NA,NA,SRX11998644,NA,NA,NA,NA,NA,NA,NA,NA
Yang J 2022,Single-cell training standard (chow) diet rep3 [TC3.scWAT],NA,adipose,white adipose tissue,NA,NA,NA,NA,NA,FALSE,TRUE,Mus musculus,GSE183288,GSM5554969,3p_v3,fastq,SRR15702763;SRR15702764,NA,SRX11998645,NA,NA,SRX11998645,NA,NA,NA,NA,NA,NA,NA,NA
Yang J 2022,Single-cell training standard (chow) diet rep4 [TC4.scWAT],NA,adipose,white adipose tissue,NA,NA,NA,NA,NA,FALSE,TRUE,Mus musculus,GSE183288,GSM5554970,3p_v3,fastq,SRR15702765;SRR15702766,NA,SRX11998646,NA,NA,SRX11998646,NA,NA,NA,NA,NA,NA,NA,NA
Yang J 2022,Single-cell sedentary high-fat diet rep1 [SH1.scWAT],NA,adipose,white adipose tissue,NA,NA,NA,NA,NA,FALSE,TRUE,Mus musculus,GSE183288,GSM5554971,3p_v3,fastq,SRR15702767;SRR15702768,NA,SRX11998647,NA,NA,SRX11998647,NA,NA,NA,NA,NA,NA,NA,NA
Yang J 2022,Single-cell sedentary high-fat diet rep2 [SH2.scWAT],NA,adipose,white adipose tissue,NA,NA,NA,NA,NA,FALSE,TRUE,Mus musculus,GSE183288,GSM5554972,3p_v3,fastq,SRR15702769;SRR15702770,NA,SRX11998648,NA,NA,SRX11998648,NA,NA,NA,NA,NA,NA,NA,NA
Yang J 2022,Single-cell sedentary high-fat diet rep3 [SH3.scWAT],NA,adipose,white adipose tissue,NA,NA,NA,NA,NA,FALSE,TRUE,Mus musculus,GSE183288,GSM5554973,3p_v3,fastq,SRR15702771;SRR15702772,NA,SRX11998649,NA,NA,SRX11998649,NA,NA,NA,NA,NA,NA,NA,NA
Yang J 2022,Single-cell training high-fat diet rep1 [TH1.scWAT],NA,adipose,white adipose tissue,NA,NA,NA,NA,NA,FALSE,TRUE,Mus musculus,GSE183288,GSM5554974,3p_v3,fastq,SRR15702773;SRR15702774,NA,SRX11998650,NA,NA,SRX11998650,NA,NA,NA,NA,NA,NA,NA,NA
Yang J 2022,Single-cell training high-fat diet rep2 [TH2.scWAT],NA,adipose,white adipose tissue,NA,NA,NA,NA,NA,FALSE,TRUE,Mus musculus,GSE183288,GSM5554975,3p_v3,fastq,SRR15702775;SRR15702776,NA,SRX11998651,NA,NA,SRX11998651,NA,NA,NA,NA,NA,NA,NA,NA
Yang J 2022,Single-cell training high-fat diet rep3 [TH3.scWAT],NA,adipose,white adipose tissue,NA,NA,NA,NA,NA,FALSE,TRUE,Mus musculus,GSE183288,GSM5554976,3p_v3,fastq,SRR15702777;SRR15702778,NA,SRX11998652,NA,NA,SRX11998652,NA,NA,NA,NA,NA,NA,NA,NA
Yang J 2022,Single-cell training high-fat diet rep4 [TH4.scWAT],NA,adipose,white adipose tissue,NA,NA,NA,NA,NA,FALSE,TRUE,Mus musculus,GSE183288,GSM5554977,3p_v3,fastq,SRR15702779;SRR15702780,NA,SRX11998653,NA,NA,SRX11998653,NA,NA,NA,NA,NA,NA,NA,NA
Yang J 2022,Single-cell sedentary standard (chow) diet rep1 [SC1.vWAT],NA,adipose,white adipose tissue,NA,NA,NA,NA,NA,FALSE,TRUE,Mus musculus,GSE183288,GSM5554978,3p_v3,fastq,SRR15702781;SRR15702782,NA,SRX11998654,NA,NA,SRX11998654,NA,NA,NA,NA,NA,NA,NA,NA
Yang J 2022,Single-cell sedentary standard (chow) diet rep2 [SC2.vWAT],NA,adipose,white adipose tissue,NA,NA,NA,NA,NA,FALSE,TRUE,Mus musculus,GSE183288,GSM5554979,3p_v3,fastq,SRR15702783;SRR15702784,NA,SRX11998655,NA,NA,SRX11998655,NA,NA,NA,NA,NA,NA,NA,NA
Yang J 2022,Single-cell sedentary standard (chow) diet rep3 [SC3.vWAT],NA,adipose,white adipose tissue,NA,NA,NA,NA,NA,FALSE,TRUE,Mus musculus,GSE183288,GSM5554980,3p_v3,fastq,SRR15702785;SRR15702786,NA,SRX11998656,NA,NA,SRX11998656,NA,NA,NA,NA,NA,NA,NA,NA
Yang J 2022,Single-cell training standard (chow) diet rep1 [TC1.vWAT],NA,adipose,white adipose tissue,NA,NA,NA,NA,NA,FALSE,TRUE,Mus musculus,GSE183288,GSM5554981,3p_v3,fastq,SRR15702787;SRR15702788,NA,SRX11998657,NA,NA,SRX11998657,NA,NA,NA,NA,NA,NA,NA,NA
Yang J 2022,Single-cell training standard (chow) diet rep2 [TC2.vWAT],NA,adipose,white adipose tissue,NA,NA,NA,NA,NA,FALSE,TRUE,Mus musculus,GSE183288,GSM5554982,3p_v3,fastq,SRR15702789;SRR15702790,NA,SRX11998658,NA,NA,SRX11998658,NA,NA,NA,NA,NA,NA,NA,NA
Yang J 2022,Single-cell training standard (chow) diet rep3 [TC3.vWAT],NA,adipose,white adipose tissue,NA,NA,NA,NA,NA,FALSE,TRUE,Mus musculus,GSE183288,GSM5554983,3p_v3,fastq,SRR15702791;SRR15702792,NA,SRX11998659,NA,NA,SRX11998659,NA,NA,NA,NA,NA,NA,NA,NA
Yang J 2022,Single-cell training standard (chow) diet rep4 [TC4.vWAT ],NA,adipose,white adipose tissue,NA,NA,NA,NA,NA,FALSE,TRUE,Mus musculus,GSE183288,GSM5554984,3p_v3,fastq,SRR15702793;SRR15702794,NA,SRX11998660,NA,NA,SRX11998660,NA,NA,NA,NA,NA,NA,NA,NA
Yang J 2022,Single-cell sedentary high-fat diet rep1 [SH1.vWAT],NA,adipose,white adipose tissue,NA,NA,NA,NA,NA,FALSE,TRUE,Mus musculus,GSE183288,GSM5554985,3p_v3,fastq,SRR15702795;SRR15702796,NA,SRX11998661,NA,NA,SRX11998661,NA,NA,NA,NA,NA,NA,NA,NA
Yang J 2022,Single-cell sedentary high-fat diet rep2 [SH2.vWAT],NA,adipose,white adipose tissue,NA,NA,NA,NA,NA,FALSE,TRUE,Mus musculus,GSE183288,GSM5554986,3p_v3,fastq,SRR15702797;SRR15702798,NA,SRX11998662,NA,NA,SRX11998662,NA,NA,NA,NA,NA,NA,NA,NA
Yang J 2022,Single-cell sedentary high-fat diet rep3 [SH3.vWAT],NA,adipose,white adipose tissue,NA,NA,NA,NA,NA,FALSE,TRUE,Mus musculus,GSE183288,GSM5554987,3p_v3,fastq,SRR15702799;SRR15702800,NA,SRX11998663,NA,NA,SRX11998663,NA,NA,NA,NA,NA,NA,NA,NA
Yang J 2022,Single-cell training high-fat diet rep1 [TH1.vWAT],NA,adipose,white adipose tissue,NA,NA,NA,NA,NA,FALSE,TRUE,Mus musculus,GSE183288,GSM5554988,3p_v3,fastq,SRR15702801;SRR15702802,NA,SRX11998664,NA,NA,SRX11998664,NA,NA,NA,NA,NA,NA,NA,NA
Yang J 2022,Single-cell training high-fat diet rep2 [TH2.vWAT],NA,adipose,white adipose tissue,NA,NA,NA,NA,NA,FALSE,TRUE,Mus musculus,GSE183288,GSM5554989,3p_v3,fastq,SRR15702803;SRR15702804,NA,SRX11998665,NA,NA,SRX11998665,NA,NA,NA,NA,NA,NA,NA,NA
Yang J 2022,Single-cell training high-fat diet rep3 [TH3.vWAT],NA,adipose,white adipose tissue,NA,NA,NA,NA,NA,FALSE,TRUE,Mus musculus,GSE183288,GSM5554990,3p_v3,fastq,SRR15702805;SRR15702806,NA,SRX11998666,NA,NA,SRX11998666,NA,NA,NA,NA,NA,NA,NA,NA
Yang J 2022,Single-cell training high-fat diet rep4 [TH4.vWAT],NA,adipose,white adipose tissue,NA,NA,NA,NA,NA,FALSE,TRUE,Mus musculus,GSE183288,GSM5554991,3p_v3,fastq,SRR15702807;SRR15702808,NA,SRX11998667,NA,NA,SRX11998667,NA,NA,NA,NA,NA,NA,NA,NA
Kulkarni 2022,Old_adipose_1,NA,adipose,stromal vascular fraction,NA,NA,NA,NA,NA,FALSE,TRUE,Mus musculus,GSE194386,GSM5834904,3p_v2,fastq,SRR17747991,NA,SRX13910429,NA,NA,SAMN25247583,NA,NA,NA,NA,NA,NA,NA,NA
Kulkarni 2022,Old_adipose_2,NA,adipose,stromal vascular fraction,NA,NA,NA,NA,NA,FALSE,TRUE,Mus musculus,GSE194386,GSM5834906,3p_v2,fastq,SRR17747989,NA,SRX13910431,NA,NA,SAMN25247581,NA,NA,NA,NA,NA,NA,NA,NA
Kulkarni 2022,Old_adipose_3,NA,adipose,stromal vascular fraction,NA,NA,NA,NA,NA,FALSE,TRUE,Mus musculus,GSE194386,GSM5834908,3p_v2,fastq,SRR17747987,NA,SRX13910433,NA,NA,SAMN25247579,NA,NA,NA,NA,NA,NA,NA,NA
Kulkarni 2022,Old_adipose_4,NA,adipose,stromal vascular fraction,NA,NA,NA,NA,NA,FALSE,TRUE,Mus musculus,GSE194386,GSM5834910,3p_v2,fastq,SRR17747985,NA,SRX13910435,NA,NA,SAMN25247577,NA,NA,NA,NA,NA,NA,NA,NA
Kulkarni 2022,Metformin-treated_adipose_1,NA,adipose,stromal vascular fraction,NA,NA,NA,NA,NA,FALSE,TRUE,Mus musculus,GSE194386,GSM5834912,3p_v2,fastq,SRR17747983,NA,SRX13910437,NA,NA,SAMN25247575,NA,NA,NA,NA,NA,NA,NA,NA
Kulkarni 2022,Metformin-treated_adipose_2,NA,adipose,stromal vascular fraction,NA,NA,NA,NA,NA,FALSE,TRUE,Mus musculus,GSE194386,GSM5834914,3p_v2,fastq,SRR17747981,NA,SRX13910439,NA,NA,SAMN25247573,NA,NA,NA,NA,NA,NA,NA,NA
Kulkarni 2022,Metformin-treated_adipose_3,NA,adipose,stromal vascular fraction,NA,NA,NA,NA,NA,FALSE,TRUE,Mus musculus,GSE194386,GSM5834916,3p_v2,fastq,SRR17747979,NA,SRX13910441,NA,NA,SAMN25247571,NA,NA,NA,NA,NA,NA,NA,NA
Kulkarni 2022,Metformin-treated_adipose_4,NA,adipose,stromal vascular fraction,NA,NA,NA,NA,NA,FALSE,TRUE,Mus musculus,GSE194386,GSM5834918,3p_v2,fastq,SRR17747977,NA,SRX13910443,NA,NA,SAMN25247569,NA,NA,NA,NA,NA,NA,NA,NA
Kulkarni 2022,Young_adipose_1,NA,adipose,stromal vascular fraction,NA,NA,NA,NA,NA,FALSE,TRUE,Mus musculus,GSE194386,GSM5834920,3p_v2,fastq,SRR17747975,NA,SRX13910445,NA,NA,SAMN25247567,NA,NA,NA,NA,NA,NA,NA,NA
Kulkarni 2022,Young_adipose_2,NA,adipose,stromal vascular fraction,NA,NA,NA,NA,NA,FALSE,TRUE,Mus musculus,GSE194386,GSM5834922,3p_v2,fastq,SRR17747973,NA,SRX13910447,NA,NA,SAMN25247565,NA,NA,NA,NA,NA,NA,NA,NA
Kulkarni 2022,Young_adipose_3,NA,adipose,stromal vascular fraction,NA,NA,NA,NA,NA,FALSE,TRUE,Mus musculus,GSE194386,GSM5834924,3p_v2,fastq,SRR17747971,NA,SRX13910449,NA,NA,SAMN25247563,NA,NA,NA,NA,NA,NA,NA,NA
Kulkarni 2022,Young_adipose_4,NA,adipose,stromal vascular fraction,NA,NA,NA,NA,NA,FALSE,TRUE,Mus musculus,GSE194386,GSM5834926,3p_v2,fastq,SRR17747969,NA,SRX13910451,NA,NA,SAMN25247561,NA,NA,NA,NA,NA,NA,NA,NA
Wang R 2021,control group,NA,bone,NA,NA,NA,NA,NA,rhapsody,FALSE,TRUE,Mus musculus,GSE132884,GSM3895612,rhapsody,fastq,SRR9317818,NA,SRX6085362,NA,NA,SAMN12084343,NA,NA,NA,NA,NA,NA,NA,NA
Wang R 2021,third day,NA,bone,NA,NA,NA,NA,NA,rhapsody,FALSE,TRUE,Mus musculus,GSE132884,GSM3895613,rhapsody,fastq,SRR9317819,NA,SRX6085363,NA,NA,SAMN12084342,NA,NA,NA,NA,NA,NA,NA,NA
Wang R 2021,seventh day,NA,bone,NA,NA,NA,NA,NA,rhapsody,FALSE,TRUE,Mus musculus,GSE132884,GSM3895614,rhapsody,fastq,SRR9317820,NA,SRX6085364,NA,NA,SAMN12084341,NA,NA,NA,NA,NA,NA,NA,NA
Wang R 2021,14th day,NA,bone,NA,NA,NA,NA,NA,rhapsody,FALSE,TRUE,Mus musculus,GSE132884,GSM3895615,rhapsody,fastq,SRR9317821,NA,SRX6085365,NA,NA,SAMN12084340,NA,NA,NA,NA,NA,NA,NA,NA
X Fu 2020,control veh,NA,bone,NA,NA,NA,NA,NA,Non-cellranger format,FALSE,TRUE,Mus musculus,GSE150291,GSM4546352,3p_v3,bam,SRR11770269,NA,SRX8323506,SRP261116,SRS6642821,SAMN14888343,NA,NA,"X Fu et al, Signal Transduct Target Ther, 2020",NA,https://pubmed.ncbi.nlm.nih.gov/33361757/,Illumina NovaSeq 6000,Kindlin-2 modulates PTH1R to regulate bone mass and PTH actions in bone,"To investigation the role of PTH and Kindlin-2 in bone development, we performed single-cell RNA-sequencing. From Con-veh, Con-PTH, cKO-veh, cKO-PTH, we profiled more than 20k single cells, including multi-potent mesenchymal stromal cells (MSC), osteoprogenitors, osteoblasts, chondrocytes, fibroblasts, endothelial cells, smooth muscle cells, skeletal muscle cells, pericytes, and schwann cells. We found proportion of part of these cells were significant altered by PTH or Kindlin-2 loss, especially for MSC, osteoblast, chondrocyte, and fibroblast. Transcriptomic analysis revealed gene expression was dramatically regulated by PTH or Kindlin-2 loss. Overall design: 3-month-old Kindlin-2f/f (control, n=6) and Dmp1-Cre; Kindlin-2f/f  (cKO, n=6) mice were treated with or without PTH daily continuously for 28d. Mice were sacrificed after the last PTH injection. Non-hematopoietic cells from bone marrow were extracted for single-cell RNA-sequencing"
X Fu 2020,control PTH,NA,bone,NA,NA,NA,NA,NA,Non-cellranger format,FALSE,TRUE,Mus musculus,GSE150291,GSM4546353,3p_v3,bam,SRR11770270,NA,SRX8323507,SRP261116,SRS6642824,SAMN14888342,NA,NA,"X Fu et al, Signal Transduct Target Ther, 2020",NA,https://pubmed.ncbi.nlm.nih.gov/33361757/,Illumina NovaSeq 6000,Kindlin-2 modulates PTH1R to regulate bone mass and PTH actions in bone,"To investigation the role of PTH and Kindlin-2 in bone development, we performed single-cell RNA-sequencing. From Con-veh, Con-PTH, cKO-veh, cKO-PTH, we profiled more than 20k single cells, including multi-potent mesenchymal stromal cells (MSC), osteoprogenitors, osteoblasts, chondrocytes, fibroblasts, endothelial cells, smooth muscle cells, skeletal muscle cells, pericytes, and schwann cells. We found proportion of part of these cells were significant altered by PTH or Kindlin-2 loss, especially for MSC, osteoblast, chondrocyte, and fibroblast. Transcriptomic analysis revealed gene expression was dramatically regulated by PTH or Kindlin-2 loss. Overall design: 3-month-old Kindlin-2f/f (control, n=6) and Dmp1-Cre; Kindlin-2f/f  (cKO, n=6) mice were treated with or without PTH daily continuously for 28d. Mice were sacrificed after the last PTH injection. Non-hematopoietic cells from bone marrow were extracted for single-cell RNA-sequencing"
X Fu 2020,cKO veh,NA,bone,NA,NA,NA,NA,NA,Non-cellranger format,FALSE,TRUE,Mus musculus,GSE150291,GSM4546354,3p_v3,bam,SRR11770271,NA,SRX8323508,SRP261116,SRS6642822,SAMN14888341,NA,NA,"X Fu et al, Signal Transduct Target Ther, 2020",NA,https://pubmed.ncbi.nlm.nih.gov/33361757/,Illumina NovaSeq 6000,Kindlin-2 modulates PTH1R to regulate bone mass and PTH actions in bone,"To investigation the role of PTH and Kindlin-2 in bone development, we performed single-cell RNA-sequencing. From Con-veh, Con-PTH, cKO-veh, cKO-PTH, we profiled more than 20k single cells, including multi-potent mesenchymal stromal cells (MSC), osteoprogenitors, osteoblasts, chondrocytes, fibroblasts, endothelial cells, smooth muscle cells, skeletal muscle cells, pericytes, and schwann cells. We found proportion of part of these cells were significant altered by PTH or Kindlin-2 loss, especially for MSC, osteoblast, chondrocyte, and fibroblast. Transcriptomic analysis revealed gene expression was dramatically regulated by PTH or Kindlin-2 loss. Overall design: 3-month-old Kindlin-2f/f (control, n=6) and Dmp1-Cre; Kindlin-2f/f  (cKO, n=6) mice were treated with or without PTH daily continuously for 28d. Mice were sacrificed after the last PTH injection. Non-hematopoietic cells from bone marrow were extracted for single-cell RNA-sequencing"
X Fu 2020,cKO PTH,NA,bone,NA,NA,NA,NA,NA,Non-cellranger format,FALSE,TRUE,Mus musculus,GSE150291,GSM4546355,3p_v3,bam,SRR11770272,NA,SRX8323509,SRP261116,SRS6642823,SAMN14888340,NA,NA,"X Fu et al, Signal Transduct Target Ther, 2020",NA,https://pubmed.ncbi.nlm.nih.gov/33361757/,Illumina NovaSeq 6000,Kindlin-2 modulates PTH1R to regulate bone mass and PTH actions in bone,"To investigation the role of PTH and Kindlin-2 in bone development, we performed single-cell RNA-sequencing. From Con-veh, Con-PTH, cKO-veh, cKO-PTH, we profiled more than 20k single cells, including multi-potent mesenchymal stromal cells (MSC), osteoprogenitors, osteoblasts, chondrocytes, fibroblasts, endothelial cells, smooth muscle cells, skeletal muscle cells, pericytes, and schwann cells. We found proportion of part of these cells were significant altered by PTH or Kindlin-2 loss, especially for MSC, osteoblast, chondrocyte, and fibroblast. Transcriptomic analysis revealed gene expression was dramatically regulated by PTH or Kindlin-2 loss. Overall design: 3-month-old Kindlin-2f/f (control, n=6) and Dmp1-Cre; Kindlin-2f/f  (cKO, n=6) mice were treated with or without PTH daily continuously for 28d. Mice were sacrificed after the last PTH injection. Non-hematopoietic cells from bone marrow were extracted for single-cell RNA-sequencing"
Al-Barghouthi 2021,Bone marrow-derived stromal cells,Bone marrow-derived stromal cells cultured from femoral bone marrow,bone,NA,NA,NA,NA,NA,Error R1 missing_fastq provided,FALSE,TRUE,Mus musculus,GSE152806,GSM4626772,3p_v2,fastq,SRR12053313;SRR12053314;SRR12053315;SRR12053316,NA,SRX8581825,SRP267947,SRS6873600,SAMN15325041,NA,NA,"Al-Barghouthi et al, Nature Communications, 2021",NA,https://pubmed.ncbi.nlm.nih.gov/34099702/,NextSeq 500,Single-cell RNA-seq of bone marrow-derived stromal cells from 5 Diversity Outbred mice,"Genome-wide association studies (GWASs) for osteoporotic traits have identified over 1000 associations; however, their impact has been limited by the difficulties of causal gene identification and a strict focus on bone mineral density (BMD). Here, we used Diversity Outbred (DO) mice to directly address these limitations by performing the first systems genetics analysis of over 50 complex skeletal phenotypes. We applied a network approach to cortical bone RNA-seq data to discover 46 genes likely to be causal for human BMD GWAS associations, including the novel genes SERTAD4 and GLT8D2. We also performed GWAS in the DO for a wide-range of bone traits and identify Qsox1 as a novel gene influencing cortical bone accrual and bone strength. Our results provide a new perspective on the genetics of osteoporosis and highlight the ability of the mouse to inform human genetics. Overall design: Here, we performed single-cell RNA-seq on pooled polyA-selected total RNA from bone marrow-derived stromal cells, cultured from the femoral bone marrow of 5 Diversity Outbred mice (1 male, 4 females). These data allowed us to profile the expression of novel bone-related genes in osteoblasts and bone marrow-derived stromal cells."
Bian 2023,"E10.5 mouse embryonic maxillary prominence, scRNA seq",NA,bone,embryonic maxillary prominence,NA,NA,NA,NA,NA,FALSE,TRUE,Mus musculus,GSE161143,GSM4890324,Microwell-seq,fastq,SRR13013017,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Bian 2023,"E11.5 mouse embryonic maxillary prominence, scRNA seq",NA,bone,embryonic maxillary prominence,NA,NA,NA,NA,NA,FALSE,TRUE,Mus musculus,GSE161143,GSM4890325,Microwell-seq,fastq,SRR13013018,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Bian 2023,"E12.5 mouse embryonic maxillary prominence, scRNA seq",NA,bone,embryonic maxillary prominence,NA,NA,NA,NA,NA,FALSE,TRUE,Mus musculus,GSE161143,GSM4890326,Microwell-seq,fastq,SRR13013019,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Bian 2023,"E14.5 mouse embryonic maxillary prominence, scRNA seq",NA,bone,embryonic maxillary prominence,NA,NA,NA,NA,NA,FALSE,TRUE,Mus musculus,GSE161143,GSM5589131,Microwell-seq,fastq,SRR15972631,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Shen 2021,MCY_Adult,CD45-Ter119-Tie2-Lepr-Cre+ cells; Long bones; Bone marrows and bone fragments; Nomal feeding,bone,NA,NA,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE138689,GSM4116165,3p_v2,fastq,SRR10257243,NA,SRX6975194,SRP225051,SRS5500579,SAMN13008864,NA,NA,unpublished,NA,unpublished,HiSeq X Ten,Transcriptomic and functional analysis of skeletal stem and progenitor cells under homeostatic and stress conditions,"Leptin receptor+ (LepR+) cells are key components of the bone marrow hematopoietic microenvironment, and highly enrich skeletal stem and progenitor cells (SSPCs) that maintain homeostasis of the adult skeleton. However, the heterogeneity and lineage hierarchy within this population has been elusive. By genetic lineage tracing and single-cell RNA-sequencing, we found that Lepr-Cre labels most bone marrow stromal cells (BMSCs) and osteogenic lineage cells in adult long bones. Integrated analysis of Lepr-Cre-traced cells under homeostatic and stress conditions revealed dynamic changes of the adipogenic, osteogenic and periosteal lineages. Importantly, we discovered a Notch3+ BMSC subpopulation that is more quiescent and closely associated with the vasculatures, as well as key transcriptional networks promoting osteo-chondrogenic differentiation. We also identified a Sca-1+ periosteal subpopulation with high clonogenic activity but limited osteo-chondrogenic potential. Together, we mapped the transcriptomic landscape of adult SSPCs, and uncovered important cellular and molecular mechanisms underlying their maintenance and lineage specification. Overall design: Single-cell transcriptomic profiling of Prrx1-Cre- and Lepr-Cre-traced stromal cells in steady state long bones from Prrx1-Cre;tdTomato;Col2.3-GFP and Lepr-Cre;tdTomato mice, respectively, as well as Lepr-Cre-traced stromal cells from Lepr-Cre;tdTomato mice under stress conditions such as aging, rosiglitazone feeding, irradiation and bone fracture. Bulk transcriptomic profiling of wild-type bone marrow stromal cells (BMSCs) cultured in 3D GelMA hydrogel alone, or 3D co-cultured with bone marrow endothelial cells (ECs)."
Shen 2021,MCY_Aging,CD45-Ter119-Tie2-Lepr-Cre+ cells; Long bones; Bone marrows and bone fragments; Nomal feeding,bone,NA,NA,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE138689,GSM4116166,3p_v2,fastq,SRR10257244,NA,SRX6975195,SRP225051,SRS5500580,SAMN13008863,NA,NA,unpublished,NA,unpublished,HiSeq X Ten,Transcriptomic and functional analysis of skeletal stem and progenitor cells under homeostatic and stress conditions,"Leptin receptor+ (LepR+) cells are key components of the bone marrow hematopoietic microenvironment, and highly enrich skeletal stem and progenitor cells (SSPCs) that maintain homeostasis of the adult skeleton. However, the heterogeneity and lineage hierarchy within this population has been elusive. By genetic lineage tracing and single-cell RNA-sequencing, we found that Lepr-Cre labels most bone marrow stromal cells (BMSCs) and osteogenic lineage cells in adult long bones. Integrated analysis of Lepr-Cre-traced cells under homeostatic and stress conditions revealed dynamic changes of the adipogenic, osteogenic and periosteal lineages. Importantly, we discovered a Notch3+ BMSC subpopulation that is more quiescent and closely associated with the vasculatures, as well as key transcriptional networks promoting osteo-chondrogenic differentiation. We also identified a Sca-1+ periosteal subpopulation with high clonogenic activity but limited osteo-chondrogenic potential. Together, we mapped the transcriptomic landscape of adult SSPCs, and uncovered important cellular and molecular mechanisms underlying their maintenance and lineage specification. Overall design: Single-cell transcriptomic profiling of Prrx1-Cre- and Lepr-Cre-traced stromal cells in steady state long bones from Prrx1-Cre;tdTomato;Col2.3-GFP and Lepr-Cre;tdTomato mice, respectively, as well as Lepr-Cre-traced stromal cells from Lepr-Cre;tdTomato mice under stress conditions such as aging, rosiglitazone feeding, irradiation and bone fracture. Bulk transcriptomic profiling of wild-type bone marrow stromal cells (BMSCs) cultured in 3D GelMA hydrogel alone, or 3D co-cultured with bone marrow endothelial cells (ECs)."
Shen 2021,MCY_Rosiglitazone,"CD45-Ter119-Tie2-Lepr-Cre+ cells; Long bones; Bone marrows and bone fragments; Fed with 20 g/kg rosiglitazone-containing chow at 5 weeks old, analyzed after 5 weeks",bone,NA,NA,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE138689,GSM4116167,3p_v2,fastq,SRR10257245,NA,SRX6975196,SRP225051,SRS5500581,SAMN13008870,NA,NA,unpublished,NA,unpublished,HiSeq X Ten,Transcriptomic and functional analysis of skeletal stem and progenitor cells under homeostatic and stress conditions,"Leptin receptor+ (LepR+) cells are key components of the bone marrow hematopoietic microenvironment, and highly enrich skeletal stem and progenitor cells (SSPCs) that maintain homeostasis of the adult skeleton. However, the heterogeneity and lineage hierarchy within this population has been elusive. By genetic lineage tracing and single-cell RNA-sequencing, we found that Lepr-Cre labels most bone marrow stromal cells (BMSCs) and osteogenic lineage cells in adult long bones. Integrated analysis of Lepr-Cre-traced cells under homeostatic and stress conditions revealed dynamic changes of the adipogenic, osteogenic and periosteal lineages. Importantly, we discovered a Notch3+ BMSC subpopulation that is more quiescent and closely associated with the vasculatures, as well as key transcriptional networks promoting osteo-chondrogenic differentiation. We also identified a Sca-1+ periosteal subpopulation with high clonogenic activity but limited osteo-chondrogenic potential. Together, we mapped the transcriptomic landscape of adult SSPCs, and uncovered important cellular and molecular mechanisms underlying their maintenance and lineage specification. Overall design: Single-cell transcriptomic profiling of Prrx1-Cre- and Lepr-Cre-traced stromal cells in steady state long bones from Prrx1-Cre;tdTomato;Col2.3-GFP and Lepr-Cre;tdTomato mice, respectively, as well as Lepr-Cre-traced stromal cells from Lepr-Cre;tdTomato mice under stress conditions such as aging, rosiglitazone feeding, irradiation and bone fracture. Bulk transcriptomic profiling of wild-type bone marrow stromal cells (BMSCs) cultured in 3D GelMA hydrogel alone, or 3D co-cultured with bone marrow endothelial cells (ECs)."
Shen 2021,MCY_Irradiation,"CD45-Ter119-Tie2-Lepr-Cre+ cells; Long bones; Bone marrows and bone fragments; Sub-lethally irradiated (5 Gy) at 7 weeks old, analyzed after one week",bone,NA,NA,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE138689,GSM4116168,3p_v2,fastq,SRR10257246,NA,SRX6975197,SRP225051,SRS5500582,SAMN13008867,NA,NA,unpublished,NA,unpublished,HiSeq X Ten,Transcriptomic and functional analysis of skeletal stem and progenitor cells under homeostatic and stress conditions,"Leptin receptor+ (LepR+) cells are key components of the bone marrow hematopoietic microenvironment, and highly enrich skeletal stem and progenitor cells (SSPCs) that maintain homeostasis of the adult skeleton. However, the heterogeneity and lineage hierarchy within this population has been elusive. By genetic lineage tracing and single-cell RNA-sequencing, we found that Lepr-Cre labels most bone marrow stromal cells (BMSCs) and osteogenic lineage cells in adult long bones. Integrated analysis of Lepr-Cre-traced cells under homeostatic and stress conditions revealed dynamic changes of the adipogenic, osteogenic and periosteal lineages. Importantly, we discovered a Notch3+ BMSC subpopulation that is more quiescent and closely associated with the vasculatures, as well as key transcriptional networks promoting osteo-chondrogenic differentiation. We also identified a Sca-1+ periosteal subpopulation with high clonogenic activity but limited osteo-chondrogenic potential. Together, we mapped the transcriptomic landscape of adult SSPCs, and uncovered important cellular and molecular mechanisms underlying their maintenance and lineage specification. Overall design: Single-cell transcriptomic profiling of Prrx1-Cre- and Lepr-Cre-traced stromal cells in steady state long bones from Prrx1-Cre;tdTomato;Col2.3-GFP and Lepr-Cre;tdTomato mice, respectively, as well as Lepr-Cre-traced stromal cells from Lepr-Cre;tdTomato mice under stress conditions such as aging, rosiglitazone feeding, irradiation and bone fracture. Bulk transcriptomic profiling of wild-type bone marrow stromal cells (BMSCs) cultured in 3D GelMA hydrogel alone, or 3D co-cultured with bone marrow endothelial cells (ECs)."
Shen 2021,MCY_Fracture,"CD45-Ter119-Tie2-Lepr-Cre+ cells; Long bones; Bone marrows and bone fragments; Femur fractured at 7 weeks old, analyzed after one week",bone,NA,NA,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE138689,GSM4116169,3p_v2,fastq,SRR10257247,NA,SRX6975198,SRP225051,SRS5500583,SAMN13008866,NA,NA,unpublished,NA,unpublished,HiSeq X Ten,Transcriptomic and functional analysis of skeletal stem and progenitor cells under homeostatic and stress conditions,"Leptin receptor+ (LepR+) cells are key components of the bone marrow hematopoietic microenvironment, and highly enrich skeletal stem and progenitor cells (SSPCs) that maintain homeostasis of the adult skeleton. However, the heterogeneity and lineage hierarchy within this population has been elusive. By genetic lineage tracing and single-cell RNA-sequencing, we found that Lepr-Cre labels most bone marrow stromal cells (BMSCs) and osteogenic lineage cells in adult long bones. Integrated analysis of Lepr-Cre-traced cells under homeostatic and stress conditions revealed dynamic changes of the adipogenic, osteogenic and periosteal lineages. Importantly, we discovered a Notch3+ BMSC subpopulation that is more quiescent and closely associated with the vasculatures, as well as key transcriptional networks promoting osteo-chondrogenic differentiation. We also identified a Sca-1+ periosteal subpopulation with high clonogenic activity but limited osteo-chondrogenic potential. Together, we mapped the transcriptomic landscape of adult SSPCs, and uncovered important cellular and molecular mechanisms underlying their maintenance and lineage specification. Overall design: Single-cell transcriptomic profiling of Prrx1-Cre- and Lepr-Cre-traced stromal cells in steady state long bones from Prrx1-Cre;tdTomato;Col2.3-GFP and Lepr-Cre;tdTomato mice, respectively, as well as Lepr-Cre-traced stromal cells from Lepr-Cre;tdTomato mice under stress conditions such as aging, rosiglitazone feeding, irradiation and bone fracture. Bulk transcriptomic profiling of wild-type bone marrow stromal cells (BMSCs) cultured in 3D GelMA hydrogel alone, or 3D co-cultured with bone marrow endothelial cells (ECs)."
Shen 2021,Prx1_BM,CD45-Ter119-Tie2-Prrx1-Cre+ Col2.3-GFP- cells; Long bones; Bone marrows and bone fragments; Nomal feeding,bone,NA,NA,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE138689,GSM4116171,3p_v2,fastq,SRR10257249,NA,SRX6975200,SRP225051,SRS5500585,SAMN13008869,NA,NA,unpublished,NA,unpublished,HiSeq X Ten,Transcriptomic and functional analysis of skeletal stem and progenitor cells under homeostatic and stress conditions,"Leptin receptor+ (LepR+) cells are key components of the bone marrow hematopoietic microenvironment, and highly enrich skeletal stem and progenitor cells (SSPCs) that maintain homeostasis of the adult skeleton. However, the heterogeneity and lineage hierarchy within this population has been elusive. By genetic lineage tracing and single-cell RNA-sequencing, we found that Lepr-Cre labels most bone marrow stromal cells (BMSCs) and osteogenic lineage cells in adult long bones. Integrated analysis of Lepr-Cre-traced cells under homeostatic and stress conditions revealed dynamic changes of the adipogenic, osteogenic and periosteal lineages. Importantly, we discovered a Notch3+ BMSC subpopulation that is more quiescent and closely associated with the vasculatures, as well as key transcriptional networks promoting osteo-chondrogenic differentiation. We also identified a Sca-1+ periosteal subpopulation with high clonogenic activity but limited osteo-chondrogenic potential. Together, we mapped the transcriptomic landscape of adult SSPCs, and uncovered important cellular and molecular mechanisms underlying their maintenance and lineage specification. Overall design: Single-cell transcriptomic profiling of Prrx1-Cre- and Lepr-Cre-traced stromal cells in steady state long bones from Prrx1-Cre;tdTomato;Col2.3-GFP and Lepr-Cre;tdTomato mice, respectively, as well as Lepr-Cre-traced stromal cells from Lepr-Cre;tdTomato mice under stress conditions such as aging, rosiglitazone feeding, irradiation and bone fracture. Bulk transcriptomic profiling of wild-type bone marrow stromal cells (BMSCs) cultured in 3D GelMA hydrogel alone, or 3D co-cultured with bone marrow endothelial cells (ECs)."
Shen 2021,MCY_Adult2,CD45-Ter119-Tie2-Lepr-Cre+ cells; Long bones; Bone marrows and bone fragments; Normal feeding,bone,NA,NA,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE138689,GSM5594805,3p_v2,fastq,SRR16021511,NA,SRX12308462,SRP225051,SRS10283328,SAMN21572422,NA,NA,unpublished,NA,unpublished,HiSeq X Ten,Transcriptomic and functional analysis of skeletal stem and progenitor cells under homeostatic and stress conditions,"Leptin receptor+ (LepR+) cells are key components of the bone marrow hematopoietic microenvironment, and highly enrich skeletal stem and progenitor cells (SSPCs) that maintain homeostasis of the adult skeleton. However, the heterogeneity and lineage hierarchy within this population has been elusive. By genetic lineage tracing and single-cell RNA-sequencing, we found that Lepr-Cre labels most bone marrow stromal cells (BMSCs) and osteogenic lineage cells in adult long bones. Integrated analysis of Lepr-Cre-traced cells under homeostatic and stress conditions revealed dynamic changes of the adipogenic, osteogenic and periosteal lineages. Importantly, we discovered a Notch3+ BMSC subpopulation that is more quiescent and closely associated with the vasculatures, as well as key transcriptional networks promoting osteo-chondrogenic differentiation. We also identified a Sca-1+ periosteal subpopulation with high clonogenic activity but limited osteo-chondrogenic potential. Together, we mapped the transcriptomic landscape of adult SSPCs, and uncovered important cellular and molecular mechanisms underlying their maintenance and lineage specification. Overall design: Single-cell transcriptomic profiling of Prrx1-Cre- and Lepr-Cre-traced stromal cells in steady state long bones from Prrx1-Cre;tdTomato;Col2.3-GFP and Lepr-Cre;tdTomato mice, respectively, as well as Lepr-Cre-traced stromal cells from Lepr-Cre;tdTomato mice under stress conditions such as aging, rosiglitazone feeding, irradiation and bone fracture. Bulk transcriptomic profiling of wild-type bone marrow stromal cells (BMSCs) cultured in 3D GelMA hydrogel alone, or 3D co-cultured with bone marrow endothelial cells (ECs)."
Shen 2021,MCY-IRRA,"CD45-Ter119-Tie2-Lepr-Cre+ cells; Long bones; Bone marrows and bone fragments; Sub-lethally irradiated (5 Gy) at 7 weeks old, analyzed after one week",bone,NA,NA,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE138689,GSM5594806,3p_v2,fastq,SRR16021513,NA,SRX12308463,SRP225051,SRS10283329,SAMN21572423,NA,NA,unpublished,NA,unpublished,Illumina NovaSeq 6000,Transcriptomic and functional analysis of skeletal stem and progenitor cells under homeostatic and stress conditions,"Leptin receptor+ (LepR+) cells are key components of the bone marrow hematopoietic microenvironment, and highly enrich skeletal stem and progenitor cells (SSPCs) that maintain homeostasis of the adult skeleton. However, the heterogeneity and lineage hierarchy within this population has been elusive. By genetic lineage tracing and single-cell RNA-sequencing, we found that Lepr-Cre labels most bone marrow stromal cells (BMSCs) and osteogenic lineage cells in adult long bones. Integrated analysis of Lepr-Cre-traced cells under homeostatic and stress conditions revealed dynamic changes of the adipogenic, osteogenic and periosteal lineages. Importantly, we discovered a Notch3+ BMSC subpopulation that is more quiescent and closely associated with the vasculatures, as well as key transcriptional networks promoting osteo-chondrogenic differentiation. We also identified a Sca-1+ periosteal subpopulation with high clonogenic activity but limited osteo-chondrogenic potential. Together, we mapped the transcriptomic landscape of adult SSPCs, and uncovered important cellular and molecular mechanisms underlying their maintenance and lineage specification. Overall design: Single-cell transcriptomic profiling of Prrx1-Cre- and Lepr-Cre-traced stromal cells in steady state long bones from Prrx1-Cre;tdTomato;Col2.3-GFP and Lepr-Cre;tdTomato mice, respectively, as well as Lepr-Cre-traced stromal cells from Lepr-Cre;tdTomato mice under stress conditions such as aging, rosiglitazone feeding, irradiation and bone fracture. Bulk transcriptomic profiling of wild-type bone marrow stromal cells (BMSCs) cultured in 3D GelMA hydrogel alone, or 3D co-cultured with bone marrow endothelial cells (ECs)."
Elliott 2020,E11.5_MNP,epithelium and mesenchyme of mandibular prominence including developing tongue bud.,bone,mandible,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE141173,GSM4196529,3p_v2,bam,SRR10560003,NA,SRX7241718,SRP234027,SRS5741203,SAMN13428587,NA,NA,"Elliott et al, elife, 2020",10.7554/eLife.56450,https://pubmed.ncbi.nlm.nih.gov/33006313/,Illumina HiSeq 2500,Single cell sequencing of dissected mouse mandibular prominence at embryonic day e11.5 and e13.5,Single cell sequencing of dissected mouse mandibular prominence at embryonic day e11.5 and e13.5 Overall design: Mouse mandibular prominences were dissected at embryonic day 11.5 and 13.5. Tissue were dissociated into single cell suspension and used for single cell RNA library preparation and sequencing using 10X Genomics platform.
Elliott 2020,E13.5_MNP,epithelium and mesenchyme of mandibular prominence including developing tongue and skeletal elements,bone,mandible,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE141173,GSM4196530,3p_v2,bam,SRR10560004,NA,SRX7241719,SRP234027,SRS5741204,SAMN13428588,NA,NA,"Elliott et al, elife, 2020",10.7554/eLife.56450,https://pubmed.ncbi.nlm.nih.gov/33006313/,Illumina HiSeq 2500,Single cell sequencing of dissected mouse mandibular prominence at embryonic day e11.5 and e13.5,Single cell sequencing of dissected mouse mandibular prominence at embryonic day e11.5 and e13.5 Overall design: Mouse mandibular prominences were dissected at embryonic day 11.5 and 13.5. Tissue were dissociated into single cell suspension and used for single cell RNA library preparation and sequencing using 10X Genomics platform.
Sivaraj 2021b,BSC Control-1 rep1,NA,bone,NA,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE154247,GSM4667551,3p_v3,fastq,SRR12199772,NA,SRX8710651,NA,NA,SAMN15508074,NA,NA,NA,NA,NA,NA,NA,NA
Sivaraj 2021b,BSC Control-1 rep2,NA,bone,NA,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE154247,GSM4667552,3p_v3,fastq,SRR12199773,NA,SRX8710652,NA,NA,SAMN15508073,NA,NA,NA,NA,NA,NA,NA,NA
Sivaraj 2021b,BSC Control-2 rep1,NA,bone,NA,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE154247,GSM4667553,3p_v3,fastq,SRR12199774,NA,SRX8710653,NA,NA,SAMN15508072,NA,NA,NA,NA,NA,NA,NA,NA
Sivaraj 2021b,BSC Control-2 rep2,NA,bone,NA,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE154247,GSM4667554,3p_v3,fastq,SRR12199775,NA,SRX8710654,NA,NA,SAMN15508071,NA,NA,NA,NA,NA,NA,NA,NA
Sivaraj 2021b,BSC Fracture-1 rep1,NA,bone,NA,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE154247,GSM4667555,3p_v3,fastq,SRR12199776,NA,SRX8710655,NA,NA,SAMN15508070,NA,NA,NA,NA,NA,NA,NA,NA
Sivaraj 2021b,BSC Fracture-1 rep2,NA,bone,NA,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE154247,GSM4667556,3p_v3,fastq,SRR12199777,NA,SRX8710656,NA,NA,SAMN15508069,NA,NA,NA,NA,NA,NA,NA,NA
Sivaraj 2021b,BSC Fracture-2 rep1,NA,bone,NA,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE154247,GSM4667557,3p_v3,fastq,SRR12199778,NA,SRX8710657,NA,NA,SAMN15508068,NA,NA,NA,NA,NA,NA,NA,NA
Sivaraj 2021b,BSC Fracture-2 rep2,NA,bone,NA,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE154247,GSM4667558,3p_v3,fastq,SRR12199779,NA,SRX8710658,NA,NA,SAMN15508067,NA,NA,NA,NA,NA,NA,NA,NA
Sivaraj 2021a,BSC rep1,Bone stromal cells,bone,NA,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE156635,GSM4735393,3p_v2,fastq,SRR12492372,NA,SRX8983987,SRP278393,SRS7238317,SAMN15877884,NA,NA,"Sivaraj et al, Cell Reports, 2021",10.1016/j.celrep.2021.109352,https://pubmed.ncbi.nlm.nih.gov/34260921/,NextSeq 500,Regional specialization and fate specification of mesenchymal stromal cells in skeletal development [scRNA-seq],"To identify cellular heterogeneity and molecular signatures of bone marrow stromal (BMSCs) cells, we performed scRNA-seq of non-hematopoietic stromal cells from 3-week-old mice. In addition, to gain further insight into MSC differentiation in vivo, Pdgfrb-CreERT2 Rosa26-mTmG (Pdgfrb-Cre R26-mT/mG) double transgenic mice were treated with tamoxifen at P1-3 and sacrificed at P21 for the isolation of GFP+ cells from long bone followed by scRNA-seq analysis. Overall design: Single cell -RNA sequencing of non-hematopoietic  bone stromal cells (BSC) postnatal day 21 old bone and PdgfrbCre-R26 mTmG GFP+ sorted cells using  10X genomics."
Sivaraj 2021a,BSC rep2,Bone stromal cells,bone,NA,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE156635,GSM4735394,3p_v2,fastq,SRR12492373,NA,SRX8983988,SRP278393,SRS7238318,SAMN15877883,NA,NA,"Sivaraj et al, Cell Reports, 2021",10.1016/j.celrep.2021.109352,https://pubmed.ncbi.nlm.nih.gov/34260921/,NextSeq 500,Regional specialization and fate specification of mesenchymal stromal cells in skeletal development [scRNA-seq],"To identify cellular heterogeneity and molecular signatures of bone marrow stromal (BMSCs) cells, we performed scRNA-seq of non-hematopoietic stromal cells from 3-week-old mice. In addition, to gain further insight into MSC differentiation in vivo, Pdgfrb-CreERT2 Rosa26-mTmG (Pdgfrb-Cre R26-mT/mG) double transgenic mice were treated with tamoxifen at P1-3 and sacrificed at P21 for the isolation of GFP+ cells from long bone followed by scRNA-seq analysis. Overall design: Single cell -RNA sequencing of non-hematopoietic  bone stromal cells (BSC) postnatal day 21 old bone and PdgfrbCre-R26 mTmG GFP+ sorted cells using  10X genomics."
Sivaraj 2021a,BSC rep3,Bone stromal cells,bone,NA,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE156635,GSM4735395,3p_v2,fastq,SRR12492374,NA,SRX8983989,SRP278393,SRS7238319,SAMN15877882,NA,NA,"Sivaraj et al, Cell Reports, 2021",10.1016/j.celrep.2021.109352,https://pubmed.ncbi.nlm.nih.gov/34260921/,NextSeq 500,Regional specialization and fate specification of mesenchymal stromal cells in skeletal development [scRNA-seq],"To identify cellular heterogeneity and molecular signatures of bone marrow stromal (BMSCs) cells, we performed scRNA-seq of non-hematopoietic stromal cells from 3-week-old mice. In addition, to gain further insight into MSC differentiation in vivo, Pdgfrb-CreERT2 Rosa26-mTmG (Pdgfrb-Cre R26-mT/mG) double transgenic mice were treated with tamoxifen at P1-3 and sacrificed at P21 for the isolation of GFP+ cells from long bone followed by scRNA-seq analysis. Overall design: Single cell -RNA sequencing of non-hematopoietic  bone stromal cells (BSC) postnatal day 21 old bone and PdgfrbCre-R26 mTmG GFP+ sorted cells using  10X genomics."
Sivaraj 2021a,BSC rep4,Bone stromal cells,bone,NA,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE156635,GSM4735396,3p_v2,fastq,SRR12492375,NA,SRX8983990,SRP278393,SRS7238320,SAMN15877881,NA,NA,"Sivaraj et al, Cell Reports, 2021",10.1016/j.celrep.2021.109352,https://pubmed.ncbi.nlm.nih.gov/34260921/,NextSeq 500,Regional specialization and fate specification of mesenchymal stromal cells in skeletal development [scRNA-seq],"To identify cellular heterogeneity and molecular signatures of bone marrow stromal (BMSCs) cells, we performed scRNA-seq of non-hematopoietic stromal cells from 3-week-old mice. In addition, to gain further insight into MSC differentiation in vivo, Pdgfrb-CreERT2 Rosa26-mTmG (Pdgfrb-Cre R26-mT/mG) double transgenic mice were treated with tamoxifen at P1-3 and sacrificed at P21 for the isolation of GFP+ cells from long bone followed by scRNA-seq analysis. Overall design: Single cell -RNA sequencing of non-hematopoietic  bone stromal cells (BSC) postnatal day 21 old bone and PdgfrbCre-R26 mTmG GFP+ sorted cells using  10X genomics."
Sivaraj 2021a,rbGFP rep1,PdgfrbCre GFP+ cells; C57BL/6 : PdgfrbCreERT2; R26 mTmG,bone,NA,cell,NA,NA,NA,NA,TRUE,FALSE,Mus musculus,GSE156635,GSM4735397,3p_v2,fastq,SRR12492376,NA,SRX8983991,SRP278393,SRS7238321,SAMN15877880,NA,NA,"Sivaraj et al, Cell Reports, 2021",10.1016/j.celrep.2021.109352,https://pubmed.ncbi.nlm.nih.gov/34260921/,NextSeq 500,Regional specialization and fate specification of mesenchymal stromal cells in skeletal development [scRNA-seq],"To identify cellular heterogeneity and molecular signatures of bone marrow stromal (BMSCs) cells, we performed scRNA-seq of non-hematopoietic stromal cells from 3-week-old mice. In addition, to gain further insight into MSC differentiation in vivo, Pdgfrb-CreERT2 Rosa26-mTmG (Pdgfrb-Cre R26-mT/mG) double transgenic mice were treated with tamoxifen at P1-3 and sacrificed at P21 for the isolation of GFP+ cells from long bone followed by scRNA-seq analysis. Overall design: Single cell -RNA sequencing of non-hematopoietic  bone stromal cells (BSC) postnatal day 21 old bone and PdgfrbCre-R26 mTmG GFP+ sorted cells using  10X genomics."
Sivaraj 2021a,rbGFP rep2,PdgfrbCre GFP+ cells; C57BL/6 : PdgfrbCreERT2; R26 mTmG,bone,NA,cell,NA,NA,NA,NA,TRUE,FALSE,Mus musculus,GSE156635,GSM4735398,3p_v2,fastq,SRR12492377,NA,SRX8983992,SRP278393,SRS7238322,SAMN15877879,NA,NA,"Sivaraj et al, Cell Reports, 2021",10.1016/j.celrep.2021.109352,https://pubmed.ncbi.nlm.nih.gov/34260921/,NextSeq 500,Regional specialization and fate specification of mesenchymal stromal cells in skeletal development [scRNA-seq],"To identify cellular heterogeneity and molecular signatures of bone marrow stromal (BMSCs) cells, we performed scRNA-seq of non-hematopoietic stromal cells from 3-week-old mice. In addition, to gain further insight into MSC differentiation in vivo, Pdgfrb-CreERT2 Rosa26-mTmG (Pdgfrb-Cre R26-mT/mG) double transgenic mice were treated with tamoxifen at P1-3 and sacrificed at P21 for the isolation of GFP+ cells from long bone followed by scRNA-seq analysis. Overall design: Single cell -RNA sequencing of non-hematopoietic  bone stromal cells (BSC) postnatal day 21 old bone and PdgfrbCre-R26 mTmG GFP+ sorted cells using  10X genomics."
Mundy 2021,Matrigel only,NA,bone,cultured primary cells,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE157679,GSM4773188,3p_v3,fastq,SRR12610990;SRR12610991;SRR12610992;SRR12610993;SRR12610994;SRR12610995,NA,SRX9094343,SRP281605,SRS7339944,SAMN16082934,NA,NA,"Mundy et al, Science Signaling, 2021",10.1126/scisignal.abd0536,https://pubmed.ncbi.nlm.nih.gov/33563697/,Illumina HiSeq 2500,Activin A promotes the development of acquired heterotopic ossification and is an effective target for disease attenuation in mice,"Heterotopic ossification (HO) is a common, potentially debilitating, acquired pathology that is instigated by tissue damage or other insults and involves inflammation followed by  chondrogenesis, osteogenesis and extraskeletal bone accumulation. Current standard of care are not very effective and have side effects, making the search for new treatments urgent. Activin A is a member of the transforming growth factor-b (TGF-b) superfamily, is produced by activated macrophages and other inflammatory cells and signals through activation of canonical SMAD2 and SMAD3 (SMAD2/3) intracellular effectors. Because HO starts with inflammation and because pSMAD2/3 activation is chondrogenic, here we tested whether activin A stimulates HO development. Using standard mouse models of acquired intramuscular and subdermal HO, we found that systemic administration of a neutralizing activin A antibody markedly reduced HO development and bone accumulation. Single-cell RNAseq and developmental trajectories showed that the antibody treatment had sharply reduced the number of Sox9+ skeletal progenitors, many of which also expressed the gene encoding activin A (Inhba), that were recruited to the HO site. In line with the latter finding, gain-of-function assays showed that treatment of progenitors with recombinant activin A enhanced their chondrogenic differentiation and did so through SMAD2/3 signaling, and inclusion of activin A to HO-inducing in vivo implants enhanced HO development. Together, our data reveal that activin A is a critical upstream signaling stimulator of HO in mice and could represent an effective therapeutic target against acquired forms of this pathology in patients. Overall design: Single cell RNA seq of cells from Ectopic masses were harvested on day 5  from mice implanted with Matrigel alone or Matrigel/rhBMP2 mixture, with the latter mice treated systemically with pre-immune control IgG or activin A neutralizing antibody"
Mundy 2021,Matrigel/rhBMP2+IgG,NA,bone,cultured primary cells,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE157679,GSM4773189,3p_v3,fastq,SRR12610996;SRR12610997;SRR12610998;SRR12610999;SRR12611000;SRR12611001,NA,SRX9094344,SRP281605,SRS7339945,SAMN16082932,NA,NA,"Mundy et al, Science Signaling, 2021",10.1126/scisignal.abd0536,https://pubmed.ncbi.nlm.nih.gov/33563697/,Illumina HiSeq 2500,Activin A promotes the development of acquired heterotopic ossification and is an effective target for disease attenuation in mice,"Heterotopic ossification (HO) is a common, potentially debilitating, acquired pathology that is instigated by tissue damage or other insults and involves inflammation followed by  chondrogenesis, osteogenesis and extraskeletal bone accumulation. Current standard of care are not very effective and have side effects, making the search for new treatments urgent. Activin A is a member of the transforming growth factor-b (TGF-b) superfamily, is produced by activated macrophages and other inflammatory cells and signals through activation of canonical SMAD2 and SMAD3 (SMAD2/3) intracellular effectors. Because HO starts with inflammation and because pSMAD2/3 activation is chondrogenic, here we tested whether activin A stimulates HO development. Using standard mouse models of acquired intramuscular and subdermal HO, we found that systemic administration of a neutralizing activin A antibody markedly reduced HO development and bone accumulation. Single-cell RNAseq and developmental trajectories showed that the antibody treatment had sharply reduced the number of Sox9+ skeletal progenitors, many of which also expressed the gene encoding activin A (Inhba), that were recruited to the HO site. In line with the latter finding, gain-of-function assays showed that treatment of progenitors with recombinant activin A enhanced their chondrogenic differentiation and did so through SMAD2/3 signaling, and inclusion of activin A to HO-inducing in vivo implants enhanced HO development. Together, our data reveal that activin A is a critical upstream signaling stimulator of HO in mice and could represent an effective therapeutic target against acquired forms of this pathology in patients. Overall design: Single cell RNA seq of cells from Ectopic masses were harvested on day 5  from mice implanted with Matrigel alone or Matrigel/rhBMP2 mixture, with the latter mice treated systemically with pre-immune control IgG or activin A neutralizing antibody"
Mundy 2021,Matrigel/rhBMP2+nAct Ab,NA,bone,cultured primary cells,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE157679,GSM4773190,3p_v3,fastq,SRR12611002;SRR12611003;SRR12611004;SRR12611005;SRR12611006;SRR12611007,NA,SRX9094345,SRP281605,SRS7339946,SAMN16082931,NA,NA,"Mundy et al, Science Signaling, 2021",10.1126/scisignal.abd0536,https://pubmed.ncbi.nlm.nih.gov/33563697/,Illumina HiSeq 2500,Activin A promotes the development of acquired heterotopic ossification and is an effective target for disease attenuation in mice,"Heterotopic ossification (HO) is a common, potentially debilitating, acquired pathology that is instigated by tissue damage or other insults and involves inflammation followed by  chondrogenesis, osteogenesis and extraskeletal bone accumulation. Current standard of care are not very effective and have side effects, making the search for new treatments urgent. Activin A is a member of the transforming growth factor-b (TGF-b) superfamily, is produced by activated macrophages and other inflammatory cells and signals through activation of canonical SMAD2 and SMAD3 (SMAD2/3) intracellular effectors. Because HO starts with inflammation and because pSMAD2/3 activation is chondrogenic, here we tested whether activin A stimulates HO development. Using standard mouse models of acquired intramuscular and subdermal HO, we found that systemic administration of a neutralizing activin A antibody markedly reduced HO development and bone accumulation. Single-cell RNAseq and developmental trajectories showed that the antibody treatment had sharply reduced the number of Sox9+ skeletal progenitors, many of which also expressed the gene encoding activin A (Inhba), that were recruited to the HO site. In line with the latter finding, gain-of-function assays showed that treatment of progenitors with recombinant activin A enhanced their chondrogenic differentiation and did so through SMAD2/3 signaling, and inclusion of activin A to HO-inducing in vivo implants enhanced HO development. Together, our data reveal that activin A is a critical upstream signaling stimulator of HO in mice and could represent an effective therapeutic target against acquired forms of this pathology in patients. Overall design: Single cell RNA seq of cells from Ectopic masses were harvested on day 5  from mice implanted with Matrigel alone or Matrigel/rhBMP2 mixture, with the latter mice treated systemically with pre-immune control IgG or activin A neutralizing antibody"
Ambrosi 2021b,2_month_old_fractured 1,NA,bone,fracture callus,cell,NA,NA,NA,~75bp R1; seq is full of Ns,TRUE,TRUE,Mus musculus,GSE166441,GSM5071238,3p_v3.1,fastq,SRR13666749,NA,SRX10058322,NA,NA,SAMN17841231,NA,NA,NA,NA,NA,NA,NA,NA
Ambrosi 2021b,2_month_old_fractured 2,NA,bone,fracture callus,cell,NA,NA,NA,~75bp R1; seq is full of Ns,TRUE,TRUE,Mus musculus,GSE166441,GSM5071239,3p_v3.1,fastq,SRR13666750,NA,SRX10058323,NA,NA,SAMN17841230,NA,NA,NA,NA,NA,NA,NA,NA
Ambrosi 2021b,2_month_old_fractured 3,NA,bone,fracture callus,cell,NA,NA,NA,~75bp R1; seq is full of Ns,TRUE,TRUE,Mus musculus,GSE166441,GSM5071240,3p_v3.1,fastq,SRR13666751,NA,SRX10058315,NA,NA,SAMN17841229,NA,NA,NA,NA,NA,NA,NA,NA
Ambrosi 2021b,12_month_old_fractured 1,NA,bone,fracture callus,cell,NA,NA,NA,~75bp R1; seq is full of Ns,TRUE,TRUE,Mus musculus,GSE166441,GSM5071241,3p_v3.1,fastq,SRR13666752,NA,SRX10058316,NA,NA,SAMN17841228,NA,NA,NA,NA,NA,NA,NA,NA
Ambrosi 2021b,12_month_old_fractured 2,NA,bone,fracture callus,cell,NA,NA,NA,~75bp R1; seq is full of Ns,TRUE,TRUE,Mus musculus,GSE166441,GSM5071242,3p_v3.1,fastq,SRR13666753,NA,SRX10058317,NA,NA,SAMN17841227,NA,NA,NA,NA,NA,NA,NA,NA
Ambrosi 2021b,12_month_old_fractured 3,NA,bone,fracture callus,cell,NA,NA,NA,~75bp R1; seq is full of Ns,TRUE,TRUE,Mus musculus,GSE166441,GSM5071243,3p_v3.1,fastq,SRR13666754,NA,SRX10058318,NA,NA,SAMN17841226,NA,NA,NA,NA,NA,NA,NA,NA
Ambrosi 2021b,24_month_old_fractured 1,NA,bone,fracture callus,cell,NA,NA,NA,~75bp R1; seq is full of Ns,TRUE,TRUE,Mus musculus,GSE166441,GSM5071244,3p_v3.1,fastq,SRR13666755,NA,SRX10058319,NA,NA,SAMN17841225,NA,NA,NA,NA,NA,NA,NA,NA
Ambrosi 2021b,24_month_old_fractured 2,NA,bone,fracture callus,cell,NA,NA,NA,~75bp R1; seq is full of Ns,TRUE,TRUE,Mus musculus,GSE166441,GSM5071245,3p_v3.1,fastq,SRR13666756,NA,SRX10058320,NA,NA,SAMN17841224,NA,NA,NA,NA,NA,NA,NA,NA
Ambrosi 2021b,24_month_old_fractured 3,NA,bone,fracture callus,cell,NA,NA,NA,~75bp R1; seq is full of Ns,TRUE,TRUE,Mus musculus,GSE166441,GSM5071246,3p_v3.1,fastq,SRR13666757,NA,SRX10058321,NA,NA,SAMN17841223,NA,NA,NA,NA,NA,NA,NA,NA
Ambrosi 2021a,Old_PBS-treated,NA,bone,NA,NA,NA,NA,NA,download issue,TRUE,TRUE,Mus musculus,GSE172149,GSM5242734,3p_v3.1,fastq,SRR14243850,NA,SRX10606482,SRP314966,SRS8707619,SAMN18747477,NA,NA,"Ambrosi et al, Nature, 2021",10.1038/s41586-021-03795-7,https://pubmed.ncbi.nlm.nih.gov/34381212/,NextSeq 500,Rejuvenating Age-impaired Fracture Healing,"Skeletal aging and disease are associated with a misbalance in the opposing actions of osteoblasts and osteoclasts that are responsible for maintaining the integrity of bone tissues. Here, we show through detailed functional and single-cell genomic studies that intrinsic aging of bona fide mouse skeletal stem cells (SSCs) alters bone marrow niche signaling and skews bone and blood lineage differentiation leading to fragile bones that regenerate poorly. Aged SSCs have diminished bone and cartilage forming potential but produce higher frequencies of stromal lineages that express high levels of pro-inflammatory and pro-resorptive cytokines. Single-cell transcriptomic studies reveal a distinct population of SSCs in aged mice that gradually outcompete their younger counterparts in the bone marrow niche. While systemic exposure to a youthful circulation through heterochronic parabiosis reduced local expression of inflammatory cytokines, it did not reverse the diminished osteochondrogenic activity of aged SSCs and was insufficient to improve bone mass and skeletal-healing parameters in aged mice. Hematopoietic reconstitution of aged mice with young hematopoietic stem cells (HSC) also did not improve bone integrity and repair. We find that deficient bone regeneration in aged mice could only be reversed by the local application of a combinatorial treatment that re-activates aged SSCs and simultaneously abates crosstalk to hematopoietic cells favoring an inflammatory milieu. This treatment expanded aged SSC pools, reduced osteoclast activity, and enhanced bone healing to youthful levels. Our findings provide mechanistic insight into the complex, multifactorial mechanisms underlying skeletal aging and offer new prospects for rejuvenating the aged skeletal system. Overall design: 10X Genomics single cell RNA-sequencing of fracture calluses from 24-months old mice at day-10 after stabilized bi-cortical fracture induction. Fracture callus tissue was harvested from 24-mo mice at day-10 after injury. Three fracture calluses treated with hydrogels containing PBS at day of injury and three fractures with hydrogels containing anti-Csf1/BMP2  were processed, digested, and prepared for FACS as described above. Single cell solutions of each treatment group were then pooled (n=3 per group) and 2x105 PI-Ter119- cells were sorted into collection tubes containing FACS buffer. Cells were then processed with 10X Chromium Next GEM Single Cell 3' GEM kit (10X Genomics Inc, v3.1) according to manufacturer's instruction."
Ambrosi 2021a,Old_Rescue_aCSF1_BMP2-treated,NA,bone,NA,NA,NA,NA,NA,download issue,TRUE,TRUE,Mus musculus,GSE172149,GSM5242735,3p_v3.1,fastq,SRR14243851,NA,SRX10606483,SRP314966,SRS8707618,SAMN18747476,NA,NA,"Ambrosi et al, Nature, 2021",10.1038/s41586-021-03795-7,https://pubmed.ncbi.nlm.nih.gov/34381212/,NextSeq 500,Rejuvenating Age-impaired Fracture Healing,"Skeletal aging and disease are associated with a misbalance in the opposing actions of osteoblasts and osteoclasts that are responsible for maintaining the integrity of bone tissues. Here, we show through detailed functional and single-cell genomic studies that intrinsic aging of bona fide mouse skeletal stem cells (SSCs) alters bone marrow niche signaling and skews bone and blood lineage differentiation leading to fragile bones that regenerate poorly. Aged SSCs have diminished bone and cartilage forming potential but produce higher frequencies of stromal lineages that express high levels of pro-inflammatory and pro-resorptive cytokines. Single-cell transcriptomic studies reveal a distinct population of SSCs in aged mice that gradually outcompete their younger counterparts in the bone marrow niche. While systemic exposure to a youthful circulation through heterochronic parabiosis reduced local expression of inflammatory cytokines, it did not reverse the diminished osteochondrogenic activity of aged SSCs and was insufficient to improve bone mass and skeletal-healing parameters in aged mice. Hematopoietic reconstitution of aged mice with young hematopoietic stem cells (HSC) also did not improve bone integrity and repair. We find that deficient bone regeneration in aged mice could only be reversed by the local application of a combinatorial treatment that re-activates aged SSCs and simultaneously abates crosstalk to hematopoietic cells favoring an inflammatory milieu. This treatment expanded aged SSC pools, reduced osteoclast activity, and enhanced bone healing to youthful levels. Our findings provide mechanistic insight into the complex, multifactorial mechanisms underlying skeletal aging and offer new prospects for rejuvenating the aged skeletal system. Overall design: 10X Genomics single cell RNA-sequencing of fracture calluses from 24-months old mice at day-10 after stabilized bi-cortical fracture induction. Fracture callus tissue was harvested from 24-mo mice at day-10 after injury. Three fracture calluses treated with hydrogels containing PBS at day of injury and three fractures with hydrogels containing anti-Csf1/BMP2  were processed, digested, and prepared for FACS as described above. Single cell solutions of each treatment group were then pooled (n=3 per group) and 2x105 PI-Ter119- cells were sorted into collection tubes containing FACS buffer. Cells were then processed with 10X Chromium Next GEM Single Cell 3' GEM kit (10X Genomics Inc, v3.1) according to manufacturer's instruction."
J He 2021,CS20_longbone_10x,NA,bone,NA,NA,NA,NA,NA,NA,TRUE,TRUE,Homo sapiens,GSE173994,GSM4274191,3p_v2,fastq,SRR10901270,NA,SRX7569448,SRP242103,SRS6005481,SAMN13869932,NA,NA,"He et al, Cell Research, 2021",10.1038/s41422-021-00467-z,https://pubmed.ncbi.nlm.nih.gov/33473154/,HiSeq X Ten,Dissecting human embryonic skeletal stem cell ontogeny by single-cell transcriptomic and functional analyses,"Mapping the transcriptional landscape of human embryonic skeletogenesis at single-cell resolution during limb bud and primary ossification center (POC) formation. We found significant heterogeneity of stromal cells within the limb bud mesenchyme that specified proximal-distal and anterior-posterior patterning. Embryonic skeletal stem and progenitor cells first appeared during POC formation, which were highly enriched by CADM1 expression and could differentiate into osteoblasts, chondrocytes and periosteal mesenchymal stromal cells. Overall design: We performed droplet-based scRNA-seq of 42,857 cells to firstly construct a molecular landscape of skeletogenesis in human embryos"
J He 2021,CS22_longbone_10x,NA,bone,NA,NA,NA,NA,NA,NA,TRUE,TRUE,Homo sapiens,GSE173994,GSM4274192,3p_v2,fastq,SRR10901271;SRR10901272;SRR10901273;SRR10901274,NA,SRX7569449,SRP242103,SRS6005482,SAMN13869931,NA,NA,"He et al, Cell Research, 2021",10.1038/s41422-021-00467-z,https://pubmed.ncbi.nlm.nih.gov/33473154/,HiSeq X Ten,Dissecting human embryonic skeletal stem cell ontogeny by single-cell transcriptomic and functional analyses,"Mapping the transcriptional landscape of human embryonic skeletogenesis at single-cell resolution during limb bud and primary ossification center (POC) formation. We found significant heterogeneity of stromal cells within the limb bud mesenchyme that specified proximal-distal and anterior-posterior patterning. Embryonic skeletal stem and progenitor cells first appeared during POC formation, which were highly enriched by CADM1 expression and could differentiate into osteoblasts, chondrocytes and periosteal mesenchymal stromal cells. Overall design: We performed droplet-based scRNA-seq of 42,857 cells to firstly construct a molecular landscape of skeletogenesis in human embryos"
J He 2021,CS22(2)_longbone_10x,NA,bone,NA,NA,NA,NA,NA,NA,TRUE,TRUE,Homo sapiens,GSE173994,GSM4274193,3p_v2,fastq,SRR10901275,NA,SRX7569450,SRP242103,SRS6005483,SAMN13869930,NA,NA,"He et al, Cell Research, 2021",10.1038/s41422-021-00467-z,https://pubmed.ncbi.nlm.nih.gov/33473154/,HiSeq X Ten,Dissecting human embryonic skeletal stem cell ontogeny by single-cell transcriptomic and functional analyses,"Mapping the transcriptional landscape of human embryonic skeletogenesis at single-cell resolution during limb bud and primary ossification center (POC) formation. We found significant heterogeneity of stromal cells within the limb bud mesenchyme that specified proximal-distal and anterior-posterior patterning. Embryonic skeletal stem and progenitor cells first appeared during POC formation, which were highly enriched by CADM1 expression and could differentiate into osteoblasts, chondrocytes and periosteal mesenchymal stromal cells. Overall design: We performed droplet-based scRNA-seq of 42,857 cells to firstly construct a molecular landscape of skeletogenesis in human embryos"
J He 2021,CS23_calvarialbone_10x,NA,bone,NA,NA,NA,NA,NA,NA,TRUE,TRUE,Homo sapiens,GSE173994,GSM4274194,3p_v2,fastq,SRR10901276,NA,SRX7569451,SRP242103,SRS6005484,SAMN13869929,NA,NA,"He et al, Cell Research, 2021",10.1038/s41422-021-00467-z,https://pubmed.ncbi.nlm.nih.gov/33473154/,HiSeq X Ten,Dissecting human embryonic skeletal stem cell ontogeny by single-cell transcriptomic and functional analyses,"Mapping the transcriptional landscape of human embryonic skeletogenesis at single-cell resolution during limb bud and primary ossification center (POC) formation. We found significant heterogeneity of stromal cells within the limb bud mesenchyme that specified proximal-distal and anterior-posterior patterning. Embryonic skeletal stem and progenitor cells first appeared during POC formation, which were highly enriched by CADM1 expression and could differentiate into osteoblasts, chondrocytes and periosteal mesenchymal stromal cells. Overall design: We performed droplet-based scRNA-seq of 42,857 cells to firstly construct a molecular landscape of skeletogenesis in human embryos"
J He 2021,CS23(2)_calvarialbone_10x,NA,bone,NA,NA,NA,NA,NA,NA,TRUE,TRUE,Homo sapiens,GSE173994,GSM4609136,3p_v2,fastq,SRR11977450;SRR11977451;SRR11977452;SRR11977453,NA,SRX8520854,SRP242103,SRS6816328,SAMN15198700,NA,NA,"He et al, Cell Research, 2021",10.1038/s41422-021-00467-z,https://pubmed.ncbi.nlm.nih.gov/33473154/,HiSeq X Ten,Dissecting human embryonic skeletal stem cell ontogeny by single-cell transcriptomic and functional analyses,"Mapping the transcriptional landscape of human embryonic skeletogenesis at single-cell resolution during limb bud and primary ossification center (POC) formation. We found significant heterogeneity of stromal cells within the limb bud mesenchyme that specified proximal-distal and anterior-posterior patterning. Embryonic skeletal stem and progenitor cells first appeared during POC formation, which were highly enriched by CADM1 expression and could differentiate into osteoblasts, chondrocytes and periosteal mesenchymal stromal cells. Overall design: We performed droplet-based scRNA-seq of 42,857 cells to firstly construct a molecular landscape of skeletogenesis in human embryos"
Xu J 2022,p75 floxed mice (p75fl/fl),NA,bone,NA,NA,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE179890,GSM5436554,3p_v3,fastq,SRR15097825;SRR15097826;SRR15097827;SRR15097828;SRR15097829;SRR15097830;SRR15097831;SRR15097832,NA,NA,SRX11407658,NA,SAMN20166699,NA,NA,NA,10.1126/sciadv.abl5716,https://pubmed.ncbi.nlm.nih.gov/35302859/,NA,NA,NA
Xu J 2022,p75 conditional knockout mice (p75PDGFRa),NA,bone,NA,NA,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE179890,GSM5436555,3p_v3,fastq,SRR15097833;SRR15097834;SRR15097835;SRR15097836;SRR15097837;SRR15097838;SRR15097839;SRR15097840,NA,NA,SRX11407659,NA,SAMN20166698,NA,NA,NA,10.1126/sciadv.abl5716,https://pubmed.ncbi.nlm.nih.gov/35302859/,NA,NA,NA
Kwon 2021,S+-01,STAT1+/-Sox2Cre+/-; male,bone,NA,NA,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE183404,GSM5556893,3p_v3,fastq,SRR15713193,NA,SRX12008780,SRP335579,SRS10014927,SAMN21216259,NA,NA,"Kwon et al, Development, 2021",10.1242/dev.199607,https://pubmed.ncbi.nlm.nih.gov/34738614/,Illumina NovaSeq 6000,Single-cell transcriptomics of cultured skeletal stem cells with a PDGFRbeta D849V mutation,"We demonstrate that skeletal stem cells (SSCs) isolated from mice with a gain-of-function D849V point mutation in PDGFRbeta exhibit colony formation defects that parallel the wasting or overgrowth phenotypes of the mice. Single-cell RNA transcriptomics with SSC-derived polyclonal colonies was performed to characterize single-cell differentiation potential and molecular signatures. This study indicates multi-lineage potential of cultured SSCs and identifies molecular alterations in osteogenic and chondrogenic precursors. Overall design: Single-cell RNA sequencing of sorted and cultured PDGFRalpha+/Sca-1+ skeletal stem cells of 3-weeks-old limb of four genotypes (STAT1+/-, STAT1-/-, PDGFRbD849V+/-STAT1+/-,PDGFRbD849V+/-STAT1-/-) of mice"
Kwon 2021,S+-02,STAT1+/-Sox2Cre+/-; female,bone,NA,NA,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE183404,GSM5556894,3p_v3,fastq,SRR15713194,NA,SRX12008781,SRP335579,SRS10014928,SAMN21216260,NA,NA,"Kwon et al, Development, 2021",10.1242/dev.199607,https://pubmed.ncbi.nlm.nih.gov/34738614/,Illumina NovaSeq 6000,Single-cell transcriptomics of cultured skeletal stem cells with a PDGFRbeta D849V mutation,"We demonstrate that skeletal stem cells (SSCs) isolated from mice with a gain-of-function D849V point mutation in PDGFRbeta exhibit colony formation defects that parallel the wasting or overgrowth phenotypes of the mice. Single-cell RNA transcriptomics with SSC-derived polyclonal colonies was performed to characterize single-cell differentiation potential and molecular signatures. This study indicates multi-lineage potential of cultured SSCs and identifies molecular alterations in osteogenic and chondrogenic precursors. Overall design: Single-cell RNA sequencing of sorted and cultured PDGFRalpha+/Sca-1+ skeletal stem cells of 3-weeks-old limb of four genotypes (STAT1+/-, STAT1-/-, PDGFRbD849V+/-STAT1+/-,PDGFRbD849V+/-STAT1-/-) of mice"
Kwon 2021,S--01,STAT1-/-Sox2Cre+/-; male,bone,NA,NA,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE183404,GSM5556895,3p_v3,fastq,SRR15713195,NA,SRX12008782,SRP335579,SRS10014930,SAMN21216261,NA,NA,"Kwon et al, Development, 2021",10.1242/dev.199607,https://pubmed.ncbi.nlm.nih.gov/34738614/,Illumina NovaSeq 6000,Single-cell transcriptomics of cultured skeletal stem cells with a PDGFRbeta D849V mutation,"We demonstrate that skeletal stem cells (SSCs) isolated from mice with a gain-of-function D849V point mutation in PDGFRbeta exhibit colony formation defects that parallel the wasting or overgrowth phenotypes of the mice. Single-cell RNA transcriptomics with SSC-derived polyclonal colonies was performed to characterize single-cell differentiation potential and molecular signatures. This study indicates multi-lineage potential of cultured SSCs and identifies molecular alterations in osteogenic and chondrogenic precursors. Overall design: Single-cell RNA sequencing of sorted and cultured PDGFRalpha+/Sca-1+ skeletal stem cells of 3-weeks-old limb of four genotypes (STAT1+/-, STAT1-/-, PDGFRbD849V+/-STAT1+/-,PDGFRbD849V+/-STAT1-/-) of mice"
Kwon 2021,S--02,STAT1-/-Sox2Cre+/-; female,bone,NA,NA,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE183404,GSM5556896,3p_v3,fastq,SRR15713196,NA,SRX12008783,SRP335579,SRS10014929,SAMN21216262,NA,NA,"Kwon et al, Development, 2021",10.1242/dev.199607,https://pubmed.ncbi.nlm.nih.gov/34738614/,Illumina NovaSeq 6000,Single-cell transcriptomics of cultured skeletal stem cells with a PDGFRbeta D849V mutation,"We demonstrate that skeletal stem cells (SSCs) isolated from mice with a gain-of-function D849V point mutation in PDGFRbeta exhibit colony formation defects that parallel the wasting or overgrowth phenotypes of the mice. Single-cell RNA transcriptomics with SSC-derived polyclonal colonies was performed to characterize single-cell differentiation potential and molecular signatures. This study indicates multi-lineage potential of cultured SSCs and identifies molecular alterations in osteogenic and chondrogenic precursors. Overall design: Single-cell RNA sequencing of sorted and cultured PDGFRalpha+/Sca-1+ skeletal stem cells of 3-weeks-old limb of four genotypes (STAT1+/-, STAT1-/-, PDGFRbD849V+/-STAT1+/-,PDGFRbD849V+/-STAT1-/-) of mice"
Kwon 2021,KS+-01,PDGFRbD849V+/-STAT1+/-Sox2Cre+/-; female,bone,NA,NA,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE183404,GSM5556897,3p_v3,fastq,SRR15713197,NA,SRX12008784,SRP335579,SRS10014931,SAMN21216263,NA,NA,"Kwon et al, Development, 2021",10.1242/dev.199607,https://pubmed.ncbi.nlm.nih.gov/34738614/,Illumina NovaSeq 6000,Single-cell transcriptomics of cultured skeletal stem cells with a PDGFRbeta D849V mutation,"We demonstrate that skeletal stem cells (SSCs) isolated from mice with a gain-of-function D849V point mutation in PDGFRbeta exhibit colony formation defects that parallel the wasting or overgrowth phenotypes of the mice. Single-cell RNA transcriptomics with SSC-derived polyclonal colonies was performed to characterize single-cell differentiation potential and molecular signatures. This study indicates multi-lineage potential of cultured SSCs and identifies molecular alterations in osteogenic and chondrogenic precursors. Overall design: Single-cell RNA sequencing of sorted and cultured PDGFRalpha+/Sca-1+ skeletal stem cells of 3-weeks-old limb of four genotypes (STAT1+/-, STAT1-/-, PDGFRbD849V+/-STAT1+/-,PDGFRbD849V+/-STAT1-/-) of mice"
Kwon 2021,KS+-02,PDGFRbD849V+/-STAT1+/-Sox2Cre+/-; male,bone,NA,NA,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE183404,GSM5556898,3p_v3,fastq,SRR15713198;SRR15713199,NA,SRX12008785,SRP335579,SRS10014932,SAMN21216264,NA,NA,"Kwon et al, Development, 2021",10.1242/dev.199607,https://pubmed.ncbi.nlm.nih.gov/34738614/,Illumina NovaSeq 6000,Single-cell transcriptomics of cultured skeletal stem cells with a PDGFRbeta D849V mutation,"We demonstrate that skeletal stem cells (SSCs) isolated from mice with a gain-of-function D849V point mutation in PDGFRbeta exhibit colony formation defects that parallel the wasting or overgrowth phenotypes of the mice. Single-cell RNA transcriptomics with SSC-derived polyclonal colonies was performed to characterize single-cell differentiation potential and molecular signatures. This study indicates multi-lineage potential of cultured SSCs and identifies molecular alterations in osteogenic and chondrogenic precursors. Overall design: Single-cell RNA sequencing of sorted and cultured PDGFRalpha+/Sca-1+ skeletal stem cells of 3-weeks-old limb of four genotypes (STAT1+/-, STAT1-/-, PDGFRbD849V+/-STAT1+/-,PDGFRbD849V+/-STAT1-/-) of mice"
Kwon 2021,KS--01,PDGFRbD849V+/-STAT1-/-Sox2Cre+/-; female,bone,NA,NA,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE183404,GSM5556899,3p_v3,fastq,SRR15713200,NA,SRX12008786,SRP335579,SRS10014933,SAMN21216266,NA,NA,"Kwon et al, Development, 2021",10.1242/dev.199607,https://pubmed.ncbi.nlm.nih.gov/34738614/,Illumina NovaSeq 6000,Single-cell transcriptomics of cultured skeletal stem cells with a PDGFRbeta D849V mutation,"We demonstrate that skeletal stem cells (SSCs) isolated from mice with a gain-of-function D849V point mutation in PDGFRbeta exhibit colony formation defects that parallel the wasting or overgrowth phenotypes of the mice. Single-cell RNA transcriptomics with SSC-derived polyclonal colonies was performed to characterize single-cell differentiation potential and molecular signatures. This study indicates multi-lineage potential of cultured SSCs and identifies molecular alterations in osteogenic and chondrogenic precursors. Overall design: Single-cell RNA sequencing of sorted and cultured PDGFRalpha+/Sca-1+ skeletal stem cells of 3-weeks-old limb of four genotypes (STAT1+/-, STAT1-/-, PDGFRbD849V+/-STAT1+/-,PDGFRbD849V+/-STAT1-/-) of mice"
Kwon 2021,KS--02,PDGFRbD849V+/-STAT1-/-Sox2Cre+/-; male,bone,NA,NA,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE183404,GSM5556900,3p_v3,fastq,SRR15713201;SRR15713202,NA,SRX12008787,SRP335579,SRS10014934,SAMN21216267,NA,NA,"Kwon et al, Development, 2021",10.1242/dev.199607,https://pubmed.ncbi.nlm.nih.gov/34738614/,Illumina NovaSeq 6000,Single-cell transcriptomics of cultured skeletal stem cells with a PDGFRbeta D849V mutation,"We demonstrate that skeletal stem cells (SSCs) isolated from mice with a gain-of-function D849V point mutation in PDGFRbeta exhibit colony formation defects that parallel the wasting or overgrowth phenotypes of the mice. Single-cell RNA transcriptomics with SSC-derived polyclonal colonies was performed to characterize single-cell differentiation potential and molecular signatures. This study indicates multi-lineage potential of cultured SSCs and identifies molecular alterations in osteogenic and chondrogenic precursors. Overall design: Single-cell RNA sequencing of sorted and cultured PDGFRalpha+/Sca-1+ skeletal stem cells of 3-weeks-old limb of four genotypes (STAT1+/-, STAT1-/-, PDGFRbD849V+/-STAT1+/-,PDGFRbD849V+/-STAT1-/-) of mice"
Olmsted-Davis 2021,HO + Callus 10X-scRNA-seq,NA,bone,NA,NA,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE185500,GSM5616860,3p_v2,fastq,SRR16230855,NA,NA,NA,NA,NA,NA,NA,NA,10.3389/fimmu.2021.686769,https://pubmed.ncbi.nlm.nih.gov/34712222/,NA,NA,NA
Long 2022,Col10a1-Cre;R26-tdTomato total bone cells e16.5 post-FACS,NA,bone,NA,NA,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE190616,GSM5726705,3p_v3,bam,SRR17190652,NA,NA,NA,NA,NA,NA,NA,NA,10.7554/eLife.76932,https://pubmed.ncbi.nlm.nih.gov/35179487/,NA,NA,NA
Lin 2022,young,NA,bone,NA,NA,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE199755,GSM5983931,3p_v3,fastq,SRR18534318;SRR18534319,NA,NA,NA,NA,SAMN27097845,NA,NA,NA,NA,NA,NA,NA,NA
Lin 2022,aged,NA,bone,NA,NA,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE199755,GSM5983932,3p_v3,fastq,SRR18534320;SRR18534321,NA,NA,NA,NA,SAMN27097846,NA,NA,NA,NA,NA,NA,NA,NA
Tang W 2022,SIFK,NA,cartilage,articular chondrocyte,NA,NA,NA,NA,NA,TRUE,FALSE,Homo sapiens,GSE215965,GSM6651688,3p_v3,fastq,SRR21937294,NA,NA,NA,NA,NA,NA,NA,NA,10.2147/JIR.S385648,https://pubmed.ncbi.nlm.nih.gov/36386577/,NA,NA,NA
Wang T 2022,healthy volunteer talus 1,NA,cartilage,talus,cell,NA,NA,NA,NA,TRUE,TRUE,Homo sapiens,GSE216578,GSM6680841,3p_v3,fastq,SRR22045703,NA,NA,NA,NA,NA,NA,NA,NA,10.3389/fcell.2022.1047119,https://pubmed.ncbi.nlm.nih.gov/36438550/,NA,NA,NA
Wang T 2022,healthy volunteer talus 2,NA,cartilage,talus,cell,NA,NA,NA,NA,TRUE,TRUE,Homo sapiens,GSE216578,GSM6680842,3p_v3,fastq,SRR22045702,NA,NA,NA,NA,NA,NA,NA,NA,10.3389/fcell.2022.1047119,https://pubmed.ncbi.nlm.nih.gov/36438550/,NA,NA,NA
Wang T 2022,healthy volunteer talus 3,NA,cartilage,talus,cell,NA,NA,NA,NA,TRUE,TRUE,Homo sapiens,GSE216578,GSM6680843,3p_v3,fastq,SRR22045701,NA,NA,NA,NA,NA,NA,NA,NA,10.3389/fcell.2022.1047119,https://pubmed.ncbi.nlm.nih.gov/36438550/,NA,NA,NA
Wang T 2022,healthy volunteer talus 4,NA,cartilage,talus,cell,NA,NA,NA,NA,TRUE,TRUE,Homo sapiens,GSE216578,GSM6680844,3p_v3,fastq,SRR22045700,NA,NA,NA,NA,NA,NA,NA,NA,10.3389/fcell.2022.1047119,https://pubmed.ncbi.nlm.nih.gov/36438550/,NA,NA,NA
Wang T 2022,healthy volunteer talus 5,NA,cartilage,talus,cell,NA,NA,NA,NA,TRUE,TRUE,Homo sapiens,GSE216578,GSM6680845,3p_v3,fastq,SRR22045699,NA,NA,NA,NA,NA,NA,NA,NA,10.3389/fcell.2022.1047119,https://pubmed.ncbi.nlm.nih.gov/36438550/,NA,NA,NA
Evseenko 2023,Osteoarthritic chondrocytes1,NA,cartilage,chondrocytes,NA,NA,NA,NA,R1 is only 25bp,FALSE,FALSE,Homo sapiens,GSE181355,GSM5495172,3p_v2,fastq,SRR15328362,NA,NA,NA,NA,SAMN20523725,NA,NA,NA,NA,NA,NA,NA,NA
Evseenko 2023,Osteoarthritic chondrocytes2,NA,cartilage,chondrocytes,NA,NA,NA,NA,R1 is only 25bp,FALSE,FALSE,Homo sapiens,GSE181355,GSM5495173,3p_v2,fastq,SRR15328363,NA,NA,NA,NA,SAMN20523726,NA,NA,NA,NA,NA,NA,NA,NA
Petrigliano 2021,ESI-017,NA,cartilage,ESC,cell,NA,NA,NA,NA,TRUE,FALSE,Homo sapiens,GSE142045,GSM5091916,3p_v3,fastq,SRR13741032;SRR13741033,NA,SRX10128164,SRP237632,SRS8282572,SAMN17980335,NA,NA,NA,10.1038/s41536-021-00187-3,https://pubmed.ncbi.nlm.nih.gov/34815400/,NA,NA,NA
Petrigliano 2021,hESDC-M1,NA,cartilage,ESC-derived chondrocytes,cell,NA,NA,NA,NA,TRUE,TRUE,Homo sapiens,GSE142045,GSM5091917,3p_v2,fastq,SRR13741034;SRR13741035;SRR13741036;SRR13741037,NA,SRX10128165,SRP237632,SRS8282573,SAMN17980334,NA,NA,NA,10.1038/s41536-021-00187-3,https://pubmed.ncbi.nlm.nih.gov/34815400/,NA,NA,NA
Petrigliano 2021,hESDC-M2,NA,cartilage,ESC-derived chondrocytes,cell,NA,NA,NA,NA,TRUE,TRUE,Homo sapiens,GSE142045,GSM5091918,3p_v2,fastq,SRR13741038;SRR13741039;SRR13741040;SRR13741041,NA,SRX10128166,SRP237632,SRS8282574,SAMN17980333,NA,NA,NA,10.1038/s41536-021-00187-3,https://pubmed.ncbi.nlm.nih.gov/34815400/,NA,NA,NA
Petrigliano 2021,Embryonic chondroprogenitor,NA,cartilage,chondrocytes,cell,NA,NA,NA,NA,TRUE,FALSE,Homo sapiens,GSE142045,GSM5091920,3p_v3,fastq,SRR13741046;SRR13741047,NA,SRX10128168,SRP237632,SRS8282576,SAMN17980331,NA,NA,NA,10.1038/s41536-021-00187-3,https://pubmed.ncbi.nlm.nih.gov/34815400/,NA,NA,NA
Petrigliano 2021,Fetal chondrocytes,NA,cartilage,chondrocytes,cell,NA,NA,NA,NA,TRUE,FALSE,Homo sapiens,GSE142045,GSM5091921,3p_v2,fastq,SRR13741048;SRR13741049;SRR13741050;SRR13741051,NA,SRX10128169,SRP237632,SRS8282577,SAMN17980330,NA,NA,NA,10.1038/s41536-021-00187-3,https://pubmed.ncbi.nlm.nih.gov/34815400/,NA,NA,NA
Petrigliano 2021,Juvenile chondrocytes,NA,cartilage,chondrocytes,cell,NA,NA,NA,NA,TRUE,FALSE,Homo sapiens,GSE142045,GSM5091922,3p_v2,fastq,SRR13741052;SRR13741053;SRR13741054;SRR13741055,NA,SRX10128169,SRP237632,SRS8282577,SAMN17980329,NA,NA,NA,10.1038/s41536-021-00187-3,https://pubmed.ncbi.nlm.nih.gov/34815400/,NA,NA,NA
Petrigliano 2021,Adult chondrocytes,NA,cartilage,chondrocytes,cell,NA,NA,NA,NA,TRUE,FALSE,Homo sapiens,GSE142045,GSM5091923,3p_v2,fastq,SRR13741056;SRR13741057;SRR13741058;SRR13741059,NA,SRX10128170,SRP237632,SRS8282578,SAMN17980328,NA,NA,NA,10.1038/s41536-021-00187-3,https://pubmed.ncbi.nlm.nih.gov/34815400/,NA,NA,NA
Laplace-Builhe 2021,Cut caudal fin_scRNA,NA,cartilage,caudal fin,cell,NA,NA,NA,Error R1 missing,TRUE,TRUE,Danio rerio,GSE158851,GSM4812243,3p_v3.1,fastq,SRR12749697;SRR12749698,NA,SRX9221654,SRP285950,SRS7455355,SAMN16320526,NA,NA,"Laplace-Builhe et al, Nature Communications, 2021",10.1038/s41467-021-26422-5,https://pubmed.ncbi.nlm.nih.gov/34732706/,Illumina NovaSeq 6000,Single-cell RNA sequencing of the cut and uncut caudal fin of zebrafish larvae,"Purpose: The goal of this study was to establish the first detailed cell atlas of the regenerating caudal fin of zebrafish larvae. Intact and regenerating caudal fin were used for single-cell RNA-sequencing with the aim to provide the first integrated model of epimorphic regeneration in zebrafish larvae and demonstrate the diversity of the cells required for blastema formation.  Methods: 150 of regenerating caudal fin (cut) and intact caudal fine (uncut) samples were dissociated and loaded into the 10x Genomics Chromium Platform, and sequenced using Illumina NovaSeq 6000.  Conclusion: Our study constitutes a resource of the gene expression profile in intact and regenerating caudal fin of zebrafish larvae. We report the application of single-molecule-based sequencing technology for high-throughput profiling of both intact (uncut) and regenerating caudal fin samples (cut) at 24hpA. We confirmed the presence of macrophage subsets, previously described by our group to govern zebrafish fin regeneration, and identified a novel blastemal cell population. Overall design: Cells from intact and regenerating caudal fin were used for single-cell RNA-sequencing (10xGenomics Chromium Platform), and sequenced using Illumina NovaSeq 6000. Cell populations were distinguished by Uniform Manifold Approximation and Projection (UMAP)."
Laplace-Builhe 2021,Uncut caudal fin_scRNA,NA,cartilage,caudal fin,cell,NA,NA,NA,Error R1 missing,TRUE,TRUE,Danio rerio,GSE158851,GSM4812244,3p_v3.1,fastq,SRR12749699;SRR12749700,NA,SRX9221655,SRP285950,SRS7455356,SAMN16320525,NA,NA,"Laplace-Builhe et al, Nature Communications, 2021",10.1038/s41467-021-26422-5,https://pubmed.ncbi.nlm.nih.gov/34732706/,Illumina NovaSeq 6000,Single-cell RNA sequencing of the cut and uncut caudal fin of zebrafish larvae,"Purpose: The goal of this study was to establish the first detailed cell atlas of the regenerating caudal fin of zebrafish larvae. Intact and regenerating caudal fin were used for single-cell RNA-sequencing with the aim to provide the first integrated model of epimorphic regeneration in zebrafish larvae and demonstrate the diversity of the cells required for blastema formation.  Methods: 150 of regenerating caudal fin (cut) and intact caudal fine (uncut) samples were dissociated and loaded into the 10x Genomics Chromium Platform, and sequenced using Illumina NovaSeq 6000.  Conclusion: Our study constitutes a resource of the gene expression profile in intact and regenerating caudal fin of zebrafish larvae. We report the application of single-molecule-based sequencing technology for high-throughput profiling of both intact (uncut) and regenerating caudal fin samples (cut) at 24hpA. We confirmed the presence of macrophage subsets, previously described by our group to govern zebrafish fin regeneration, and identified a novel blastemal cell population. Overall design: Cells from intact and regenerating caudal fin were used for single-cell RNA-sequencing (10xGenomics Chromium Platform), and sequenced using Illumina NovaSeq 6000. Cell populations were distinguished by Uniform Manifold Approximation and Projection (UMAP)."
Gan 2021,human_NP_1,NA,cartilage,NA,cell,NA,NA,NA,NA,TRUE,FALSE,Homo sapiens,GSE160756,GSM4878538,3p_v3,fastq,SRR12973953;SRR12973954;SRR12973955;SRR12973955;SRR12973956;SRR12973957;SRR12973958;SRR12973959;SRR12973960,NA,SRX9426285,NA,NA,SAMN16644284,NA,NA,NA,NA,NA,NA,NA,NA
Gan 2021,human_NP_2,NA,cartilage,NA,cell,NA,NA,NA,NA,TRUE,FALSE,Homo sapiens,GSE160756,GSM4878539,3p_v3,fastq,SRR12973961;SRR12973962;SRR12973963;SRR12973964,NA,SRX9426286,NA,NA,SAMN16644283,NA,NA,NA,NA,NA,NA,NA,NA
Gan 2021,human_NP_3,NA,cartilage,NA,cell,NA,NA,NA,NA,TRUE,FALSE,Homo sapiens,GSE160756,GSM4878540,3p_v3,fastq,SRR12973965;SRR12973966;SRR12973967;SRR12973968,NA,SRX9426287,NA,NA,SAMN16644282,NA,NA,NA,NA,NA,NA,NA,NA
Gan 2021,human_CEP_1,NA,cartilage,NA,cell,NA,NA,NA,NA,TRUE,FALSE,Homo sapiens,GSE160756,GSM4878541,3p_v3,fastq,SRR12973969;SRR12973970;SRR12973971;SRR12973972,NA,SRX9426288,NA,NA,SAMN16644281,NA,NA,NA,NA,NA,NA,NA,NA
Gan 2021,human_CEP_2,NA,cartilage,NA,cell,NA,NA,NA,NA,TRUE,FALSE,Homo sapiens,GSE160756,GSM4878542,3p_v3,fastq,SRR12973973;SRR12973974;SRR12973975;SRR12973976,NA,SRX9426289,NA,NA,SAMN16644280,NA,NA,NA,NA,NA,NA,NA,NA
Gan 2021,human_AF_1,NA,cartilage,NA,cell,NA,NA,NA,NA,TRUE,FALSE,Homo sapiens,GSE160756,GSM4878543,3p_v3,fastq,SRR12973977;SRR12973978;SRR12973979;SRR12973980;SRR12973981;SRR12973982;SRR12973983;SRR12973984,NA,SRX9426290,NA,NA,SAMN16644279,NA,NA,NA,NA,NA,NA,NA,NA
Gan 2021,human_AF_2,NA,cartilage,NA,cell,NA,NA,NA,NA,TRUE,FALSE,Homo sapiens,GSE160756,GSM4878544,3p_v3,fastq,SRR12973985;SRR12973986;SRR12973987;SRR12973988;SRR12973989;SRR12973990;SRR12973991;SRR12973992,NA,SRX9426291,NA,NA,SAMN16644278,NA,NA,NA,NA,NA,NA,NA,NA
Hung 2022,Single Cell GEM well 1 (NA19160_NA18855_NA18856),NA,cartilage,chondrocytes,cell,NA,NA,NA,NA,TRUE,TRUE,Homo sapiens,GSE165874,GSM5051909,3p_v3,fastq,SRR13600604,NA,SRX9995016,NA,NA,SAMN17727486,NA,NA,NA,NA,NA,NA,NA,NA
Hung 2022,Single Cell GEM well 2 (NA19160_NA18855),NA,cartilage,chondrocytes,cell,NA,NA,NA,NA,TRUE,TRUE,Homo sapiens,GSE165874,GSM5051910,3p_v3,fastq,SRR13600605,NA,SRX9995017,NA,NA,SAMN17727485,NA,NA,NA,NA,NA,NA,NA,NA
Fu 2022,normal1,NA,cartilage,chondrocytes,cell,NA,NA,NA,NA,TRUE,TRUE,Homo sapiens,GSE169454,GSM5203389,3p_v3,bam,SRR14048704,NA,SRX10424647,NA,NA,SAMN18444947,NA,NA,NA,NA,NA,NA,NA,NA
Fu 2022,normal2,NA,cartilage,chondrocytes,cell,NA,NA,NA,NA,TRUE,TRUE,Homo sapiens,GSE169454,GSM5203390,3p_v3,bam,SRR14048705,NA,SRX10424648,NA,NA,SAMN18444946,NA,NA,NA,NA,NA,NA,NA,NA
Fu 2022,normal3,NA,cartilage,chondrocytes,cell,NA,NA,NA,NA,TRUE,TRUE,Homo sapiens,GSE169454,GSM5203391,3p_v3,bam,SRR14048706,NA,SRX10424649,NA,NA,SAMN18444945,NA,NA,NA,NA,NA,NA,NA,NA
Fu 2022,OA1,NA,cartilage,chondrocytes,cell,NA,NA,NA,NA,TRUE,TRUE,Homo sapiens,GSE169454,GSM5203392,3p_v3,bam,SRR14048707,NA,SRX10424650,NA,NA,SAMN18444944,NA,NA,NA,NA,NA,NA,NA,NA
Fu 2022,OA2,NA,cartilage,chondrocytes,cell,NA,NA,NA,NA,TRUE,TRUE,Homo sapiens,GSE169454,GSM5203393,3p_v3,bam,SRR14048708,NA,SRX10424651,NA,NA,SAMN18444943,NA,NA,NA,NA,NA,NA,NA,NA
Fu 2022,OA3,NA,cartilage,chondrocytes,cell,NA,NA,NA,NA,TRUE,TRUE,Homo sapiens,GSE169454,GSM5203394,3p_v3,bam,SRR14048709,NA,SRX10424652,NA,NA,SAMN18444942,NA,NA,NA,NA,NA,NA,NA,NA
Fu 2022,OA4,NA,cartilage,chondrocytes,cell,NA,NA,NA,NA,TRUE,TRUE,Homo sapiens,GSE169454,GSM5203395,3p_v3,bam,SRR14048710,NA,SRX10424653,NA,NA,SAMN18444941,NA,NA,NA,NA,NA,NA,NA,NA
Sebastian 2021,Uninjured,NA,cartilage,knee,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE172500,GSM5258024,3p_v3,bam,SRR14294973,NA,SRX10652879,SRP315738,NA,SAMN18822180,NA,NA,"Sebastian et al, Cells, 2021",10.3390/cells10061462,https://pubmed.ncbi.nlm.nih.gov/34200880/,NA,NA,NA
Sebastian 2021,3 DPI,NA,cartilage,knee,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE172500,GSM5258025,3p_v3,bam,SRR14294974,NA,SRX10652880,SRP315738,NA,SAMN18822179,NA,NA,"Sebastian et al, Cells, 2021",10.3390/cells10061462,https://pubmed.ncbi.nlm.nih.gov/34200880/,NA,NA,NA
Sebastian 2021,7 DPI,NA,cartilage,knee,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE172500,GSM5258026,3p_v3,bam,SRR14294975,NA,SRX10652881,SRP315738,NA,SAMN18822178,NA,NA,"Sebastian et al, Cells, 2021",10.3390/cells10061462,https://pubmed.ncbi.nlm.nih.gov/34200880/,NA,NA,NA
Brachvogel 2021,Cre,NA,cartilage,knee,cell,female,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE173204,GSM5261801,3p_v3,bam,SRR14310180,NA,SRX10665412,NA,NA,SAMN18848200,NA,NA,NA,10.1016/j.jbc.2021.101224,https://pubmed.ncbi.nlm.nih.gov/34560099/,NA,NA,NA
Brachvogel 2021,CreTW,NA,cartilage,knee,cell,female,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE173204,GSM5261802,3p_v3,bam,SRR14310181,NA,SRX10665413,NA,NA,SAMN18848199,NA,NA,NA,10.1016/j.jbc.2021.101224,https://pubmed.ncbi.nlm.nih.gov/34560099/,NA,NA,NA
Ma J 2021,C1,NA,cartilage,auricular,cell,NA,NA,NA,NA,TRUE,TRUE,Homo sapiens,GSE179135,GSM5410484,3p_v3,fastq,SRR14972272;SRR14972274;SRR14972276;SRR14972278,NA,SRX11287778,NA,NA,SAMN19948087,NA,NA,NA,10.1002/ctm2.702,https://pubmed.ncbi.nlm.nih.gov/35184397/,NA,NA,NA
Ma J 2021,C2,NA,cartilage,auricular,cell,NA,NA,NA,NA,TRUE,TRUE,Homo sapiens,GSE179135,GSM5410485,3p_v3,fastq,SRR14972280;SRR14972282;SRR14972284;SRR14972286;SRR14972288;SRR14972290;SRR14972292;SRR14972294,NA,SRX11287779,NA,NA,SAMN19948086,NA,NA,NA,10.1002/ctm2.702,https://pubmed.ncbi.nlm.nih.gov/35184397/,NA,NA,NA
Ma J 2021,C3,NA,cartilage,auricular,cell,NA,NA,NA,NA,TRUE,TRUE,Homo sapiens,GSE179135,GSM5410486,3p_v3,fastq,SRR14972296;SRR14972298;SRR14972300;SRR14972302;SRR14972304;SRR14972306;SRR14972308;SRR14972310,NA,SRX11287780,NA,NA,SAMN19948085,NA,NA,NA,10.1002/ctm2.702,https://pubmed.ncbi.nlm.nih.gov/35184397/,NA,NA,NA
Ma J 2021,C4,NA,cartilage,auricular,cell,NA,NA,NA,NA,TRUE,TRUE,Homo sapiens,GSE179135,GSM5410487,3p_v3,fastq,SRR14972312;SRR14972314;SRR14972316;SRR14972318,NA,SRX11287781,NA,NA,SAMN19948083,NA,NA,NA,10.1002/ctm2.702,https://pubmed.ncbi.nlm.nih.gov/35184397/,NA,NA,NA
Ma J 2021,C5,NA,cartilage,auricular,cell,NA,NA,NA,NA,TRUE,TRUE,Homo sapiens,GSE179135,GSM5410488,3p_v3,fastq,SRR14972320;SRR14972322;SRR14972324;SRR14972326,NA,SRX11287782,NA,NA,SAMN19948082,NA,NA,NA,10.1002/ctm2.702,https://pubmed.ncbi.nlm.nih.gov/35184397/,NA,NA,NA
Ma J 2021,C6,NA,cartilage,auricular,cell,NA,NA,NA,NA,TRUE,TRUE,Homo sapiens,GSE179135,GSM5410489,3p_v3,fastq,SRR14972328;SRR14972330;SRR14972332;SRR14972334,NA,SRX11287783,NA,NA,SAMN19948081,NA,NA,NA,10.1002/ctm2.702,https://pubmed.ncbi.nlm.nih.gov/35184397/,NA,NA,NA
Ma J 2021,M1,NA,cartilage,auricular,cell,NA,NA,NA,NA,TRUE,TRUE,Homo sapiens,GSE179135,GSM5410490,3p_v3,fastq,SRR14972336;SRR14972337;SRR14972339;SRR14972340,NA,SRX11287784,NA,NA,SAMN19948080,NA,NA,NA,10.1002/ctm2.702,https://pubmed.ncbi.nlm.nih.gov/35184397/,NA,NA,NA
Ma J 2021,M2,NA,cartilage,auricular,cell,NA,NA,NA,NA,TRUE,TRUE,Homo sapiens,GSE179135,GSM5410491,3p_v3,fastq,SRR14972342;SRR14972343;SRR14972345;SRR14972346,NA,SRX11287785,NA,NA,SAMN19948079,NA,NA,NA,10.1002/ctm2.702,https://pubmed.ncbi.nlm.nih.gov/35184397/,NA,NA,NA
Ma J 2021,M3,NA,cartilage,auricular,cell,NA,NA,NA,NA,TRUE,TRUE,Homo sapiens,GSE179135,GSM5410492,3p_v3,fastq,SRR14972348;SRR14972349;SRR14972351;SRR14972353,NA,SRX11287786,NA,NA,SAMN19948078,NA,NA,NA,10.1002/ctm2.702,https://pubmed.ncbi.nlm.nih.gov/35184397/,NA,NA,NA
Liu NQ 2022,Stat3fl/fl,NA,cartilage,NA,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE184406,GSM5587074,3p_v3,fastq,SRR15965269,NA,NA,NA,NA,NA,NA,NA,NA,10.1038/s42003-021-02944-y,https://pubmed.ncbi.nlm.nih.gov/35039652/,NA,NA,NA
Liu NQ 2022,Acan-Cre+/Cre;Stat3fl/fl,NA,cartilage,NA,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE184406,GSM5587075,3p_v3,fastq,SRR15965270,NA,NA,NA,NA,NA,NA,NA,NA,10.1038/s42003-021-02944-y,https://pubmed.ncbi.nlm.nih.gov/35039652/,NA,NA,NA
Crump 2021,scRNAseq_Sox10_Cre_bact_BtR_1.5dpf_rep_1,NA,embryo,cranial neural crest,NA,NA,NA,NA,NA,TRUE,TRUE,Danio rerio,GSE178969,GSM5402428,3p_v2,fastq,SRR14923950;SRR14923951;SRR14923952;SRR14923953,NA,SRX11237256,NA,NA,SAMN19903687,NA,NA,NA,NA,NA,NA,NA,NA
Crump 2021,scRNAseq_fliIa_eGFP_Sox10_dsRed_1.5dpf_rep_1,NA,embryo,cranial neural crest,NA,NA,NA,NA,NA,TRUE,TRUE,Danio rerio,GSE178969,GSM5402429,3p_v2,fastq,SRR14923954;SRR14923955;SRR14923956;SRR14923957,NA,SRX11237257,NA,NA,SAMN19903686,NA,NA,NA,NA,NA,NA,NA,NA
Crump 2021,scRNAseq_Sox10_Cre_bact_BtR_2dpf_rep_1,NA,embryo,cranial neural crest,NA,NA,NA,NA,NA,TRUE,TRUE,Danio rerio,GSE178969,GSM5402430,3p_v2,fastq,SRR14923958;SRR14923959;SRR14923960;SRR14923961,NA,SRX11237258,NA,NA,SAMN19903685,NA,NA,NA,NA,NA,NA,NA,NA
Crump 2021,scRNAseq_Sox10_Cre_bact_BtR_3dpf_rep_1,NA,embryo,cranial neural crest,NA,NA,NA,NA,NA,TRUE,TRUE,Danio rerio,GSE178969,GSM5402431,3p_v2,fastq,SRR14923962;SRR14923963;SRR14923964;SRR14923965,NA,SRX11237259,NA,NA,SAMN19903684,NA,NA,NA,NA,NA,NA,NA,NA
Crump 2021,scRNAseq_Sox10_Cre_bact_BtR_3dpf_rep_2,NA,embryo,cranial neural crest,NA,NA,NA,NA,NA,TRUE,TRUE,Danio rerio,GSE178969,GSM5402432,3p_v2,fastq,SRR14923966;SRR14923967;SRR14923968;SRR14923969,NA,SRX11237260,NA,NA,SAMN19903683,NA,NA,NA,NA,NA,NA,NA,NA
Crump 2021,scRNAseq_Sox10_Cre_bact_BtR_3dpf_rep_3,NA,embryo,cranial neural crest,NA,NA,NA,NA,NA,TRUE,TRUE,Danio rerio,GSE178969,GSM5402433,3p_v2,fastq,SRR14923970;SRR14923971;SRR14923972;SRR14923973,NA,SRX11237261,NA,NA,SAMN19903682,NA,NA,NA,NA,NA,NA,NA,NA
Crump 2021,scRNAseq_Sox10_Cre_bact_BtR_5dpf_rep_1,NA,embryo,cranial neural crest,NA,NA,NA,NA,NA,TRUE,TRUE,Danio rerio,GSE178969,GSM5402434,3p_v2,fastq,SRR14923974;SRR14923975;SRR14923976;SRR14923977,NA,SRX11237262,NA,NA,SAMN19903681,NA,NA,NA,NA,NA,NA,NA,NA
Crump 2021,scRNAseq_Sox10_Cre_bact_BtR_5dpf_rep_2,NA,embryo,cranial neural crest,NA,NA,NA,NA,NA,TRUE,TRUE,Danio rerio,GSE178969,GSM5402435,3p_v2,fastq,SRR14923978;SRR14923979;SRR14923980;SRR14923981,NA,SRX11237263,NA,NA,SAMN19903680,NA,NA,NA,NA,NA,NA,NA,NA
Crump 2021,scRNAseq_Sox10_Cre_bact_BtR_14dpf_rep_1,NA,embryo,cranial neural crest,NA,NA,NA,NA,NA,TRUE,TRUE,Danio rerio,GSE178969,GSM5402436,3p_v2,fastq,SRR14923982;SRR14923983;SRR14923984;SRR14923985,NA,SRX11237264,NA,NA,SAMN19903679,NA,NA,NA,NA,NA,NA,NA,NA
Crump 2021,scRNAseq_Sox10_Cre_bact_BtR_14dpf_rep_2,NA,embryo,cranial neural crest,NA,NA,NA,NA,NA,TRUE,TRUE,Danio rerio,GSE178969,GSM5402437,3p_v2,fastq,SRR14923986;SRR14923987;SRR14923988;SRR14923989,NA,SRX11237265,NA,NA,SAMN19903678,NA,NA,NA,NA,NA,NA,NA,NA
Crump 2021,scRNAseq_Sox10_Cre_bact_BtR_14dpf_rep_ceratohyal,NA,embryo,cranial neural crest,NA,NA,NA,NA,NA,TRUE,TRUE,Danio rerio,GSE178969,GSM5402438,3p_v2,fastq,SRR14923990;SRR14923991;SRR14923992;SRR14923993,NA,SRX11237266,NA,NA,SAMN19903677,NA,NA,NA,NA,NA,NA,NA,NA
Crump 2021,scRNAseq_Sox10_Cre_bact_BtR_60dpf_rep_1,NA,embryo,cranial neural crest,NA,NA,NA,NA,NA,TRUE,TRUE,Danio rerio,GSE178969,GSM5402439,3p_v2,fastq,SRR14923994;SRR14923995;SRR14923996;SRR14923997,NA,SRX11237267,NA,NA,SAMN19903676,NA,NA,NA,NA,NA,NA,NA,NA
Crump 2021,scRNAseq_Sox10_Cre_bact_BtR_60dpf_rep_2,NA,embryo,cranial neural crest,NA,NA,NA,NA,NA,TRUE,TRUE,Danio rerio,GSE178969,GSM5402440,3p_v2,fastq,SRR14923998;SRR14923999;SRR14924000;SRR14924001,NA,SRX11237268,NA,NA,SAMN19903675,NA,NA,NA,NA,NA,NA,NA,NA
Crump 2021,scRNAseq_Sox10_Cre_bact_BtR_150dpf_rep_1,NA,embryo,cranial neural crest,NA,NA,NA,NA,NA,TRUE,TRUE,Danio rerio,GSE178969,GSM5402441,3p_v2,fastq,SRR14924002;SRR14924003;SRR14924004;SRR14924005,NA,SRX11237269,NA,NA,SAMN19903674,NA,NA,NA,NA,NA,NA,NA,NA
Crump 2021,scRNAseq_Sox10_Cre_bact_BtR_150dpf_rep_2,NA,embryo,cranial neural crest,NA,NA,NA,NA,NA,TRUE,TRUE,Danio rerio,GSE178969,GSM5402442,3p_v2,fastq,SRR14924006;SRR14924007;SRR14924008;SRR14924009,NA,SRX11237270,NA,NA,SAMN19903673,NA,NA,NA,NA,NA,NA,NA,NA
Crump 2021,scRNAseq_Sox10_Cre_bact_BtR_150dpf_rep_3,NA,embryo,cranial neural crest,NA,NA,NA,NA,NA,TRUE,TRUE,Danio rerio,GSE178969,GSM5402443,3p_v2,fastq,SRR14924010;SRR14924011;SRR14924012;SRR14924013,NA,SRX11237271,NA,NA,SAMN19903672,NA,NA,NA,NA,NA,NA,NA,NA
Gage 2023,Multiome_control_nr5a2_GFP_2.5dpf_head (snRNA-seq),NA,embryo,jaw mesenchyme,NA,NA,NA,NA,29bp R1; multiome dataset,TRUE,FALSE,Danio rerio,GSE210251,GSM6424703,3p_v3.1,fastq,SRR20737630,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Gage 2023,Multiome_mutant_nr5a2_GFP_2.5dpf_head (snRNA-seq),NA,embryo,jaw mesenchyme,NA,NA,NA,NA,29bp R1; multiome dataset,TRUE,FALSE,Danio rerio,GSE210251,GSM6424705,3p_v3.1,fastq,SRR20737632,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Hota 2022,WT MES,NA,heart,mesoderma,cell,NA,NA,NA,1 fq file downloaded,FALSE,TRUE,Homo sapiens,GSE116293,GSM3227600,3p_v2,bam,SRR7430961,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Hota 2022,Brm KO MES,NA,heart,mesoderma,cell,NA,NA,NA,1 fq file downloaded,FALSE,TRUE,Homo sapiens,GSE116293,GSM3227601,3p_v2,bam,SRR7430962,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Hota 2022,WT CM,NA,heart,cardiomyocytes,cell,NA,NA,NA,1 fq file downloaded,FALSE,TRUE,Homo sapiens,GSE116293,GSM3227602,3p_v2,bam,SRR7430963,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Hota 2022,BRM KO CM,NA,heart,cardiomyocytes,cell,NA,NA,NA,1 fq file downloaded,FALSE,TRUE,Homo sapiens,GSE116293,GSM3227603,3p_v2,bam,SRR7430964,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Steimle 2022,snRNA-Pitx2-LA-WT,NA,heart,left atrium,NA,NA,NA,NA,renaming issues (only R2 & R3 remain?),FALSE,TRUE,Homo sapiens,GSE183310,GSM5555380,3p_v3,fastq,SRR15703042;SRR15703043;SRR15703044;SRR15703045,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Steimle 2022,snRNA-Pitx2-LA-MUT,NA,heart,left atrium,NA,NA,NA,NA,renaming issues (only R2 & R3 remain?),FALSE,TRUE,Homo sapiens,GSE183310,GSM5555381,3p_v3,fastq,SRR15703046;SRR15703047;SRR15703048;SRR15703049,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Steimle 2022,snRNA-Pitx2-PV-WT,NA,heart,pulmonary vein,NA,NA,NA,NA,renaming issues (only R2 & R3 remain?),FALSE,TRUE,Homo sapiens,GSE183310,GSM5555382,3p_v3,fastq,SRR15703050;SRR15703051;SRR15703052;SRR15703053,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Steimle 2022,snRNA-Pitx2-PV-MUT,NA,heart,pulmonary vein,NA,NA,NA,NA,renaming issues (only R2 & R3 remain?),FALSE,TRUE,Homo sapiens,GSE183310,GSM5555383,3p_v3,fastq,SRR15703054;SRR15703055;SRR15703056;SRR15703057,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Esfandyari 2022,healthy_hiPSCCM_mimic365,NA,heart,IPSC-derived organoid,NA,NA,NA,NA,fasterq err 2 and 3,FALSE,FALSE,Homo sapiens,GSE185690,GSM5621619,3p_v2,fastq,SRR16293215,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Esfandyari 2022,healthy_hiPSCCM_antimiR365,NA,heart,IPSC-derived organoid,NA,NA,NA,NA,fasterq err 2 and 3,FALSE,FALSE,Homo sapiens,GSE185690,GSM5621620,3p_v2,fastq,SRR16293216,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Esfandyari 2022,LQT1_hiPSCCM_gene expression_multiplex_untreated_antimiRCtrl_antimiR365,NA,heart,IPSC-derived organoid,NA,NA,NA,NA,fasterq err 2 and 3,FALSE,FALSE,Homo sapiens,GSE185690,GSM5621621,3p_v3.1,fastq,SRR16293217;SRR16293218;SRR16293219;SRR16293220;SRR16293221;SRR16293222;SRR16293223;SRR16293224,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Hong 2022,"Cardiac NCCs, KO",NA,heart,neural crest cells,NA,NA,NA,NA,1 fq file downloaded,FALSE,TRUE,Mus musculus,GSE195589,GSM5841323,3p_v3,fastq,SRR17793021;SRR17793022;SRR17793023;SRR17793024,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Hong 2022,"Cardiac NCCs, WT",NA,heart,neural crest cells,NA,NA,NA,NA,1 fq file downloaded,FALSE,TRUE,Mus musculus,GSE195589,GSM5841324,3p_v3,fastq,SRR17793017;SRR17793018;SRR17793019;SRR17793020,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Ranade 2022,WT_E775_1 [scRNAseq],NA,heart,NA,NA,NA,NA,NA,1 fq file downloaded,FALSE,TRUE,Mus musculus,GSE198562,GSM5952282,3p_v3.1,bam,SRR18342524,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Ranade 2022,WT_E775_2 [scRNAseq],NA,heart,NA,NA,NA,NA,NA,NA,FALSE,TRUE,Mus musculus,GSE198562,GSM5952283,3p_v3.1,bam,SRR18342525,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Ranade 2022,WT_E775_3 [scRNAseq],NA,heart,NA,NA,NA,NA,NA,NA,FALSE,TRUE,Mus musculus,GSE198562,GSM5952284,3p_v3.1,bam,SRR18342526,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Ranade 2022,WT_E775_4 [scRNAseq],NA,heart,NA,NA,NA,NA,NA,NA,FALSE,TRUE,Mus musculus,GSE198562,GSM5952285,3p_v3.1,bam,SRR18342527,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Ranade 2022,WT_E775_5 [scRNAseq],NA,heart,NA,NA,NA,NA,NA,NA,FALSE,TRUE,Mus musculus,GSE198562,GSM5952286,3p_v3.1,bam,SRR18342528,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Ranade 2022,WT_E825_1 [scRNAseq],NA,heart,NA,NA,NA,NA,NA,NA,FALSE,TRUE,Mus musculus,GSE198562,GSM5952287,3p_v3.1,bam,SRR18342529,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Ranade 2022,WT_E825_2 [scRNAseq],NA,heart,NA,NA,NA,NA,NA,NA,FALSE,TRUE,Mus musculus,GSE198562,GSM5952288,3p_v3.1,bam,SRR18342530,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Ranade 2022,WT_E95_1 [scRNAseq],NA,heart,NA,NA,NA,NA,NA,NA,FALSE,TRUE,Mus musculus,GSE198562,GSM5952289,3p_v3.1,bam,SRR18342531,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Ranade 2022,WT_E95_2 [scRNAseq],NA,heart,NA,NA,NA,NA,NA,NA,FALSE,TRUE,Mus musculus,GSE198562,GSM5952290,3p_v3.1,bam,SRR18342532,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Ranade 2022,WT_E95_3 [scRNAseq],NA,heart,NA,NA,NA,NA,NA,NA,FALSE,TRUE,Mus musculus,GSE198562,GSM5952291,3p_v3.1,bam,SRR18342533,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Ranade 2022,WT_E95_4 [scRNAseq],NA,heart,NA,NA,NA,NA,NA,NA,FALSE,TRUE,Mus musculus,GSE198562,GSM5952292,3p_v3.1,bam,SRR18342534,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Ranade 2022,WT_E105_1 [scRNAseq],NA,heart,NA,NA,NA,NA,NA,NA,FALSE,TRUE,Mus musculus,GSE198562,GSM5952293,3p_v3.1,bam,SRR18342535,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Ranade 2022,WT_E105_2 [scRNAseq],NA,heart,NA,NA,NA,NA,NA,NA,FALSE,TRUE,Mus musculus,GSE198562,GSM5952294,3p_v3.1,bam,SRR18342536,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Ranade 2022,WT_E105_3 [scRNAseq],NA,heart,NA,NA,NA,NA,NA,NA,FALSE,TRUE,Mus musculus,GSE198562,GSM5952295,3p_v3.1,bam,SRR18342537,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Ranade 2022,WT_E105_4 [scRNAseq],NA,heart,NA,NA,NA,NA,NA,NA,FALSE,TRUE,Mus musculus,GSE198562,GSM5952296,3p_v3.1,bam,SRR18342538,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Ranade 2022,WT_E115_1 [scRNAseq],NA,heart,NA,NA,NA,NA,NA,NA,FALSE,TRUE,Mus musculus,GSE198562,GSM5952297,3p_v3.1,bam,SRR18342539,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Ranade 2022,WT_E115_2 [scRNAseq],NA,heart,NA,NA,NA,NA,NA,NA,FALSE,TRUE,Mus musculus,GSE198562,GSM5952298,3p_v3.1,bam,SRR18342540,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Ranade 2022,KO_E925_1 [scRNAseq],NA,heart,NA,NA,NA,NA,NA,NA,FALSE,TRUE,Mus musculus,GSE198562,GSM5952299,3p_v3.1,bam,SRR18342541,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Ranade 2022,KO_E925_2 [scRNAseq],NA,heart,NA,NA,NA,NA,NA,NA,FALSE,TRUE,Mus musculus,GSE198562,GSM5952300,3p_v3.1,bam,SRR18342542,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Ranade 2022,KO_E105_1 [scRNAseq],NA,heart,NA,NA,NA,NA,NA,NA,FALSE,TRUE,Mus musculus,GSE198562,GSM5952301,3p_v3.1,bam,SRR18342543,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Ranade 2022,KO_E105_2 [scRNAseq],NA,heart,NA,NA,NA,NA,NA,fasterq-dump quit with error code 3,FALSE,TRUE,Mus musculus,GSE198562,GSM5952302,3p_v3.1,bam,SRR18342544,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Ranade 2022,KO_E115_1 [scRNAseq],NA,heart,NA,NA,NA,NA,NA,fasterq-dump quit with error code 3,FALSE,TRUE,Mus musculus,GSE198562,GSM5952303,3p_v3.1,bam,SRR18342545,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Ranade 2022,KO_E115_2 [scRNAseq],NA,heart,NA,NA,NA,NA,NA,NA,FALSE,TRUE,Mus musculus,GSE198562,GSM5952304,3p_v3.1,bam,SRR18342546,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Ranade 2022,KO_E115_3 [scRNAseq],NA,heart,NA,NA,NA,NA,NA,NA,FALSE,TRUE,Mus musculus,GSE198562,GSM5952305,3p_v3.1,bam,SRR18342547,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Yan 2022,C,NA,heart,mitral leaflet,NA,NA,NA,NA,2 3 4 remaining,FALSE,TRUE,Mus musculus,GSE207226,GSM6281853,3p_v3,fastq,SRR19903534,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Yan 2022,M,NA,heart,mitral leaflet,NA,NA,NA,NA,2 3 4 remaining,FALSE,TRUE,Mus musculus,GSE207226,GSM6281854,3p_v3,fastq,SRR19903533,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Zhou 2022,"Gata4_het_1, scRNAseq",NA,heart,NA,NA,NA,NA,NA,download issue,FALSE,TRUE,Mus musculus,GSE208162,GSM6338301,3p_v2,fastq,SRR20173383,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Zhou 2022,"Gata4_het_2, scRNAseq",NA,heart,NA,NA,NA,NA,NA,download issue,FALSE,TRUE,Mus musculus,GSE208162,GSM6338302,3p_v2,fastq,SRR20173382,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Zhou 2022,"Gata4_KO_1, scRNAseq",NA,heart,NA,NA,NA,NA,NA,download issue,FALSE,TRUE,Mus musculus,GSE208162,GSM6338303,3p_v2,fastq,SRR20173381,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Zhou 2022,"Gata4_KO_2, scRNAseq",NA,heart,NA,NA,NA,NA,NA,download issue,FALSE,TRUE,Mus musculus,GSE208162,GSM6338304,3p_v2,fastq,SRR20173380,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Tabula Microcebus 2022,NA,NA,heart,NA,cell,NA,NA,NA,Data not yet public,FALSE,TRUE,Microcebus murinus,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,https://registry.opendata.aws/tabula-sapiens/,"Tabula Sapiens Consortium et al, bioRxiv, 2021",NA,https://www.biorxiv.org/content/10.1101/2021.07.19.452956v2,NA,NA,NA
Tabula Muris 2018,10X_P7_4,NA,heart,NA,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE109774,GSM3040902,3p_v2,bam,SRR6835856,NA,NA,NA,NA,NA,NA,NA,"Tabula Muris, Nature, 2018",10.1038/s41586-018-0590-4,https://pubmed.ncbi.nlm.nih.gov/30283141/,Illumina NovaSeq 6000,Tabula Muris: Transcriptomic characterization of 20 organs and tissues from Mus musculus at single cell resolution,We have created a resource of single cell transcriptome data from the model organism Mus musculus. Contributor: The Tabula Muris Consortium The full list of contributors to this dataset can be found in the corresponding publication. Overall design: Single cell RNA sequencing of single cells across 20 tissues of 3 month aged mice
de Soysa 2019,E775_WT1,NA,heart,Cardiac Crescent region,NA,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE126128,GSM3592142,3p_v2,bam,SRR8535078,NA,SRX5337567,NA,NA,SAMN10878133,NA,NA,NA,10.1038/s41586-019-1414-x,https://pubmed.ncbi.nlm.nih.gov/31341279,Illumina HiSeq 4000,NA,NA
de Soysa 2019,E775_WT2,NA,heart,Cardiac Crescent region,NA,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE126128,GSM3592143,3p_v2,bam,SRR8535079,NA,SRX5337568,NA,NA,SAMN10878132,NA,NA,NA,10.1038/s41586-019-1414-x,https://pubmed.ncbi.nlm.nih.gov/31341279,Illumina HiSeq 4000,NA,NA
de Soysa 2019,E775_WT3,NA,heart,Cardiac Crescent region,NA,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE126128,GSM3592144,3p_v2,bam,SRR8535080,NA,SRX5337569,NA,NA,SAMN10878131,NA,NA,NA,10.1038/s41586-019-1414-x,https://pubmed.ncbi.nlm.nih.gov/31341279,Illumina HiSeq 4000,NA,NA
de Soysa 2019,E775_WT4,NA,heart,Cardiac Crescent region,NA,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE126128,GSM3592145,3p_v2,bam,SRR8535081,NA,SRX5337570,NA,NA,SAMN10878130,NA,NA,NA,10.1038/s41586-019-1414-x,https://pubmed.ncbi.nlm.nih.gov/31341279,Illumina HiSeq 4000,NA,NA
de Soysa 2019,E775_WT5,NA,heart,Cardiac Crescent region,NA,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE126128,GSM3592146,3p_v2,bam,SRR8535082,NA,SRX5337571,NA,NA,SAMN10878129,NA,NA,NA,10.1038/s41586-019-1414-x,https://pubmed.ncbi.nlm.nih.gov/31341279,Illumina HiSeq 4000,NA,NA
de Soysa 2019,E825_WT1,NA,heart,Heart tube and SHF region,NA,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE126128,GSM3592147,3p_v2,bam,SRR8535083,NA,SRX5337572,NA,NA,SAMN10878128,NA,NA,NA,10.1038/s41586-019-1414-x,https://pubmed.ncbi.nlm.nih.gov/31341279,NextSeq 500,NA,NA
de Soysa 2019,E825_WT2,NA,heart,Heart tube and SHF region,NA,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE126128,GSM3592148,3p_v2,bam,SRR8535084,NA,SRX5337573,NA,NA,SAMN10878127,NA,NA,NA,10.1038/s41586-019-1414-x,https://pubmed.ncbi.nlm.nih.gov/31341279,NextSeq 500,NA,NA
de Soysa 2019,E925_WT1,NA,heart,"Looped heart, SHF and pharyngeal arch region",NA,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE126128,GSM3592149,3p_v2,bam,SRR8535085,NA,SRX5337574,NA,NA,SAMN10878126,NA,NA,NA,10.1038/s41586-019-1414-x,https://pubmed.ncbi.nlm.nih.gov/31341279,NextSeq 500,NA,NA
de Soysa 2019,E925_WT2,NA,heart,"Looped heart, SHF and pharyngeal arch region",NA,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE126128,GSM3592150,3p_v2,bam,SRR8535086,NA,SRX5337575,NA,NA,SAMN10878125,NA,NA,NA,10.1038/s41586-019-1414-x,https://pubmed.ncbi.nlm.nih.gov/31341279,NextSeq 500,NA,NA
de Soysa 2019,E775_Hand2_KO1,NA,heart,Cardiac Crescent region,NA,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE126128,GSM3592151,3p_v2,bam,SRR8535087,NA,SRX5337576,NA,NA,SAMN10878124,NA,NA,NA,10.1038/s41586-019-1414-x,https://pubmed.ncbi.nlm.nih.gov/31341279,Illumina HiSeq 4000,NA,NA
de Soysa 2019,E775_Hand2_KO2,NA,heart,Cardiac Crescent region,NA,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE126128,GSM3592152,3p_v2,bam,SRR8535088,NA,SRX5337577,NA,NA,SAMN10878123,NA,NA,NA,10.1038/s41586-019-1414-x,https://pubmed.ncbi.nlm.nih.gov/31341279,Illumina HiSeq 4000,NA,NA
de Soysa 2019,E775_Hand2_KO3,NA,heart,Cardiac Crescent region,NA,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE126128,GSM3592153,3p_v2,bam,SRR8535089,NA,SRX5337578,NA,NA,SAMN10878122,NA,NA,NA,10.1038/s41586-019-1414-x,https://pubmed.ncbi.nlm.nih.gov/31341279,Illumina HiSeq 4000,NA,NA
de Soysa 2019,E825_Hand2_KO1,NA,heart,Heart tube and SHF region,NA,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE126128,GSM3592154,3p_v2,bam,SRR8535090,NA,SRX5337579,NA,NA,SAMN10878121,NA,NA,NA,10.1038/s41586-019-1414-x,https://pubmed.ncbi.nlm.nih.gov/31341279,NextSeq 500,NA,NA
de Soysa 2019,E825_Hand2_KO2,NA,heart,Heart tube and SHF region,NA,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE126128,GSM3592155,3p_v2,bam,SRR8535091,NA,SRX5337580,NA,NA,SAMN10878120,NA,NA,NA,10.1038/s41586-019-1414-x,https://pubmed.ncbi.nlm.nih.gov/31341279,NextSeq 500,NA,NA
de Soysa 2019,E925_Hand2_KO1,NA,heart,"Looped heart, SHF and pharyngeal arch region",NA,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE126128,GSM3592156,3p_v2,bam,SRR8535092,NA,SRX5337581,NA,NA,SAMN10878119,NA,NA,NA,10.1038/s41586-019-1414-x,https://pubmed.ncbi.nlm.nih.gov/31341279,NextSeq 500,NA,NA
de Soysa 2019,E925_Hand2_KO2,NA,heart,"Looped heart, SHF and pharyngeal arch region",NA,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE126128,GSM3592157,3p_v2,bam,SRR8535093,NA,SRX5337582,NA,NA,SAMN10878118,NA,NA,NA,10.1038/s41586-019-1414-x,https://pubmed.ncbi.nlm.nih.gov/31341279,NextSeq 500,NA,NA
Tabula Muris Senis 2020,MACA_21m_F_HEART_4CHAMBERS_54,NA,heart,NA,cell,female,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE132042,MACA_21m_F_HEART_4CHAMBERS_54,3p_v2,aws,NA,https://czb-tabula-muris-senis.s3.us-west-2.amazonaws.com/10x/FASTQs/MACA_21m_F_HEART_4CHAMBERS_54/MACA_21m_F_HEART_4CHAMBERS_54_S5_L001_R1_001.fastq.gz;https://czb-tabula-muris-senis.s3.us-west-2.amazonaws.com/10x/FASTQs/MACA_21m_F_HEART_4CHAMBERS_54/MACA_21m_F_HEART_4CHAMBERS_54_S5_L002_R1_001.fastq.gz;https://czb-tabula-muris-senis.s3.us-west-2.amazonaws.com/10x/FASTQs/MACA_21m_F_HEART_4CHAMBERS_54/MACA_21m_F_HEART_4CHAMBERS_54_S5_L001_R2_001.fastq.gz;https://czb-tabula-muris-senis.s3.us-west-2.amazonaws.com/10x/FASTQs/MACA_21m_F_HEART_4CHAMBERS_54/MACA_21m_F_HEART_4CHAMBERS_54_S5_L002_R2_001.fastq.gz,NA,NA,NA,NA,NA,NA,"Tabula Muris Senis, Nature, 2020",10.1038/s41586-020-2496-1,https://pubmed.ncbi.nlm.nih.gov/32669714/,NA,NA,NA
Tabula Muris Senis 2020,MACA_21m_F_HEART_4CHAMBERS_55,NA,heart,NA,cell,female,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE132042,MACA_21m_F_HEART_4CHAMBERS_55,3p_v2,aws,NA,https://czb-tabula-muris-senis.s3.us-west-2.amazonaws.com/10x/FASTQs/MACA_21m_F_HEART_4CHAMBERS_55/MACA_21m_F_HEART_4CHAMBERS_55_S5_L001_R1_001.fastq.gz;https://czb-tabula-muris-senis.s3.us-west-2.amazonaws.com/10x/FASTQs/MACA_21m_F_HEART_4CHAMBERS_55/MACA_21m_F_HEART_4CHAMBERS_55_S5_L002_R1_001.fastq.gz;https://czb-tabula-muris-senis.s3.us-west-2.amazonaws.com/10x/FASTQs/MACA_21m_F_HEART_4CHAMBERS_55/MACA_21m_F_HEART_4CHAMBERS_55_S5_L001_R2_001.fastq.gz;https://czb-tabula-muris-senis.s3.us-west-2.amazonaws.com/10x/FASTQs/MACA_21m_F_HEART_4CHAMBERS_55/MACA_21m_F_HEART_4CHAMBERS_55_S5_L002_R2_001.fastq.gz,NA,NA,NA,NA,NA,NA,"Tabula Muris Senis, Nature, 2020",10.1038/s41586-020-2496-1,https://pubmed.ncbi.nlm.nih.gov/32669714/,NA,NA,NA
Tabula Muris Senis 2020,MACA_24m_M_HEART_58,NA,heart,NA,cell,male,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE132042,MACA_24m_M_HEART_58,3p_v2,aws,NA,https://czb-tabula-muris-senis.s3.us-west-2.amazonaws.com/10x/FASTQs/MACA_24m_M_HEART_58/MACA_24m_M_HEART_58_S13_L001_R1_001.fastq.gz;https://czb-tabula-muris-senis.s3.us-west-2.amazonaws.com/10x/FASTQs/MACA_24m_M_HEART_58/MACA_24m_M_HEART_58_S13_L001_R2_001.fastq.gz;https://czb-tabula-muris-senis.s3.us-west-2.amazonaws.com/10x/FASTQs/MACA_24m_M_HEART_58/MACA_24m_M_HEART_58_S13_L002_R1_001.fastq.gz;https://czb-tabula-muris-senis.s3.us-west-2.amazonaws.com/10x/FASTQs/MACA_24m_M_HEART_58/MACA_24m_M_HEART_58_S13_L002_R2_001.fastq.gz,NA,NA,NA,NA,NA,NA,"Tabula Muris Senis, Nature, 2020",10.1038/s41586-020-2496-1,https://pubmed.ncbi.nlm.nih.gov/32669714/,NA,NA,NA
Tabula Muris Senis 2020,MACA_24m_M_HEART_59,NA,heart,NA,cell,male,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE132042,MACA_24m_M_HEART_59,3p_v2,aws,NA,https://czb-tabula-muris-senis.s3.us-west-2.amazonaws.com/10x/FASTQs/MACA_24m_M_HEART_59/MACA_24m_M_HEART_59_S14_L001_R1_001.fastq.gz;https://czb-tabula-muris-senis.s3.us-west-2.amazonaws.com/10x/FASTQs/MACA_24m_M_HEART_59/MACA_24m_M_HEART_59_S14_L001_R2_001.fastq.gz;https://czb-tabula-muris-senis.s3.us-west-2.amazonaws.com/10x/FASTQs/MACA_24m_M_HEART_59/MACA_24m_M_HEART_59_S14_L002_R1_001.fastq.gz;https://czb-tabula-muris-senis.s3.us-west-2.amazonaws.com/10x/FASTQs/MACA_24m_M_HEART_59/MACA_24m_M_HEART_59_S14_L002_R2_001.fastq.gz,NA,NA,NA,NA,NA,NA,"Tabula Muris Senis, Nature, 2020",10.1038/s41586-020-2496-1,https://pubmed.ncbi.nlm.nih.gov/32669714/,NA,NA,NA
Tabula Muris Senis 2020,MACA_24m_M_HEART_60,NA,heart,NA,cell,male,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE132042,MACA_24m_M_HEART_60,3p_v2,aws,NA,https://czb-tabula-muris-senis.s3.us-west-2.amazonaws.com/10x/FASTQs/MACA_24m_M_HEART_60/MACA_24m_M_HEART_60_S5_L001_R1_001.fastq.gz;https://czb-tabula-muris-senis.s3.us-west-2.amazonaws.com/10x/FASTQs/MACA_24m_M_HEART_60/MACA_24m_M_HEART_60_S5_L001_R2_001.fastq.gz;https://czb-tabula-muris-senis.s3.us-west-2.amazonaws.com/10x/FASTQs/MACA_24m_M_HEART_60/MACA_24m_M_HEART_60_S5_L002_R1_001.fastq.gz;https://czb-tabula-muris-senis.s3.us-west-2.amazonaws.com/10x/FASTQs/MACA_24m_M_HEART_60/MACA_24m_M_HEART_60_S5_L002_R2_001.fastq.gz,NA,NA,NA,NA,NA,NA,"Tabula Muris Senis, Nature, 2020",10.1038/s41586-020-2496-1,https://pubmed.ncbi.nlm.nih.gov/32669714/,NA,NA,NA
Tabula Muris Senis 2020,MACA_24m_M_HEART_61,NA,heart,NA,cell,male,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE132042,MACA_24m_M_HEART_61,3p_v2,aws,NA,https://czb-tabula-muris-senis.s3.us-west-2.amazonaws.com/10x/FASTQs/MACA_24m_M_HEART_61/MACA_24m_M_HEART_61_S6_L001_R1_001.fastq.gz;https://czb-tabula-muris-senis.s3.us-west-2.amazonaws.com/10x/FASTQs/MACA_24m_M_HEART_61/MACA_24m_M_HEART_61_S6_L001_R2_001.fastq.gz;https://czb-tabula-muris-senis.s3.us-west-2.amazonaws.com/10x/FASTQs/MACA_24m_M_HEART_61/MACA_24m_M_HEART_61_S6_L002_R1_001.fastq.gz;https://czb-tabula-muris-senis.s3.us-west-2.amazonaws.com/10x/FASTQs/MACA_24m_M_HEART_61/MACA_24m_M_HEART_61_S6_L002_R2_001.fastq.gz,NA,NA,NA,NA,NA,NA,"Tabula Muris Senis, Nature, 2020",10.1038/s41586-020-2496-1,https://pubmed.ncbi.nlm.nih.gov/32669714/,NA,NA,NA
Tabula Muris Senis 2020,MOUSE_CARDIOMYOCYTE_2,NA,heart,cardiomyocytes,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE132042,MOUSE_CARDIOMYOCYTE_2,3p_v2,aws,NA,https://czb-tabula-muris-senis.s3.us-west-2.amazonaws.com/10x/FASTQs/MOUSE_CARDIOMYOCYTE_2/MOUSE_CARDIOMYOCYTE_2_S20_L001_R1_001.fastq.gz;https://czb-tabula-muris-senis.s3.us-west-2.amazonaws.com/10x/FASTQs/MOUSE_CARDIOMYOCYTE_2/MOUSE_CARDIOMYOCYTE_2_S20_L001_R2_001.fastq.gz;https://czb-tabula-muris-senis.s3.us-west-2.amazonaws.com/10x/FASTQs/MOUSE_CARDIOMYOCYTE_2/MOUSE_CARDIOMYOCYTE_2_S20_L002_R1_001.fastq.gz;https://czb-tabula-muris-senis.s3.us-west-2.amazonaws.com/10x/FASTQs/MOUSE_CARDIOMYOCYTE_2/MOUSE_CARDIOMYOCYTE_2_S20_L002_R2_001.fastq.gz,NA,NA,NA,NA,NA,NA,"Tabula Muris Senis, Nature, 2020",10.1038/s41586-020-2496-1,https://pubmed.ncbi.nlm.nih.gov/32669714/,NA,NA,NA
Koth 2020,587680_45,NA,heart,NA,NA,NA,NA,NA,NA,TRUE,TRUE,Danio rerio,GSE138181,GSM4101380,3p_v2,fastq,SRR10203906,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Koth 2020,587680_46,NA,heart,NA,NA,NA,NA,NA,NA,TRUE,TRUE,Danio rerio,GSE138181,GSM4101381,3p_v2,fastq,SRR10203907,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Koth 2020,587680_47,NA,heart,NA,NA,NA,NA,NA,NA,TRUE,TRUE,Danio rerio,GSE138181,GSM4101382,3p_v2,fastq,SRR10203908,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Emechebe 2021,Heart Endothelial 3 mo rep1,NA,heart,endothelial cells,cell,NA,NA,NA,NA,TRUE,FALSE,Mus musculus,GSE163822,GSM4987951,3p_v2,bam,SRR13302415,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Emechebe 2021,Heart Endothelial 3 mo rep2,NA,heart,endothelial cells,cell,NA,NA,NA,NA,TRUE,FALSE,Mus musculus,GSE163822,GSM4987952,3p_v2,bam,SRR13302416,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Emechebe 2021,Heart Endothelial 3 mo rep3,NA,heart,endothelial cells,cell,NA,NA,NA,NA,TRUE,FALSE,Mus musculus,GSE163822,GSM4987953,3p_v2,bam,SRR13302417,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Emechebe 2021,Heart Endothelial 24 mo rep1,NA,heart,endothelial cells,cell,NA,NA,NA,NA,TRUE,FALSE,Mus musculus,GSE163822,GSM4987954,3p_v2,bam,SRR13302418,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Emechebe 2021,Heart Endothelial 24 mo rep2,NA,heart,endothelial cells,cell,NA,NA,NA,NA,TRUE,FALSE,Mus musculus,GSE163822,GSM4987955,3p_v2,bam,SRR13302419,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Emechebe 2021,Heart Endothelial 24 mo rep3,NA,heart,endothelial cells,cell,NA,NA,NA,NA,TRUE,FALSE,Mus musculus,GSE163822,GSM4987956,3p_v2,bam,SRR13302420,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Galow 2021,iSABs,NA,heart,NA,NA,NA,NA,NA,NA,TRUE,FALSE,Mus musculus,GSE174233,GSM5289681,3p_v3,fastq,SRR14494827,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Lasrado 2022,Healthy Controls 1,NA,heart,NA,NA,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE174458,GSM5311767,NA,fastq,SRR14539831,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Lasrado 2022,Healthy Controls 2,NA,heart,NA,NA,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE174458,GSM5311768,NA,fastq,SRR14539832,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Lasrado 2022,Myocarditis 1,NA,heart,NA,NA,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE174458,GSM5311769,NA,fastq,SRR14539833,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Lasrado 2022,Myocarditis 2,NA,heart,NA,NA,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE174458,GSM5311770,NA,fastq,SRR14539834,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Zhang Q 2022,E7.25,NA,heart,NA,NA,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE176306,GSM5362454,3p_v2,bam,SRR14750747,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Zhang Q 2022,E7.5 sample 1,NA,heart,NA,NA,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE176306,GSM5362455,3p_v2,bam,SRR14750748,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Zhang Q 2022,E7.5 sample 2,NA,heart,NA,NA,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE176306,GSM5362456,3p_v2,bam,SRR14750749,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Zhang Q 2022,E7.5 sample 3,NA,heart,NA,NA,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE176306,GSM5362457,3p_v2,bam,SRR14750750,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Zhang Q 2022,E7.5 sample 4,NA,heart,NA,NA,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE176306,GSM5362458,3p_v2,bam,SRR14750751,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Zhang Q 2022,E7.75 sample 1,NA,heart,NA,NA,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE176306,GSM5362459,3p_v2,bam,SRR14750752,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Zhang Q 2022,E7.75 sample 2,NA,heart,NA,NA,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE176306,GSM5362460,3p_v2,bam,SRR14750753,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Zhang Q 2022,E8.25 sample 1,NA,heart,NA,NA,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE176306,GSM5362461,3p_v2,bam,SRR14750754,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Zhang Q 2022,E8.25 sample 2,NA,heart,NA,NA,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE176306,GSM5362462,3p_v2,bam,SRR14750755,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Zhang Q 2022,E8.25 sample 3,NA,heart,NA,NA,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE176306,GSM5362463,3p_v2,bam,SRR14750756,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Wu 2021,Heart.scRNA.Prdm16cKO1,NA,heart,NA,NA,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE179390,GSM5416737,3p_v3.1,fastq,SRR15035106,NA,SRX11346596,NA,NA,SAMN20054507,NA,NA,NA,NA,NA,NA,NA,NA
Wu 2021,Heart.scRNA.Prdm16cKO2,NA,heart,NA,NA,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE179390,GSM5416738,3p_v3.1,fastq,SRR15035107,NA,SRX11346597,NA,NA,SAMN20054506,NA,NA,NA,NA,NA,NA,NA,NA
Wu 2021,Heart.scRNA.WT1,NA,heart,NA,NA,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE179390,GSM5416739,3p_v3.1,fastq,SRR15035108,NA,SRX11346598,NA,NA,SAMN20054505,NA,NA,NA,NA,NA,NA,NA,NA
Wu 2021,Heart.scRNA.WT2,NA,heart,NA,NA,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE179390,GSM5416740,3p_v3.1,fastq,SRR15035109,NA,SRX11346599,NA,NA,SAMN20054504,NA,NA,NA,NA,NA,NA,NA,NA
Liao 2022,Lyz2-Cre,NA,heart,Non-myocytes,NA,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE185756,GSM5623255,3p_v3,fastq,SRR16301630,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Liao 2022,Lyz2-KLF2-KO,NA,heart,Non-myocytes,NA,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE185756,GSM5623256,3p_v3,fastq,SRR16301631,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Sussman 2021a,Lin28_SN_cK_N,NA,heart,cardiac interstitial cells,NA,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE186176,GSM5639808,3p_v3.1,bam,SRR16491018,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Sussman 2021a,Lin28_SP_cK_N,NA,heart,cardiac interstitial cells,NA,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE186176,GSM5639809,3p_v3.1,bam,SRR16491019,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Sussman 2021a,Lin28_SP_cK_P,NA,heart,cardiac interstitial cells,NA,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE186176,GSM5639810,3p_v3.1,bam,SRR16491020,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Cosacak 2022,AS2,NA,heart,NA,NA,NA,NA,NA,NA,TRUE,TRUE,Danio rerio,GSE186874,GSM5662814,NA,bam,SRR16646359,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Sussman 2021b,cKit_N_DDR2_P,NA,heart,cardiac interstitial cells,NA,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE188804,GSM5690358,3p_v3.1,bam,SRR16946483,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Sussman 2021b,cKit_P_DDR2_N,NA,heart,cardiac interstitial cells,NA,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE188804,GSM5690359,3p_v3.1,bam,SRR16946484,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Sussman 2021b,cKit_P_DDR2_N_1,NA,heart,cardiac interstitial cells,NA,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE188804,GSM5690360,3p_v3.1,bam,SRR16946485,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Sussman 2021b,cKit_P_DDR2_P_CD45_N,NA,heart,cardiac interstitial cells,NA,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE188804,GSM5690361,3p_v3.1,bam,SRR16946486,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Sussman 2021b,CND_cKit_P_DDR2_P,NA,heart,cardiac interstitial cells,NA,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE188804,GSM5690362,3p_v3.1,bam,SRR16946487,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
McCracken 2022,13_week_cardiac_EC,NA,heart,fetal,NA,NA,NA,NA,NA,TRUE,TRUE,Homo sapiens,GSE195911,GSM5856284,3p_v3.1,fastq,SRR17848279,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
McCracken 2022,14_week_cardiac_EC,NA,heart,fetal,NA,NA,NA,NA,R1 download issue,TRUE,TRUE,Homo sapiens,GSE195911,GSM5856285,3p_v3.1,fastq,SRR17848278,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
McCracken 2022,hESC-EC_siRNA_MECOM_1,NA,heart,NA,NA,NA,NA,NA,NA,TRUE,FALSE,Homo sapiens,GSE195911,GSM5856286,3p_v3.1,fastq,SRR17848277,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
McCracken 2022,hESC-EC_siRNA_MECOM_2,NA,heart,NA,NA,NA,NA,NA,NA,TRUE,FALSE,Homo sapiens,GSE195911,GSM5856287,3p_v3.1,fastq,SRR17848276,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
McCracken 2022,hESC-EC_siRNA_MECOM_3,NA,heart,NA,NA,NA,NA,NA,NA,TRUE,FALSE,Homo sapiens,GSE195911,GSM5856288,3p_v3.1,fastq,SRR17848275,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
McCracken 2022,hESC-EC_siRNA_MECOM_4,NA,heart,NA,NA,NA,NA,NA,NA,TRUE,FALSE,Homo sapiens,GSE195911,GSM5856289,3p_v3.1,fastq,SRR17848274,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
McCracken 2022,hESC-EC_siRNA_control_1,NA,heart,NA,NA,NA,NA,NA,NA,TRUE,FALSE,Homo sapiens,GSE195911,GSM5856290,3p_v3.1,fastq,SRR17848273,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
McCracken 2022,hESC-EC_siRNA_control_2,NA,heart,NA,NA,NA,NA,NA,NA,TRUE,FALSE,Homo sapiens,GSE195911,GSM5856291,3p_v3.1,fastq,SRR17848272,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
McCracken 2022,hESC-EC_siRNA_control_3,NA,heart,NA,NA,NA,NA,NA,NA,TRUE,FALSE,Homo sapiens,GSE195911,GSM5856292,3p_v3.1,fastq,SRR17848271,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
McCracken 2022,hESC-EC_siRNA_control_4,NA,heart,NA,NA,NA,NA,NA,NA,TRUE,FALSE,Homo sapiens,GSE195911,GSM5856293,3p_v3.1,fastq,SRR17848270,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Jiang 2022,day 14 GFP+ split A,NA,heart,iPSC,cell,NA,NA,NA,NA,TRUE,FALSE,Homo sapiens,GSE198729,GSM5955898,3p_v3,fastq,SRR18335029,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Jiang 2022,day 14 GFP+ split B,NA,heart,iPSC,cell,NA,NA,NA,NA,TRUE,FALSE,Homo sapiens,GSE198729,GSM5955899,3p_v3,fastq,SRR18335028,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Jiang 2022,day 14 GFP- split B,NA,heart,iPSC,cell,NA,NA,NA,NA,TRUE,FALSE,Homo sapiens,GSE198729,GSM5955900,3p_v3,fastq,SRR18335027,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Jiang 2022,GFP+ hiPS,NA,heart,iPSC,cell,NA,NA,NA,NA,TRUE,FALSE,Homo sapiens,GSE198729,GSM5955901,3p_v3,fastq,SRR18335026,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Brian 2022,"CD31Neg Non-myo, replicate 1, scRNAseq",NA,heart,Non-myocytes,NA,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE200067,GSM6008295,3p_v2,fastq,SRR18590332;SRR18590333;SRR18590334;SRR18590335,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Gurung 2022,GFP+mCherry+ cells (etv2 and kdrl positive cells),NA,heart,NA,NA,NA,NA,NA,NA,TRUE,FALSE,Danio rerio,GSE202912,GSM6138416,3p_v3,fastq,SRR19180493;SRR19180494,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Gurung 2022,GFP+mCherry- cells (etv2 positive and kdrl negative cells),NA,heart,NA,NA,NA,NA,NA,NA,TRUE,FALSE,Danio rerio,GSE202912,GSM6138417,3p_v3,fastq,SRR19180491;SRR19180492,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Hill 2022,"P8, snrna, rep1",NA,heart,NA,NA,NA,NA,NA,"raw data available, need to add",TRUE,TRUE,Homo sapiens,GSE203274,GSM6165791,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Hill 2022,"P8, snrna, rep2",NA,heart,NA,NA,NA,NA,NA,"raw data available, need to add",TRUE,TRUE,Homo sapiens,GSE203274,GSM6165792,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Hill 2022,"P26, snrna, rep1",NA,heart,NA,NA,NA,NA,NA,"raw data available, need to add",TRUE,TRUE,Homo sapiens,GSE203274,GSM6165793,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Hill 2022,"P26, snrna, rep2",NA,heart,NA,NA,NA,NA,NA,"raw data available, need to add",TRUE,TRUE,Homo sapiens,GSE203274,GSM6165794,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Hill 2022,"P28, snrna, rep1",NA,heart,NA,NA,NA,NA,NA,"raw data available, need to add",TRUE,TRUE,Homo sapiens,GSE203274,GSM6165795,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Hill 2022,"P28, snrna, rep2",NA,heart,NA,NA,NA,NA,NA,"raw data available, need to add",TRUE,TRUE,Homo sapiens,GSE203274,GSM6165796,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Hill 2022,"P33, snrna, rep1",NA,heart,NA,NA,NA,NA,NA,"raw data available, need to add",TRUE,TRUE,Homo sapiens,GSE203274,GSM6165797,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Hill 2022,"P33, snrna, rep2",NA,heart,NA,NA,NA,NA,NA,"raw data available, need to add",TRUE,TRUE,Homo sapiens,GSE203274,GSM6165798,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Hill 2022,"P36, snrna, rep1",NA,heart,NA,NA,NA,NA,NA,"raw data available, need to add",TRUE,TRUE,Homo sapiens,GSE203274,GSM6165799,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Hill 2022,"P36, snrna, rep2",NA,heart,NA,NA,NA,NA,NA,"raw data available, need to add",TRUE,TRUE,Homo sapiens,GSE203274,GSM6165800,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Hill 2022,"P40, snrna, rep1",NA,heart,NA,NA,NA,NA,NA,"raw data available, need to add",TRUE,TRUE,Homo sapiens,GSE203274,GSM6165801,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Hill 2022,"P40, snrna, rep2",NA,heart,NA,NA,NA,NA,NA,"raw data available, need to add",TRUE,TRUE,Homo sapiens,GSE203274,GSM6165802,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Hill 2022,"P64, snrna, rep1",NA,heart,NA,NA,NA,NA,NA,"raw data available, need to add",TRUE,TRUE,Homo sapiens,GSE203274,GSM6165803,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Hill 2022,"P64, snrna, rep2",NA,heart,NA,NA,NA,NA,NA,"raw data available, need to add",TRUE,TRUE,Homo sapiens,GSE203274,GSM6165804,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Hill 2022,"P75, snrna, rep1",NA,heart,NA,NA,NA,NA,NA,"raw data available, need to add",TRUE,TRUE,Homo sapiens,GSE203274,GSM6165805,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Hill 2022,"P75, snrna, rep2",NA,heart,NA,NA,NA,NA,NA,"raw data available, need to add",TRUE,TRUE,Homo sapiens,GSE203274,GSM6165806,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Hill 2022,"P86, snrna, rep1",NA,heart,NA,NA,NA,NA,NA,"raw data available, need to add",TRUE,TRUE,Homo sapiens,GSE203274,GSM6165807,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Hill 2022,"P86, snrna, rep2",NA,heart,NA,NA,NA,NA,NA,"raw data available, need to add",TRUE,TRUE,Homo sapiens,GSE203274,GSM6165808,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Hill 2022,"UK2, snrna, rep1",NA,heart,NA,NA,NA,NA,NA,"raw data available, need to add",TRUE,TRUE,Homo sapiens,GSE203274,GSM6165809,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Hill 2022,"UK2, snrna, rep2",NA,heart,NA,NA,NA,NA,NA,"raw data available, need to add",TRUE,TRUE,Homo sapiens,GSE203274,GSM6165810,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Hill 2022,"UK2, snrna, rep3",NA,heart,NA,NA,NA,NA,NA,"raw data available, need to add",TRUE,TRUE,Homo sapiens,GSE203274,GSM6165811,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Hill 2022,"UK1, snrna, rep1",NA,heart,NA,NA,NA,NA,NA,"raw data available, need to add",TRUE,TRUE,Homo sapiens,GSE203274,GSM6165812,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Hill 2022,"UK1, snrna, rep2",NA,heart,NA,NA,NA,NA,NA,"raw data available, need to add",TRUE,TRUE,Homo sapiens,GSE203274,GSM6165813,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Hill 2022,"UK1, snrna, rep3",NA,heart,NA,NA,NA,NA,NA,"raw data available, need to add",TRUE,TRUE,Homo sapiens,GSE203274,GSM6165814,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Hill 2022,"WU198LV, snrna, rep1",NA,heart,NA,NA,NA,NA,NA,"raw data available, need to add",TRUE,TRUE,Homo sapiens,GSE203274,GSM6165815,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Hill 2022,"WU198LV, snrna, rep2",NA,heart,NA,NA,NA,NA,NA,"raw data available, need to add",TRUE,TRUE,Homo sapiens,GSE203274,GSM6165816,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Hill 2022,"WU198RV, snrna, rep1",NA,heart,NA,NA,NA,NA,NA,"raw data available, need to add",TRUE,TRUE,Homo sapiens,GSE203274,GSM6165817,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Hill 2022,"WU198RV, snrna, rep2",NA,heart,NA,NA,NA,NA,NA,"raw data available, need to add",TRUE,TRUE,Homo sapiens,GSE203274,GSM6165818,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Hill 2022,"WU13235, snrna, rep1",NA,heart,NA,NA,NA,NA,NA,"raw data available, need to add",TRUE,TRUE,Homo sapiens,GSE203274,GSM6165819,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Hill 2022,"WU13235, snrna, rep2",NA,heart,NA,NA,NA,NA,NA,"raw data available, need to add",TRUE,TRUE,Homo sapiens,GSE203274,GSM6165820,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Gonzalez 2022,"E8.25, CC Stage, 3 pooled embryos, scRNAseq",NA,heart,NA,NA,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE205950,GSM6235981,3p_v3,fastq,SRR19632791;SRR19632792;SRR19632793;SRR19632794;SRR19632795;SRR19632796;SRR19632797;SRR19632798;SRR19632799;SRR19632800;SRR19632801;SRR19632802;SRR19632803;SRR19632804;SRR19632805;SRR19632806,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Gonzalez 2022,"E8.75, PHT Stage, 3 pooled embryos, scRNAseq",NA,heart,NA,NA,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE205950,GSM6235982,3p_v3,fastq,SRR19632772;SRR19632773;SRR19632774;SRR19632775;SRR19632776;SRR19632777;SRR19632778;SRR19632779;SRR19632780;SRR19632781;SRR19632782;SRR19632783;SRR19632784;SRR19632785;SRR19632786;SRR19632787;SRR19632788;SRR19632789;SRR19632790,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Gonzalez 2022,"E9.25, HT Stage, 3 pooled embryos, scRNAseq",NA,heart,NA,NA,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE205950,GSM6235983,3p_v3,fastq,SRR19632752;SRR19632753;SRR19632754;SRR19632755;SRR19632756;SRR19632757;SRR19632758;SRR19632759;SRR19632760;SRR19632761;SRR19632762;SRR19632763;SRR19632764;SRR19632765;SRR19632766;SRR19632767;SRR19632768;SRR19632769;SRR19632770;SRR19632771,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Gonzalez 2022,"RA-exposed CC Stage embryos (E8.25), 3 pooled embryos, scRNAseq",NA,heart,NA,NA,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE205950,GSM6235984,3p_v3,fastq,SRR19632740;SRR19632741;SRR19632742;SRR19632743;SRR19632744;SRR19632745;SRR19632746;SRR19632747;SRR19632748;SRR19632749;SRR19632750;SRR19632751,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Gonzalez 2022,"RA-exposed PHT Stage embryos (E8.75), 3 pooled embryos, scRNAseq",NA,heart,NA,NA,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE205950,GSM6235985,3p_v3,fastq,SRR19632726;SRR19632727;SRR19632728;SRR19632729;SRR19632730;SRR19632731;SRR19632732;SRR19632733;SRR19632734;SRR19632735;SRR19632736;SRR19632737;SRR19632738;SRR19632739,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Gonzalez 2022,"RA-exposed HT Stage embryos (E9.25), 3 pooled embryos, scRNAseq",NA,heart,NA,NA,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE205950,GSM6235986,3p_v3,fastq,SRR19632710;SRR19632711;SRR19632712;SRR19632713;SRR19632714;SRR19632715;SRR19632716;SRR19632717;SRR19632718;SRR19632719;SRR19632720;SRR19632721;SRR19632722;SRR19632723;SRR19632724;SRR19632725,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Sun 2023,OC-Heart,NA,heart,NA,NA,NA,NA,NA,no methods released at the time of recording,TRUE,TRUE,Mus musculus,PRJCA009794,CRX456253,3p_v3,ngdc_fastq,CRR516190,https://download.cncb.ac.cn/gsa2/CRA007207/CRR516190_f1_fastq.gz https://download.cncb.ac.cn/gsa2/CRA007207/CRR516190_r2.fastq.gz,CRX456253,PRJCA009794,SAMC801330,NA,NA,NA,NA,NA,NA,NA,NA,NA
Sun 2023,OE-Heart,NA,heart,NA,NA,NA,NA,NA,no methods released at the time of recording,TRUE,TRUE,Mus musculus,PRJCA009794,CRX456254,3p_v3,ngdc_fastq,CRR516191,https://download.cncb.ac.cn/gsa2/CRA007207/CRR516191_f1_fastq.gz https://download.cncb.ac.cn/gsa2/CRA007207/CRR516191_r2.fastq.gz,CRX456254,PRJCA009794,SAMC801331,NA,NA,NA,NA,NA,NA,NA,NA,NA
Sun 2023,YC-Heart,NA,heart,NA,NA,NA,NA,NA,no methods released at the time of recording,TRUE,TRUE,Mus musculus,PRJCA009794,CRX456255,3p_v3,ngdc_fastq,CRR516192,https://download.cncb.ac.cn/gsa2/CRA007207/CRR516192_f1_fastq.gz https://download.cncb.ac.cn/gsa2/CRA007207/CRR516192_r2.fastq.gz,CRX456255,PRJCA009794,SAMC801332,NA,NA,NA,NA,NA,NA,NA,NA,NA
Sun 2023,YE-Heart,NA,heart,NA,NA,NA,NA,NA,no methods released at the time of recording,TRUE,TRUE,Mus musculus,PRJCA009794,CRX456256,3p_v3,ngdc_fastq,CRR516193,https://download.cncb.ac.cn/gsa2/CRA007207/CRR516193_f1_fastq.gz https://download.cncb.ac.cn/gsa2/CRA007207/CRR516193_r2.fastq.gz,CRX456256,PRJCA009794,SAMC801333,NA,NA,NA,NA,NA,NA,NA,NA,NA
Sun 2023,Heart-OC-1,NA,heart,NA,NA,NA,NA,NA,no methods released at the time of recording,TRUE,TRUE,Mus musculus,PRJCA009794,CRX469735,3p_v3,ngdc_fastq,CRR529857,https://download.cncb.ac.cn/gsa2/CRA007207/CRR529857_f1_fastq.gz https://download.cncb.ac.cn/gsa2/CRA007207/CRR529857_r2.fastq.gz,CRX469735,PRJCA009794,SAMC816654,NA,NA,NA,NA,NA,NA,NA,NA,NA
Sun 2023,Heart-OC-2,NA,heart,NA,NA,NA,NA,NA,no methods released at the time of recording,TRUE,TRUE,Mus musculus,PRJCA009794,CRX469736,3p_v3,ngdc_fastq,CRR529858,https://download.cncb.ac.cn/gsa2/CRA007207/CRR529858_f1_fastq.gz https://download.cncb.ac.cn/gsa2/CRA007207/CRR529858_r2.fastq.gz,CRX469736,PRJCA009794,SAMC816655,NA,NA,NA,NA,NA,NA,NA,NA,NA
Sun 2023,Heart-OC-3,NA,heart,NA,NA,NA,NA,NA,no methods released at the time of recording,TRUE,TRUE,Mus musculus,PRJCA009794,CRX469737,3p_v3,ngdc_fastq,CRR529859,https://download.cncb.ac.cn/gsa2/CRA007207/CRR529859_f1_fastq.gz https://download.cncb.ac.cn/gsa2/CRA007207/CRR529859_r2.fastq.gz,CRX469737,PRJCA009794,SAMC816656,NA,NA,NA,NA,NA,NA,NA,NA,NA
Sun 2023,Heart-OE-1,NA,heart,NA,NA,NA,NA,NA,no methods released at the time of recording,TRUE,TRUE,Mus musculus,PRJCA009794,CRX469738,3p_v3,ngdc_fastq,CRR529860,https://download.cncb.ac.cn/gsa2/CRA007207/CRR529860_f1_fastq.gz https://download.cncb.ac.cn/gsa2/CRA007207/CRR529860_r2.fastq.gz,CRX469738,PRJCA009794,SAMC816657,NA,NA,NA,NA,NA,NA,NA,NA,NA
Sun 2023,Heart-OE-2,NA,heart,NA,NA,NA,NA,NA,no methods released at the time of recording,TRUE,TRUE,Mus musculus,PRJCA009794,CRX469739,3p_v3,ngdc_fastq,CRR529861,https://download.cncb.ac.cn/gsa2/CRA007207/CRR529861_f1_fastq.gz https://download.cncb.ac.cn/gsa2/CRA007207/CRR529861_r2.fastq.gz,CRX469739,PRJCA009794,SAMC816658,NA,NA,NA,NA,NA,NA,NA,NA,NA
Sun 2023,Heart-OE-3,NA,heart,NA,NA,NA,NA,NA,no methods released at the time of recording,TRUE,TRUE,Mus musculus,PRJCA009794,CRX469740,3p_v3,ngdc_fastq,CRR529862,https://download.cncb.ac.cn/gsa2/CRA007207/CRR529862_f1_fastq.gz https://download.cncb.ac.cn/gsa2/CRA007207/CRR529862_r2.fastq.gz,CRX469740,PRJCA009794,SAMC816659,NA,NA,NA,NA,NA,NA,NA,NA,NA
Sun 2023,Heart-YC-1,NA,heart,NA,NA,NA,NA,NA,no methods released at the time of recording,TRUE,TRUE,Mus musculus,PRJCA009794,CRX469741,3p_v3,ngdc_fastq,CRR529863,https://download.cncb.ac.cn/gsa2/CRA007207/CRR529863_f1_fastq.gz https://download.cncb.ac.cn/gsa2/CRA007207/CRR529863_r2.fastq.gz,CRX469741,PRJCA009794,SAMC816660,NA,NA,NA,NA,NA,NA,NA,NA,NA
Sun 2023,Heart-YC-2,NA,heart,NA,NA,NA,NA,NA,no methods released at the time of recording,TRUE,TRUE,Mus musculus,PRJCA009794,CRX469742,3p_v3,ngdc_fastq,CRR529864,https://download.cncb.ac.cn/gsa2/CRA007207/CRR529864_f1_fastq.gz https://download.cncb.ac.cn/gsa2/CRA007207/CRR529864_r2.fastq.gz,CRX469742,PRJCA009794,SAMC816661,NA,NA,NA,NA,NA,NA,NA,NA,NA
Sun 2023,Heart-YC-3,NA,heart,NA,NA,NA,NA,NA,no methods released at the time of recording,TRUE,TRUE,Mus musculus,PRJCA009794,CRX469743,3p_v3,ngdc_fastq,CRR529865,https://download.cncb.ac.cn/gsa2/CRA007207/CRR529865_f1_fastq.gz https://download.cncb.ac.cn/gsa2/CRA007207/CRR529865_r2.fastq.gz,CRX469743,PRJCA009794,SAMC816662,NA,NA,NA,NA,NA,NA,NA,NA,NA
Sun 2023,Heart-YE-1,NA,heart,NA,NA,NA,NA,NA,no methods released at the time of recording,TRUE,TRUE,Mus musculus,PRJCA009794,CRX469744,3p_v3,ngdc_fastq,CRR529866,https://download.cncb.ac.cn/gsa2/CRA007207/CRR529866_f1_fastq.gz https://download.cncb.ac.cn/gsa2/CRA007207/CRR529866_r2.fastq.gz,CRX469744,PRJCA009794,SAMC816663,NA,NA,NA,NA,NA,NA,NA,NA,NA
Sun 2023,Heart-YE-2,NA,heart,NA,NA,NA,NA,NA,no methods released at the time of recording,TRUE,TRUE,Mus musculus,PRJCA009794,CRX469745,3p_v3,ngdc_fastq,CRR529867,https://download.cncb.ac.cn/gsa2/CRA007207/CRR529867_f1_fastq.gz https://download.cncb.ac.cn/gsa2/CRA007207/CRR529867_r2.fastq.gz,CRX469745,PRJCA009794,SAMC816664,NA,NA,NA,NA,NA,NA,NA,NA,NA
Sun 2023,Heart-YE-3,NA,heart,NA,NA,NA,NA,NA,no methods released at the time of recording,TRUE,TRUE,Mus musculus,PRJCA009794,CRX469746,3p_v3,ngdc_fastq,CRR529868,https://download.cncb.ac.cn/gsa2/CRA007207/CRR529868_f1_fastq.gz https://download.cncb.ac.cn/gsa2/CRA007207/CRR529868_r2.fastq.gz,CRX469746,PRJCA009794,SAMC816665,NA,NA,NA,NA,NA,NA,NA,NA,NA
Bian 2022,e17_5,NA,joint,joint,NA,NA,NA,NA,not yet public,FALSE,TRUE,Mus musculus,GSE179701,GSM5429626,NA,NA,NOT_PUBLIC,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Pistorius 2022,M1,NA,joint,paw,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE174118,GSM5287500,3p_v2,fastq,SRR14475511;SRR14475512;SRR14475513;SRR14475514,NA,SRX10823751,NA,NA,SAMN19080958,NA,NA,NA,NA,NA,NA,NA,NA
Pistorius 2022,M3,NA,joint,paw,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE174118,GSM5287501,3p_v2,fastq,SRR14475515;SRR14475516;SRR14475517;SRR14475518,NA,SRX10823752,NA,NA,SAMN19080957,NA,NA,NA,NA,NA,NA,NA,NA
Pistorius 2022,M4,NA,joint,paw,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE174118,GSM5287502,3p_v2,fastq,SRR14475519;SRR14475520;SRR14475521;SRR14475522,NA,SRX10823753,NA,NA,SAMN19080956,NA,NA,NA,NA,NA,NA,NA,NA
Pistorius 2022,M5,NA,joint,paw,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE174118,GSM5287503,3p_v2,fastq,SRR14475523;SRR14475524;SRR14475526;SRR14475527,NA,SRX10823754,NA,NA,SAMN19080955,NA,NA,NA,NA,NA,NA,NA,NA
Pistorius 2022,M7,NA,joint,paw,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE174118,GSM5287504,3p_v2,fastq,SRR14475527;SRR14475528;SRR14475529;SRR14475530,NA,SRX10823755,NA,NA,SAMN19080954,NA,NA,NA,NA,NA,NA,NA,NA
Pistorius 2022,M9,NA,joint,paw,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE174118,GSM5287505,3p_v2,fastq,SRR14475531;SRR14475532;SRR14475533;SRR14475534,NA,SRX10823756,NA,NA,SAMN19080953,NA,NA,NA,NA,NA,NA,NA,NA
Pistorius 2022,M10,NA,joint,paw,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE174118,GSM5287506,3p_v2,fastq,SRR14475535;SRR14475536;SRR14475537;SRR14475538,NA,SRX10823757,NA,NA,SAMN19080952,NA,NA,NA,NA,NA,NA,NA,NA
Pistorius 2022,M12,NA,joint,paw,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE174118,GSM5287507,3p_v2,fastq,SRR14475539;SRR14475540;SRR14475541;SRR14475542,NA,SRX10823758,NA,NA,SAMN19080951,NA,NA,NA,NA,NA,NA,NA,NA
Smeeton 2021,sox10:DsRed-enriched,NA,joint,NA,NA,NA,NA,NA,NA,TRUE,TRUE,Danio rerio,GSE184403,GSM5587034,3p_v2,fastq,SRR15964630;SRR15964631,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Smeeton 2021,trps1:eGFP-enriched,NA,joint,NA,NA,NA,NA,NA,NA,TRUE,TRUE,Danio rerio,GSE184403,GSM5587035,3p_v2,fastq,SRR15964632;SRR15964633,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Loots 2022,Control_Uninjured,NA,joint,knee,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE198837,GSM5957780,3p_v3,bam,SRR18355760,NA,SRX14491058,NA,NA,SAMN26748223,NA,NA,NA,10.1002/jbm4.10625,https://pubmed.ncbi.nlm.nih.gov/35509635/,NA,NA,NA
Loots 2022,Control_Injured,NA,joint,knee,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE198837,GSM5957781,3p_v3,bam,SRR18355761,NA,SRX14491057,NA,NA,SAMN26748222,NA,NA,NA,10.1002/jbm4.10625,https://pubmed.ncbi.nlm.nih.gov/35509635/,NA,NA,NA
Loots 2022,T1DM_Uninjured,NA,joint,knee,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE198837,GSM5957782,3p_v3,bam,SRR18355759,NA,SRX14491059,NA,NA,SAMN26748221,NA,NA,NA,10.1002/jbm4.10625,https://pubmed.ncbi.nlm.nih.gov/35509635/,NA,NA,NA
Loots 2022,T1DM_Injured,NA,joint,knee,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE198837,GSM5957783,3p_v3,bam,SRR18355762,NA,SRX14491056,NA,NA,SAMN26748220,NA,NA,NA,10.1002/jbm4.10625,https://pubmed.ncbi.nlm.nih.gov/35509635/,NA,NA,NA
Floudas 2022,PSA patient 1,NA,joint,knee,cell,NA,NA,NA,NA,TRUE,TRUE,Homo sapiens,GSE200815,GSM6044087,3p_v3,fastq,SRR18758456;SRR18758457,NA,SRX14858018,NA,NA,SAMN27585191,NA,NA,NA,10.1136/annrheumdis-2021-221761,https://pubmed.ncbi.nlm.nih.gov/35701153/,NA,NA,NA
Floudas 2022,PSA patient 2,NA,joint,knee,cell,NA,NA,NA,NA,TRUE,TRUE,Homo sapiens,GSE200815,GSM6044088,3p_v3,fastq,SRR18758458;SRR18758459,NA,SRX14858017,NA,NA,SAMN27585193,NA,NA,NA,10.1136/annrheumdis-2021-221761,https://pubmed.ncbi.nlm.nih.gov/35701153/,NA,NA,NA
Floudas 2022,PSA patient 3,NA,joint,knee,cell,NA,NA,NA,NA,TRUE,TRUE,Homo sapiens,GSE200815,GSM6044089,3p_v3,fastq,SRR18758460;SRR18758461,NA,SRX14858016,NA,NA,SAMN27585199,NA,NA,NA,10.1136/annrheumdis-2021-221761,https://pubmed.ncbi.nlm.nih.gov/35701153/,NA,NA,NA
Floudas 2022,PSA patient 4,NA,joint,knee,cell,NA,NA,NA,NA,TRUE,TRUE,Homo sapiens,GSE200815,GSM6044090,3p_v3,fastq,SRR18758462;SRR18758463,NA,SRX14858015,NA,NA,SAMN27585192,NA,NA,NA,10.1136/annrheumdis-2021-221761,https://pubmed.ncbi.nlm.nih.gov/35701153/,NA,NA,NA
Floudas 2022,PSA patient 5,NA,joint,knee,cell,NA,NA,NA,NA,TRUE,TRUE,Homo sapiens,GSE200815,GSM6044091,3p_v3,fastq,SRR18758464;SRR18758465,NA,SRX14858014,NA,NA,SAMN27585194,NA,NA,NA,10.1136/annrheumdis-2021-221761,https://pubmed.ncbi.nlm.nih.gov/35701153/,NA,NA,NA
Floudas 2022,RA patient 1,NA,joint,knee,cell,NA,NA,NA,NA,TRUE,TRUE,Homo sapiens,GSE200815,GSM6044092,3p_v3,fastq,SRR18758466;SRR18758467,NA,SRX14858012,NA,NA,SAMN27585196,NA,NA,NA,10.1136/annrheumdis-2021-221761,https://pubmed.ncbi.nlm.nih.gov/35701153/,NA,NA,NA
Floudas 2022,RA patient 2,NA,joint,knee,cell,NA,NA,NA,NA,TRUE,TRUE,Homo sapiens,GSE200815,GSM6044093,3p_v3,fastq,SRR18758468;SRR18758469,NA,SRX14858010,NA,NA,SAMN27585198,NA,NA,NA,10.1136/annrheumdis-2021-221761,https://pubmed.ncbi.nlm.nih.gov/35701153/,NA,NA,NA
Floudas 2022,RA patient 3,NA,joint,knee,cell,NA,NA,NA,NA,TRUE,TRUE,Homo sapiens,GSE200815,GSM6044094,3p_v3,fastq,SRR18758470;SRR18758471,NA,SRX14858011,NA,NA,SAMN27585197,NA,NA,NA,10.1136/annrheumdis-2021-221761,https://pubmed.ncbi.nlm.nih.gov/35701153/,NA,NA,NA
Floudas 2022,RA patient 4,NA,joint,knee,cell,NA,NA,NA,NA,TRUE,TRUE,Homo sapiens,GSE200815,GSM6044095,3p_v3,fastq,SRR18758472;SRR18758473,NA,SRX14858013,NA,NA,SAMN27585195,NA,NA,NA,10.1136/annrheumdis-2021-221761,https://pubmed.ncbi.nlm.nih.gov/35701153/,NA,NA,NA
Fuji 2022,Control,NA,ligament,anterior cruciate ligament,cell,NA,NA,NA,issues with fastqs  R2 is same size as R1 after trimming,TRUE,TRUE,Mus musculus,GSE171479,GSM5226207,3p_v3,fastq,SRR14143472;SRR14143473,NA,SRX10512836,NA,NA,SAMN18617843,NA,NA,NA,NA,NA,Illumina NovaSeq 6000,NA,NA
Fuji 2022,postoperative day 1,NA,ligament,anterior cruciate ligament,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE171479,GSM5226208,3p_v3,fastq,SRR14143474,NA,SRX10512837,NA,NA,SAMN18617842,NA,NA,NA,NA,NA,Illumina HiSeq 4000,NA,NA
Fuji 2022,postoperative day 3,NA,ligament,anterior cruciate ligament,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE171479,GSM5226209,3p_v3,fastq,SRR14143475,NA,SRX10512838,NA,NA,SAMN18617841,NA,NA,NA,NA,NA,Illumina HiSeq 4000,NA,NA
Fuji 2022,postoperative day 7,NA,ligament,anterior cruciate ligament,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE171479,GSM5226210,3p_v3,fastq,SRR14143476,NA,SRX10512839,NA,NA,SAMN18617840,NA,NA,NA,NA,NA,Illumina HiSeq 4000,NA,NA
Fuji 2022,postoperative day 14,NA,ligament,anterior cruciate ligament,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE171479,GSM5226211,3p_v3,fastq,SRR14143477,NA,SRX10512840,NA,NA,SAMN18617839,NA,NA,NA,NA,NA,Illumina HiSeq 4000,NA,NA
Zhao H 2022,ACL-201112-L,NA,ligament,ACL,cell,NA,NA,NA,NA,TRUE,TRUE,Homo sapiens,GSE199280,GSM5968653,3p_v3,fastq,SRR18458448,NA,SRX14591075,NA,NA,SAMN26900343,NA,NA,NA,NA,NA,NA,NA,NA
Zhao H 2022,ACL-201112-R,NA,ligament,ACL,cell,NA,NA,NA,NA,TRUE,TRUE,Homo sapiens,GSE199280,GSM5968654,3p_v3,fastq,SRR18458447,NA,SRX14591076,NA,NA,SAMN26900342,NA,NA,NA,NA,NA,NA,NA,NA
Zhao H 2022,ACL-201120,NA,ligament,ACL,cell,NA,NA,NA,NA,TRUE,TRUE,Homo sapiens,GSE199280,GSM5968655,3p_v3,fastq,SRR18458446,NA,SRX14591077,NA,NA,SAMN26900341,NA,NA,NA,NA,NA,NA,NA,NA
Zhao H 2022,ACL-T-201116-10XSC3,NA,ligament,ACL,cell,NA,NA,NA,NA,TRUE,TRUE,Homo sapiens,GSE199280,GSM5968656,3p_v3,fastq,SRR18458445,NA,SRX14591078,NA,NA,SAMN26900340,NA,NA,NA,NA,NA,NA,NA,NA
Zhao H 2022,ACL-201120-T,NA,ligament,ACL,cell,NA,NA,NA,NA,TRUE,TRUE,Homo sapiens,GSE199280,GSM5968657,3p_v3,fastq,SRR18458444,NA,SRX14591079,NA,NA,SAMN26900339,NA,NA,NA,NA,NA,NA,NA,NA
Zhao H 2022,ACL-201118-T-10XSC3,NA,ligament,ACL,cell,NA,NA,NA,NA,TRUE,TRUE,Homo sapiens,GSE199280,GSM5968658,3p_v3,fastq,SRR18458443,NA,SRX14591080,NA,NA,SAMN26900338,NA,NA,NA,NA,NA,NA,NA,NA
Fuiten 2023,"Day 2, replicate A, scRNAseq",NA,limb,in vitro,cell,female,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE221883,GSM6908653,3p_v3.1,fastq,SRR22924618;SRR22924619,NA,NA,NA,NA,NA,NA,NA,NA,10.3389/fcell.2023.1135025,https://pubmed.ncbi.nlm.nih.gov/36994104/,NA,NA,NA
Fuiten 2023,"Day 2, replicate B, scRNAseq",NA,limb,in vitro,cell,female,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE221883,GSM6908654,3p_v3.1,fastq,SRR22924616;SRR22924617,NA,NA,NA,NA,NA,NA,NA,NA,10.3389/fcell.2023.1135025,https://pubmed.ncbi.nlm.nih.gov/36994104/,NA,NA,NA
Fuiten 2023,"Day 7, replicate A, scRNAseq",NA,limb,in vitro,cell,female,NA,NA,"index read treated as R1, R1 treated as R2, R2 tossed",TRUE,TRUE,Mus musculus,GSE221883,GSM6908655,3p_v3.1,fastq,SRR22924614;SRR22924615,NA,NA,NA,NA,NA,NA,NA,NA,10.3389/fcell.2023.1135025,https://pubmed.ncbi.nlm.nih.gov/36994104/,NA,NA,NA
Fuiten 2023,"Day 7, replicate B, scRNAseq",NA,limb,in vitro,cell,female,NA,NA,"index read treated as R1, R1 treated as R2, R2 tossed",TRUE,TRUE,Mus musculus,GSE221883,GSM6908656,3p_v3.1,fastq,SRR22924612;SRR22924613,NA,NA,NA,NA,NA,NA,NA,NA,10.3389/fcell.2023.1135025,https://pubmed.ncbi.nlm.nih.gov/36994104/,NA,NA,NA
Fuiten 2023,"Day 10, replicate A, scRNAseq",NA,limb,in vitro,cell,female,NA,NA,"index read treated as R1, R1 treated as R2, R2 tossed",TRUE,TRUE,Mus musculus,GSE221883,GSM6908657,3p_v3.1,fastq,SRR22924610;SRR22924611,NA,NA,NA,NA,NA,NA,NA,NA,10.3389/fcell.2023.1135025,https://pubmed.ncbi.nlm.nih.gov/36994104/,NA,NA,NA
Fuiten 2023,"Day 10, replicate B, scRNAseq",NA,limb,in vitro,cell,female,NA,NA,"index read treated as R1, R1 treated as R2, R2 tossed",TRUE,TRUE,Mus musculus,GSE221883,GSM6908658,3p_v3.1,fastq,SRR22924608;SRR22924609,NA,NA,NA,NA,NA,NA,NA,NA,10.3389/fcell.2023.1135025,https://pubmed.ncbi.nlm.nih.gov/36994104/,NA,NA,NA
Sacher 2019,HH25 scRNA-seq,Whole autopod; HH25,limb,limb bud,cell,NA,NA,NA,NA,TRUE,TRUE,Gallus gallus,GSE130439,GSM3738693,3p_v2,fastq,SRR8985028;SRR8985029;SRR8985030;SRR8985031;SRR8985032;SRR8985033;SRR8985034;SRR8985035,NA,SRX5764290,SRP194133,SRS4698684,SAMN11526604,NA,NA,"Sacher et al, Matrix Biol Plus, 2021",10.1016/j.mbplus.2021.100069,https://pubmed.ncbi.nlm.nih.gov/34195598/,NextSeq 500,"Single cell transcriptomes of developing chicken hind limbs at stages HH25, HH29 and HH31","We sequenced 17'628 cells coming from three key developmental stages of chicken autopod patterning. We identified 23 cell populations with distinct transcriptional profiles, including essential populations like the apical ectodermal ridge. We also inferred gene co-expression modules that coincide with distinct tissue types across developmental time, and used them to track patterning-relevant cell populations of the forming digits. The supplementary file contains processed UMI count matrices, which also include meta data of each cell, e.g. cluster. Overall design: Droplet-based single cell RNA-seq of dissociated developing limbs of chicken at three different stages"
Sacher 2019,HH31 scRNA-seq,Tip of digit 4; HH31,limb,limb bud,cell,NA,NA,NA,NA,TRUE,TRUE,Gallus gallus,GSE130439,GSM3738695,3p_v2,fastq,SRR8985039;SRR8985040;SRR8985041;SRR8985042;SRR8985043;SRR8985044;SRR8985045;SRR8985046,NA,SRX5764292,SRP194133,SRS4698686,SAMN11526602,NA,NA,"Sacher et al, Matrix Biol Plus, 2021",10.1016/j.mbplus.2021.100069,https://pubmed.ncbi.nlm.nih.gov/34195598/,NextSeq 500,"Single cell transcriptomes of developing chicken hind limbs at stages HH25, HH29 and HH31","We sequenced 17'628 cells coming from three key developmental stages of chicken autopod patterning. We identified 23 cell populations with distinct transcriptional profiles, including essential populations like the apical ectodermal ridge. We also inferred gene co-expression modules that coincide with distinct tissue types across developmental time, and used them to track patterning-relevant cell populations of the forming digits. The supplementary file contains processed UMI count matrices, which also include meta data of each cell, e.g. cluster. Overall design: Droplet-based single cell RNA-seq of dissociated developing limbs of chicken at three different stages"
Kelly 2019,E11.5,embryonic day 11.5,limb,limb bud,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE142425,GSM4227224,3p_v2,fastq,SRR10745783;SRR10745784,NA,SRX7421171,SRP238355,SRS5867775,SAMN13653645,NA,NA,"Kelly et al, Matrix Biology, 2019",10.1016/j.matbio.2019.12.004,https://pubmed.ncbi.nlm.nih.gov/31874220/,Illumina NovaSeq 6000,Single cell RNA-sequencing reveals cellular heterogeneity and trajectories of lineage specification during murine embryonic limb development,"The coordinated spatial and temporal regulation of gene expression in the murine hindlimb determines the identity of mesenchymal progenitors and the development of diversity of musculoskeletal tissues they form. Hindlimb development has historically been studied with lineage tracing of individual genes selected a priori, or at the bulk tissue level, which does not allow for the determination of single cell transcriptional programs yielding mature cell types and tissues. To identify the cellular trajectories of lineage specification during limb bud development, we used single cell mRNA sequencing (scRNA-seq) to profile the developing murine hindlimb between embryonic days (E)11.5-E18.5. We found cell type heterogeneity at all time points, and the expected cell types that form the mouse hindlimb. In addition, we used RNA fluorescence in situ hybridization (FISH) to examine the spatial locations of cell types and cell trajectories to understand the ancestral continuum of cell maturation. This data provides a resource for the transcriptional program of hindlimb development that will support future studies of musculoskeletal development and generate hypotheses for tissue regeneration. Overall design: Four samples from murine embryonic hindlimb tissue at E11.5, E13.5, E15.5, and E18.5"
Kelly 2019,E13.5,embryonic day 13.5,limb,limb bud,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE142425,GSM4227225,3p_v2,fastq,SRR10745785;SRR10745786,NA,SRX7421172,SRP238355,SRS5867776,SAMN13653635,NA,NA,"Kelly et al, Matrix Biology, 2019",10.1016/j.matbio.2019.12.004,https://pubmed.ncbi.nlm.nih.gov/31874220/,Illumina NovaSeq 6000,Single cell RNA-sequencing reveals cellular heterogeneity and trajectories of lineage specification during murine embryonic limb development,"The coordinated spatial and temporal regulation of gene expression in the murine hindlimb determines the identity of mesenchymal progenitors and the development of diversity of musculoskeletal tissues they form. Hindlimb development has historically been studied with lineage tracing of individual genes selected a priori, or at the bulk tissue level, which does not allow for the determination of single cell transcriptional programs yielding mature cell types and tissues. To identify the cellular trajectories of lineage specification during limb bud development, we used single cell mRNA sequencing (scRNA-seq) to profile the developing murine hindlimb between embryonic days (E)11.5-E18.5. We found cell type heterogeneity at all time points, and the expected cell types that form the mouse hindlimb. In addition, we used RNA fluorescence in situ hybridization (FISH) to examine the spatial locations of cell types and cell trajectories to understand the ancestral continuum of cell maturation. This data provides a resource for the transcriptional program of hindlimb development that will support future studies of musculoskeletal development and generate hypotheses for tissue regeneration. Overall design: Four samples from murine embryonic hindlimb tissue at E11.5, E13.5, E15.5, and E18.5"
Kelly 2019,E15.5,embryonic day 15.5,limb,limb bud,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE142425,GSM4227226,3p_v2,fastq,SRR10745787;SRR10745788,NA,SRX7421173,SRP238355,SRS5867777,SAMN13653610,NA,NA,"Kelly et al, Matrix Biology, 2019",10.1016/j.matbio.2019.12.004,https://pubmed.ncbi.nlm.nih.gov/31874220/,Illumina NovaSeq 6000,Single cell RNA-sequencing reveals cellular heterogeneity and trajectories of lineage specification during murine embryonic limb development,"The coordinated spatial and temporal regulation of gene expression in the murine hindlimb determines the identity of mesenchymal progenitors and the development of diversity of musculoskeletal tissues they form. Hindlimb development has historically been studied with lineage tracing of individual genes selected a priori, or at the bulk tissue level, which does not allow for the determination of single cell transcriptional programs yielding mature cell types and tissues. To identify the cellular trajectories of lineage specification during limb bud development, we used single cell mRNA sequencing (scRNA-seq) to profile the developing murine hindlimb between embryonic days (E)11.5-E18.5. We found cell type heterogeneity at all time points, and the expected cell types that form the mouse hindlimb. In addition, we used RNA fluorescence in situ hybridization (FISH) to examine the spatial locations of cell types and cell trajectories to understand the ancestral continuum of cell maturation. This data provides a resource for the transcriptional program of hindlimb development that will support future studies of musculoskeletal development and generate hypotheses for tissue regeneration. Overall design: Four samples from murine embryonic hindlimb tissue at E11.5, E13.5, E15.5, and E18.5"
Kelly 2019,E18.5,embryonic day 18.5,limb,limb bud,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE142425,GSM4227227,3p_v2,fastq,SRR10745789;SRR10745790,NA,SRX7421174,SRP238355,SRS5867778,SAMN13653580,NA,NA,"Kelly et al, Matrix Biology, 2019",10.1016/j.matbio.2019.12.004,https://pubmed.ncbi.nlm.nih.gov/31874220/,Illumina NovaSeq 6000,Single cell RNA-sequencing reveals cellular heterogeneity and trajectories of lineage specification during murine embryonic limb development,"The coordinated spatial and temporal regulation of gene expression in the murine hindlimb determines the identity of mesenchymal progenitors and the development of diversity of musculoskeletal tissues they form. Hindlimb development has historically been studied with lineage tracing of individual genes selected a priori, or at the bulk tissue level, which does not allow for the determination of single cell transcriptional programs yielding mature cell types and tissues. To identify the cellular trajectories of lineage specification during limb bud development, we used single cell mRNA sequencing (scRNA-seq) to profile the developing murine hindlimb between embryonic days (E)11.5-E18.5. We found cell type heterogeneity at all time points, and the expected cell types that form the mouse hindlimb. In addition, we used RNA fluorescence in situ hybridization (FISH) to examine the spatial locations of cell types and cell trajectories to understand the ancestral continuum of cell maturation. This data provides a resource for the transcriptional program of hindlimb development that will support future studies of musculoskeletal development and generate hypotheses for tissue regeneration. Overall design: Four samples from murine embryonic hindlimb tissue at E11.5, E13.5, E15.5, and E18.5"
de Lima 2021,"Forelimb,_E4",NA,limb,NA,NA,NA,NA,NA,NCBI entry missing on SRA?,TRUE,TRUE,Gallus gallus,GSE166981,GSM5090142,3p_v3,fastq,SRR13733760,NA,SRX10121386,SRP306879,SRS8276066,SAMN17965279,NA,NA,"de Lima et al, Nature Communications, 2021",10.1038/s41467-021-24157-x,https://pubmed.ncbi.nlm.nih.gov/34158501/,NextSeq 500,Unexpected contribution of fibroblasts to the muscle lineage during foetal myogenesis and role of BMP signalling in this process,"Purpose : Positional information driving limb muscle patterning is considered to be contained in lateral plate mesoderm-derived tissues, such as tendon or muscle connective tissue and not in myogenic cells themselves. The current consensus is that myogenic cells originate from somites, while connective tissue fibroblasts originate from the lateral plate mesoderm. We challenged this model by cell and genetic lineage tracing experiments and identified that a subpopulation of limb myogenic cells did not originate from somite or Pax3 lineage, but rather originated from the lateral plate mesoderm and were derived from Osr1 and Scx lineages. Results: Analysis of single-cell RNA-sequencing data obtained from limb cells at successive developmental stages identified a subpopulation of cells displaying a dual muscle and connective tissue signature, in addition to independent muscle and connective tissue populations. Active BMP signalling was detected in this junctional cell sub-population and at the tendon/muscle interface in developing limbs. BMP gain- and loss-of-function experiments performed in vivo and in vitro showed that this signalling pathway regulated a fibroblast-to-myoblast conversion. Conclusions: We propose that localised BMP signalling converts a subset of lateral plate mesoderm-derived fibroblasts to a myogenic fate and establishes a boundary of fibroblast-derived myonuclei at the tendon/muscle interface to control the muscle pattern during limb development and myotendinous formation. Overall design: Single cell mRNA profiles of whole forelimbs in wild type chicken embryos at three developmental stages (E4, E6 and E10)"
de Lima 2021,"Forelimb,_E6",NA,limb,NA,NA,NA,NA,NA,NCBI entry missing on SRA?,TRUE,TRUE,Gallus gallus,GSE166981,GSM5090143,3p_v3,fastq,SRR13733761,NA,SRX10121387,SRP306879,SRS8276068,SAMN17965275,NA,NA,"de Lima et al, Nature Communications, 2021",10.1038/s41467-021-24157-x,https://pubmed.ncbi.nlm.nih.gov/34158501/,NextSeq 500,Unexpected contribution of fibroblasts to the muscle lineage during foetal myogenesis and role of BMP signalling in this process,"Purpose : Positional information driving limb muscle patterning is considered to be contained in lateral plate mesoderm-derived tissues, such as tendon or muscle connective tissue and not in myogenic cells themselves. The current consensus is that myogenic cells originate from somites, while connective tissue fibroblasts originate from the lateral plate mesoderm. We challenged this model by cell and genetic lineage tracing experiments and identified that a subpopulation of limb myogenic cells did not originate from somite or Pax3 lineage, but rather originated from the lateral plate mesoderm and were derived from Osr1 and Scx lineages. Results: Analysis of single-cell RNA-sequencing data obtained from limb cells at successive developmental stages identified a subpopulation of cells displaying a dual muscle and connective tissue signature, in addition to independent muscle and connective tissue populations. Active BMP signalling was detected in this junctional cell sub-population and at the tendon/muscle interface in developing limbs. BMP gain- and loss-of-function experiments performed in vivo and in vitro showed that this signalling pathway regulated a fibroblast-to-myoblast conversion. Conclusions: We propose that localised BMP signalling converts a subset of lateral plate mesoderm-derived fibroblasts to a myogenic fate and establishes a boundary of fibroblast-derived myonuclei at the tendon/muscle interface to control the muscle pattern during limb development and myotendinous formation. Overall design: Single cell mRNA profiles of whole forelimbs in wild type chicken embryos at three developmental stages (E4, E6 and E10)"
de Lima 2021,"Forelimb,_E10",NA,limb,NA,NA,NA,NA,NA,NCBI entry missing on SRA?,TRUE,TRUE,Gallus gallus,GSE166981,GSM5090144,3p_v3,fastq,SRR13733762,NA,SRX10121388,SRP306879,SRS8276069,SAMN17965276,NA,NA,"de Lima et al, Nature Communications, 2021",10.1038/s41467-021-24157-x,https://pubmed.ncbi.nlm.nih.gov/34158501/,NextSeq 500,Unexpected contribution of fibroblasts to the muscle lineage during foetal myogenesis and role of BMP signalling in this process,"Purpose : Positional information driving limb muscle patterning is considered to be contained in lateral plate mesoderm-derived tissues, such as tendon or muscle connective tissue and not in myogenic cells themselves. The current consensus is that myogenic cells originate from somites, while connective tissue fibroblasts originate from the lateral plate mesoderm. We challenged this model by cell and genetic lineage tracing experiments and identified that a subpopulation of limb myogenic cells did not originate from somite or Pax3 lineage, but rather originated from the lateral plate mesoderm and were derived from Osr1 and Scx lineages. Results: Analysis of single-cell RNA-sequencing data obtained from limb cells at successive developmental stages identified a subpopulation of cells displaying a dual muscle and connective tissue signature, in addition to independent muscle and connective tissue populations. Active BMP signalling was detected in this junctional cell sub-population and at the tendon/muscle interface in developing limbs. BMP gain- and loss-of-function experiments performed in vivo and in vitro showed that this signalling pathway regulated a fibroblast-to-myoblast conversion. Conclusions: We propose that localised BMP signalling converts a subset of lateral plate mesoderm-derived fibroblasts to a myogenic fate and establishes a boundary of fibroblast-derived myonuclei at the tendon/muscle interface to control the muscle pattern during limb development and myotendinous formation. Overall design: Single cell mRNA profiles of whole forelimbs in wild type chicken embryos at three developmental stages (E4, E6 and E10)"
J He 2021,CS13_limbbud_10x,NA,limb,limb bud,cell,NA,NA,NA,NA,TRUE,TRUE,Homo sapiens,GSE173994,GSM4274188,3p_v2,fastq,SRR10901267,NA,SRX7569445,SRP242103,SRS6005478,SAMN13869935,NA,NA,"He et al, Cell Research, 2021",10.1038/s41422-021-00467-z,https://pubmed.ncbi.nlm.nih.gov/33473154/,HiSeq X Ten,Dissecting human embryonic skeletal stem cell ontogeny by single-cell transcriptomic and functional analyses,"Mapping the transcriptional landscape of human embryonic skeletogenesis at single-cell resolution during limb bud and primary ossification center (POC) formation. We found significant heterogeneity of stromal cells within the limb bud mesenchyme that specified proximal-distal and anterior-posterior patterning. Embryonic skeletal stem and progenitor cells first appeared during POC formation, which were highly enriched by CADM1 expression and could differentiate into osteoblasts, chondrocytes and periosteal mesenchymal stromal cells. Overall design: We performed droplet-based scRNA-seq of 42,857 cells to firstly construct a molecular landscape of skeletogenesis in human embryos"
J He 2021,CS15_limbbud_10x,NA,limb,limb bud,cell,NA,NA,NA,NA,TRUE,TRUE,Homo sapiens,GSE173994,GSM4274189,3p_v2,fastq,SRR10901268,NA,SRX7569446,SRP242103,SRS6005479,SAMN13869934,NA,NA,"He et al, Cell Research, 2021",10.1038/s41422-021-00467-z,https://pubmed.ncbi.nlm.nih.gov/33473154/,HiSeq X Ten,Dissecting human embryonic skeletal stem cell ontogeny by single-cell transcriptomic and functional analyses,"Mapping the transcriptional landscape of human embryonic skeletogenesis at single-cell resolution during limb bud and primary ossification center (POC) formation. We found significant heterogeneity of stromal cells within the limb bud mesenchyme that specified proximal-distal and anterior-posterior patterning. Embryonic skeletal stem and progenitor cells first appeared during POC formation, which were highly enriched by CADM1 expression and could differentiate into osteoblasts, chondrocytes and periosteal mesenchymal stromal cells. Overall design: We performed droplet-based scRNA-seq of 42,857 cells to firstly construct a molecular landscape of skeletogenesis in human embryos"
J He 2021,CS15(2)_limbbud_10x,NA,limb,limb bud,cell,NA,NA,NA,NA,TRUE,TRUE,Homo sapiens,GSE173994,GSM4274190,3p_v2,fastq,SRR10901269,NA,SRX7569447,SRP242103,SRS6005480,SAMN13869933,NA,NA,"He et al, Cell Research, 2021",10.1038/s41422-021-00467-z,https://pubmed.ncbi.nlm.nih.gov/33473154/,HiSeq X Ten,Dissecting human embryonic skeletal stem cell ontogeny by single-cell transcriptomic and functional analyses,"Mapping the transcriptional landscape of human embryonic skeletogenesis at single-cell resolution during limb bud and primary ossification center (POC) formation. We found significant heterogeneity of stromal cells within the limb bud mesenchyme that specified proximal-distal and anterior-posterior patterning. Embryonic skeletal stem and progenitor cells first appeared during POC formation, which were highly enriched by CADM1 expression and could differentiate into osteoblasts, chondrocytes and periosteal mesenchymal stromal cells. Overall design: We performed droplet-based scRNA-seq of 42,857 cells to firstly construct a molecular landscape of skeletogenesis in human embryos"
Van Deusen 2023b,"Adult, uninjured, rep1 snRNA-seq",NA,muscle,tibialis anterior,nucleus,male,C57BL/6J,NA,NA,FALSE,TRUE,Mus musculus,GSE180225,GSM5456281,3p_v3,fastq,SRR15169919,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Van Deusen 2023b,"Adult, uninjured, rep2 snRNA-seq",NA,muscle,tibialis anterior,nucleus,male,C57BL/6J,NA,NA,FALSE,TRUE,Mus musculus,GSE180225,GSM5456282,3p_v3,fastq,SRR15169920,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Van Deusen 2023b,"Aged, uninjured, rep1 snRNA-seq",NA,muscle,tibialis anterior,nucleus,male,C57BL/6J,NA,NA,FALSE,TRUE,Mus musculus,GSE180225,GSM5456283,3p_v3,fastq,SRR15169921,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Van Deusen 2023b,"Aged, uninjured, rep2 snRNA-seq",NA,muscle,tibialis anterior,nucleus,male,C57BL/6J,NA,NA,FALSE,TRUE,Mus musculus,GSE180225,GSM5456284,3p_v3,fastq,SRR15169922,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Van Deusen 2023b,"Adult, 4 days post-injury snRNA-seq",NA,muscle,tibialis anterior,nucleus,male,C57BL/6J,NA,NA,FALSE,TRUE,Mus musculus,GSE180225,GSM5456285,3p_v3,fastq,SRR15169923,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Van Deusen 2023b,"Adult, 7 days post-injury snRNA-seq",NA,muscle,tibialis anterior,nucleus,male,C57BL/6J,NA,NA,FALSE,TRUE,Mus musculus,GSE180225,GSM5456286,3p_v3,fastq,SRR15169924,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Van Deusen 2023b,"Aged, 4 days post-injury snRNA-seq",NA,muscle,tibialis anterior,nucleus,male,C57BL/6J,NA,NA,FALSE,TRUE,Mus musculus,GSE180225,GSM5456287,3p_v3,fastq,SRR15169925,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Van Deusen 2023b,"Aged, 7 days post-injury snRNA-seq",NA,muscle,tibialis anterior,nucleus,male,C57BL/6J,NA,NA,FALSE,TRUE,Mus musculus,GSE180225,GSM5456288,3p_v3,fastq,SRR15169926,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Liu L 2023,Y1ex,NA,muscle,extensor digitorum longus,cell,male,C57BL/6,NA,NA,FALSE,TRUE,Mus musculus,GSE196364,GSM5778080,SmartSeq4,fastq,SRR17492734,NA,SRX13662920,,NA,SAMN24727980,,NA,NA,NA,https://pubmed.ncbi.nlm.nih.gov/37080206/,NA,NA,NA
Liu L 2023,Y2ex,NA,muscle,extensor digitorum longus,cell,male,C57BL/6,NA,NA,FALSE,TRUE,Mus musculus,GSE196364,GSM5778081,SmartSeq4,fastq,SRR17492733,NA,SRX13662921,,NA,SAMN24727979,,NA,NA,NA,https://pubmed.ncbi.nlm.nih.gov/37080206/,NA,NA,NA
Liu L 2023,Y3ex,NA,muscle,extensor digitorum longus,cell,male,C57BL/6,NA,NA,FALSE,TRUE,Mus musculus,GSE196364,GSM5778082,SmartSeq4,fastq,SRR17492732,NA,SRX13662922,,NA,SAMN24727978,,NA,NA,NA,https://pubmed.ncbi.nlm.nih.gov/37080206/,NA,NA,NA
Liu L 2023,Y1e4,NA,muscle,extensor digitorum longus,cell,male,C57BL/6,NA,NA,FALSE,TRUE,Mus musculus,GSE196364,GSM5778083,SmartSeq4,fastq,SRR17492731,NA,SRX13662923,,NA,SAMN24727977,,NA,NA,NA,https://pubmed.ncbi.nlm.nih.gov/37080206/,NA,NA,NA
Liu L 2023,Y5c,NA,muscle,extensor digitorum longus,cell,male,C57BL/6,NA,NA,FALSE,TRUE,Mus musculus,GSE196364,GSM5778084,SmartSeq4,fastq,SRR17492730,NA,SRX13662924,,NA,SAMN24727976,,NA,NA,NA,https://pubmed.ncbi.nlm.nih.gov/37080206/,NA,NA,NA
Liu L 2023,Y6c,NA,muscle,extensor digitorum longus,cell,male,C57BL/6,NA,NA,FALSE,TRUE,Mus musculus,GSE196364,GSM5778085,SmartSeq4,fastq,SRR17492729,NA,SRX13662925,,NA,SAMN24727975,,NA,NA,NA,https://pubmed.ncbi.nlm.nih.gov/37080206/,NA,NA,NA
Liu L 2023,Y7c,NA,muscle,extensor digitorum longus,cell,male,C57BL/6,NA,NA,FALSE,TRUE,Mus musculus,GSE196364,GSM5778086,SmartSeq4,fastq,SRR17492728,NA,SRX13662926,,NA,SAMN24727974,,NA,NA,NA,https://pubmed.ncbi.nlm.nih.gov/37080206/,NA,NA,NA
Liu L 2023,Y8c,NA,muscle,extensor digitorum longus,cell,male,C57BL/6,NA,NA,FALSE,TRUE,Mus musculus,GSE196364,GSM5778087,SmartSeq4,fastq,SRR17492727,NA,SRX13662927,,NA,SAMN24727973,,NA,NA,NA,https://pubmed.ncbi.nlm.nih.gov/37080206/,NA,NA,NA
Liu L 2023,O1ex,NA,muscle,extensor digitorum longus,cell,male,C57BL/6,NA,NA,FALSE,TRUE,Mus musculus,GSE196364,GSM5778088,SmartSeq4,fastq,SRR17492726,NA,SRX13662928,,NA,SAMN24727972,,NA,NA,NA,https://pubmed.ncbi.nlm.nih.gov/37080206/,NA,NA,NA
Liu L 2023,O2ex,NA,muscle,extensor digitorum longus,cell,male,C57BL/6,NA,NA,FALSE,TRUE,Mus musculus,GSE196364,GSM5778089,SmartSeq4,fastq,SRR17492725,NA,SRX13662929,,NA,SAMN24727971,,NA,NA,NA,https://pubmed.ncbi.nlm.nih.gov/37080206/,NA,NA,NA
Liu L 2023,O3ex,NA,muscle,extensor digitorum longus,cell,male,C57BL/6,NA,NA,FALSE,TRUE,Mus musculus,GSE196364,GSM5778090,SmartSeq4,fastq,SRR17492724,NA,SRX13662930,,NA,SAMN24727970,,NA,NA,NA,https://pubmed.ncbi.nlm.nih.gov/37080206/,NA,NA,NA
Liu L 2023,O1e4,NA,muscle,extensor digitorum longus,cell,male,C57BL/6,NA,NA,FALSE,TRUE,Mus musculus,GSE196364,GSM5778091,SmartSeq4,fastq,SRR17492723,NA,SRX13662931,,NA,SAMN24727969,,NA,NA,NA,https://pubmed.ncbi.nlm.nih.gov/37080206/,NA,NA,NA
Liu L 2023,O5c,NA,muscle,extensor digitorum longus,cell,male,C57BL/6,NA,NA,FALSE,TRUE,Mus musculus,GSE196364,GSM5778092,SmartSeq4,fastq,SRR17492722,NA,SRX13662932,,NA,SAMN24727968,,NA,NA,NA,https://pubmed.ncbi.nlm.nih.gov/37080206/,NA,NA,NA
Liu L 2023,O6c,NA,muscle,extensor digitorum longus,cell,male,C57BL/6,NA,NA,FALSE,TRUE,Mus musculus,GSE196364,GSM5778093,SmartSeq4,fastq,SRR17492721,NA,SRX13662933,,NA,SAMN24727967,,NA,NA,NA,https://pubmed.ncbi.nlm.nih.gov/37080206/,NA,NA,NA
Liu L 2023,O7c,NA,muscle,extensor digitorum longus,cell,male,C57BL/6,NA,NA,FALSE,TRUE,Mus musculus,GSE196364,GSM5778094,SmartSeq4,fastq,SRR17492720,NA,SRX13662934,,NA,SAMN24727966,,NA,NA,NA,https://pubmed.ncbi.nlm.nih.gov/37080206/,NA,NA,NA
Liu L 2023,O8c,NA,muscle,extensor digitorum longus,cell,male,C57BL/6,NA,NA,FALSE,TRUE,Mus musculus,GSE196364,GSM5778095,SmartSeq4,fastq,SRR17492719,NA,SRX13662935,,NA,SAMN24727965,,NA,NA,NA,https://pubmed.ncbi.nlm.nih.gov/37080206/,NA,NA,NA
Liu L 2023,Yex1mu,NA,muscle,hindlimb,cell,male,C57BL/6,NA,NA,TRUE,TRUE,Mus musculus,GSE196364,GSM5876610,3p_v3,fastq,SRR17944901;SRR17944902;SRR17944903;SRR17944904;SRR17944905;SRR17944906;SRR17944907;SRR17944908;SRR17944909;SRR17944910;SRR17944911;SRR17944912;SRR17944913;SRR17944914;SRR17944915;SRR17944916;,NA,NA,NA,NA,NA,NA,NA,NA,NA,https://pubmed.ncbi.nlm.nih.gov/37080206/,NA,NA,NA
Liu L 2023,Yex2mu,NA,muscle,hindlimb,cell,male,C57BL/6,NA,NA,TRUE,TRUE,Mus musculus,GSE196364,GSM5876611,3p_v3,fastq,SRR17944885;SRR17944886;SRR17944887;SRR17944888;SRR17944889;SRR17944890;SRR17944891;SRR17944892;SRR17944893;SRR17944894;SRR17944895;SRR17944896;SRR17944897;SRR17944898;SRR17944899;SRR17944900;,NA,NA,NA,NA,NA,NA,NA,NA,NA,https://pubmed.ncbi.nlm.nih.gov/37080206/,NA,NA,NA
Liu L 2023,Yex3mu,NA,muscle,hindlimb,cell,male,C57BL/6,NA,NA,TRUE,TRUE,Mus musculus,GSE196364,GSM5876612,3p_v3,fastq,SRR17944869;SRR17944870;SRR17944871;SRR17944872;SRR17944873;SRR17944874;SRR17944875;SRR17944876;SRR17944877;SRR17944878;SRR17944879;SRR17944880;SRR17944881;SRR17944882;SRR17944883;SRR17944884;,NA,NA,NA,NA,NA,NA,NA,NA,NA,https://pubmed.ncbi.nlm.nih.gov/37080206/,NA,NA,NA
Liu L 2023,Yex4mu,NA,muscle,hindlimb,cell,male,C57BL/6,NA,NA,TRUE,TRUE,Mus musculus,GSE196364,GSM5876613,3p_v3,fastq,SRR17944851;SRR17944830;SRR17944831;SRR17944832;SRR17944833;SRR17944834;SRR17944852;SRR17944853;SRR17944854;SRR17944855;SRR17944856;SRR17944857;SRR17944858;SRR17944859;SRR17944860;SRR17944861;,NA,NA,NA,NA,NA,NA,NA,NA,NA,https://pubmed.ncbi.nlm.nih.gov/37080206/,NA,NA,NA
Liu L 2023,Yc1mu,NA,muscle,hindlimb,cell,male,C57BL/6,NA,NA,TRUE,TRUE,Mus musculus,GSE196364,GSM5876614,3p_v3,fastq,SRR17944798;SRR17944799;SRR17944800;SRR17944801;SRR17944802;SRR17944803;SRR17944804;SRR17944805;SRR17944806;SRR17944807;SRR17944808;SRR17944809;SRR17944810;SRR17944811;SRR17944812;SRR17944813;,NA,NA,NA,NA,NA,NA,NA,NA,NA,https://pubmed.ncbi.nlm.nih.gov/37080206/,NA,NA,NA
Liu L 2023,Yc2mu,NA,muscle,hindlimb,cell,male,C57BL/6,NA,NA,TRUE,TRUE,Mus musculus,GSE196364,GSM5876615,3p_v3,fastq,SRR17944782;SRR17944783;SRR17944784;SRR17944785;SRR17944786;SRR17944787;SRR17944788;SRR17944789;SRR17944790;SRR17944791;SRR17944792;SRR17944793;SRR17944794;SRR17944795;SRR17944796;SRR17944797;,NA,NA,NA,NA,NA,NA,NA,NA,NA,https://pubmed.ncbi.nlm.nih.gov/37080206/,NA,NA,NA
Liu L 2023,Yc3mu,NA,muscle,hindlimb,cell,male,C57BL/6,NA,NA,TRUE,TRUE,Mus musculus,GSE196364,GSM5876616,3p_v3,fastq,SRR17944766;SRR17944767;SRR17944768;SRR17944769;SRR17944770;SRR17944771;SRR17944772;SRR17944773;SRR17944774;SRR17944775;SRR17944776;SRR17944777;SRR17944778;SRR17944779;SRR17944780;SRR17944781;,NA,NA,NA,NA,NA,NA,NA,NA,NA,https://pubmed.ncbi.nlm.nih.gov/37080206/,NA,NA,NA
Liu L 2023,Yc4mu,NA,muscle,hindlimb,cell,male,C57BL/6,NA,NA,TRUE,TRUE,Mus musculus,GSE196364,GSM5876617,3p_v3,fastq,SRR17944750;SRR17944751;SRR17944752;SRR17944753;SRR17944754;SRR17944755;SRR17944756;SRR17944757;SRR17944758;SRR17944759;SRR17944760;SRR17944761;SRR17944762;SRR17944763;SRR17944764;SRR17944765;,NA,NA,NA,NA,NA,NA,NA,NA,NA,https://pubmed.ncbi.nlm.nih.gov/37080206/,NA,NA,NA
Liu L 2023,Oex1mu,NA,muscle,hindlimb,cell,male,C57BL/6,NA,NA,TRUE,TRUE,Mus musculus,GSE196364,GSM5876618,3p_v3,fastq,SRR17944734;SRR17944735;SRR17944736;SRR17944737;SRR17944738;SRR17944739;SRR17944740;SRR17944741;SRR17944742;SRR17944743;SRR17944744;SRR17944745;SRR17944746;SRR17944747;SRR17944748;SRR17944749;,NA,NA,NA,NA,NA,NA,NA,NA,NA,https://pubmed.ncbi.nlm.nih.gov/37080206/,NA,NA,NA
Liu L 2023,Oex2mu,NA,muscle,hindlimb,cell,male,C57BL/6,NA,NA,TRUE,TRUE,Mus musculus,GSE196364,GSM5876619,3p_v3,fastq,SRR17944718;SRR17944719;SRR17944720;SRR17944721;SRR17944722;SRR17944723;SRR17944724;SRR17944725;SRR17944726;SRR17944727;SRR17944728;SRR17944729;SRR17944730;SRR17944731;SRR17944732;SRR17944733;,NA,NA,NA,NA,NA,NA,NA,NA,NA,https://pubmed.ncbi.nlm.nih.gov/37080206/,NA,NA,NA
Liu L 2023,Oex3mu,NA,muscle,hindlimb,cell,male,C57BL/6,NA,NA,TRUE,TRUE,Mus musculus,GSE196364,GSM5876620,3p_v3,fastq,SRR17944702;SRR17944703;SRR17944704;SRR17944705;SRR17944706;SRR17944707;SRR17944708;SRR17944709;SRR17944710;SRR17944711;SRR17944712;SRR17944713;SRR17944714;SRR17944715;SRR17944716;SRR17944717;,NA,NA,NA,NA,NA,NA,NA,NA,NA,https://pubmed.ncbi.nlm.nih.gov/37080206/,NA,NA,NA
Liu L 2023,Oex4mu,NA,muscle,hindlimb,cell,male,C57BL/6,NA,NA,TRUE,TRUE,Mus musculus,GSE196364,GSM5876621,3p_v3,fastq,SRR17944686;SRR17944687;SRR17944688;SRR17944689;SRR17944690;SRR17944691;SRR17944692;SRR17944693;SRR17944694;SRR17944695;SRR17944696;SRR17944697;SRR17944698;SRR17944699;SRR17944700;SRR17944701;,NA,NA,NA,NA,NA,NA,NA,NA,NA,https://pubmed.ncbi.nlm.nih.gov/37080206/,NA,NA,NA
Liu L 2023,Oc1mu,NA,muscle,hindlimb,cell,male,C57BL/6,NA,NA,TRUE,TRUE,Mus musculus,GSE196364,GSM5876622,3p_v3,fastq,SRR17944670;SRR17944671;SRR17944672;SRR17944673;SRR17944674;SRR17944675;SRR17944676;SRR17944677;SRR17944678;SRR17944679;SRR17944680;SRR17944681;SRR17944682;SRR17944683;SRR17944684;SRR17944685;,NA,NA,NA,NA,NA,NA,NA,NA,NA,https://pubmed.ncbi.nlm.nih.gov/37080206/,NA,NA,NA
Liu L 2023,Oc2mu,NA,muscle,hindlimb,cell,male,C57BL/6,NA,NA,TRUE,TRUE,Mus musculus,GSE196364,GSM5876623,3p_v3,fastq,SRR17944661;SRR17944662;SRR17944663;SRR17944664;SRR17944665;SRR17944666;SRR17944667;SRR17944668;SRR17944669;SRR17944862;SRR17944863;SRR17944864;SRR17944865;SRR17944866;SRR17944867;SRR17944868;,NA,NA,NA,NA,NA,NA,NA,NA,NA,https://pubmed.ncbi.nlm.nih.gov/37080206/,NA,NA,NA
Liu L 2023,Oc3mu,NA,muscle,hindlimb,cell,male,C57BL/6,NA,NA,TRUE,TRUE,Mus musculus,GSE196364,GSM5876624,3p_v3,fastq,SRR17944835;SRR17944836;SRR17944837;SRR17944838;SRR17944839;SRR17944840;SRR17944841;SRR17944842;SRR17944843;SRR17944844;SRR17944845;SRR17944846;SRR17944847;SRR17944848;SRR17944849;SRR17944850;,NA,NA,NA,NA,NA,NA,NA,NA,NA,https://pubmed.ncbi.nlm.nih.gov/37080206/,NA,NA,NA
Liu L 2023,Oc4mu,NA,muscle,hindlimb,cell,male,C57BL/6,NA,NA,TRUE,TRUE,Mus musculus,GSE196364,GSM5876625,3p_v3,fastq,SRR17944814;SRR17944815;SRR17944816;SRR17944817;SRR17944818;SRR17944819;SRR17944820;SRR17944821;SRR17944822;SRR17944823;SRR17944824;SRR17944825;SRR17944826;SRR17944827;SRR17944828;SRR17944829;,NA,NA,NA,NA,NA,NA,NA,NA,NA,https://pubmed.ncbi.nlm.nih.gov/37080206/,NA,NA,NA
Fitzgerald 2023,RF1,NA,muscle,rectus femoris,nucleus,NA,NA,NA,NA,TRUE,TRUE,Homo sapiens,GSE200487,GSM6034993,3p_v3.1,fastq,SRR18686431,NA,SRX14787461,NA,NA,SAMN27479204,NA,NA,NA,10.1038/s42003-023-04504-y,https://pubmed.ncbi.nlm.nih.gov/36707617/,NA,NA,NA
Fitzgerald 2023,RF2,NA,muscle,rectus femoris,nucleus,NA,NA,NA,NA,TRUE,TRUE,Homo sapiens,GSE200487,GSM6034994,3p_v3.1,fastq,SRR18686430,NA,SRX14787462,NA,NA,SAMN27479203,NA,NA,NA,10.1038/s42003-023-04504-y,https://pubmed.ncbi.nlm.nih.gov/36707617/,NA,NA,NA
Fitzgerald 2023,GM1,NA,muscle,gluteus minimus,nucleus,NA,NA,NA,NA,TRUE,TRUE,Homo sapiens,GSE200487,GSM6034995,3p_v3.1,fastq,SRR18686429,NA,SRX14787463,NA,NA,SAMN27479202,NA,NA,NA,10.1038/s42003-023-04504-y,https://pubmed.ncbi.nlm.nih.gov/36707617/,NA,NA,NA
Fitzgerald 2023,GM2,NA,muscle,gluteus minimus,nucleus,NA,NA,NA,NA,TRUE,TRUE,Homo sapiens,GSE200487,GSM6034996,3p_v3.1,fastq,SRR18686428,NA,SRX14787464,NA,NA,SAMN27479201,NA,NA,NA,10.1038/s42003-023-04504-y,https://pubmed.ncbi.nlm.nih.gov/36707617/,NA,NA,NA
Fitzgerald 2023,schulthess_10_RF1,NA,muscle,rectus femoris,cell,NA,NA,NA,NA,TRUE,TRUE,Homo sapiens,GSE200487,GSM6034997,3p_v2,fastq,SRR18686427;SRR18686426,NA,SRX14787465,NA,NA,SAMN27479200,NA,NA,NA,10.1038/s42003-023-04504-y,https://pubmed.ncbi.nlm.nih.gov/36707617/,NA,NA,NA
Fitzgerald 2023,schulthess_10_GM,NA,muscle,gluteus minimus,cell,NA,NA,NA,NA,TRUE,TRUE,Homo sapiens,GSE200487,GSM6034998,3p_v2,fastq,SRR18686425;SRR18686424,NA,SRX14787466,NA,NA,SAMN27479199,NA,NA,NA,10.1038/s42003-023-04504-y,https://pubmed.ncbi.nlm.nih.gov/36707617/,NA,NA,NA
Fitzgerald 2023,FAPS30_all_E1,NA,muscle,hindlimb,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE200487,GSM6034999,3p_v2,fastq,SRR18686423;SRR18686422,NA,SRX14787467,NA,NA,SAMN27479198,NA,NA,NA,10.1038/s42003-023-04504-y,https://pubmed.ncbi.nlm.nih.gov/36707617/,NA,NA,NA
Conte 2023,"Muscle, control,3 samples pooled, scRNA-seq",NA,muscle,myoblasts,cell,mixed,NA,CD56,very low mapping rate,FALSE,FALSE,Homo sapiens,GSE208360,GSM6341891,3p_v3.1,fastq,SRR20281136,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Conte 2023,"Muscle, patient,3 samples pooled, scRNA-seq",NA,muscle,myoblasts,cell,mixed,NA,CD56,very low mapping rate,FALSE,FALSE,Homo sapiens,GSE208360,GSM6341892,3p_v3.1,fastq,SRR20281135,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Wang Y 2023,"EV, replicate 1, scRNAseq",NA,muscle,electric organ,cell,NA,NA,NA,NA,TRUE,TRUE,Electrophorus voltai,GSE228466,GSM7122392,3p_v3.1,fastq,SRR24003747;SRR24003748;SRR24003749;SRR24003750,NA,SRX19807151,NA,NA,SAMN33965470,NA,NA,NA,NA,NA,NA,NA,NA
Ly 2021,P1_Quiescent_HighGlucose,NA,muscle,NA,NA,NA,NA,NA,"32bp R1, only 12bp of non-N sequence",FALSE,TRUE,Mus musculus,GSE117386,GSM3293675,NA,fastq,SRR7541458,NA,SRX4408985,NA,NA,SAMN09692750,NA,NA,NA,NA,NA,NA,NA,NA
Ly 2021,P2_LowGlucose_Galactose,NA,muscle,NA,NA,NA,NA,NA,"32bp R1, only 12bp of non-N sequence",FALSE,TRUE,Mus musculus,GSE117386,GSM3293676,NA,fastq,SRR7541459,NA,SRX4408986,NA,NA,SAMN09692749,NA,NA,NA,NA,NA,NA,NA,NA
Incitti 2019,"iPax3 single-cell RNA-Seq, 2",ES-derived myogenic progenitors,muscle,iPSC,cell,NA,NA,NA,NA,FALSE,TRUE,Mus musculus,GSE121469,GSM3494414,NA,fastq,SRR8256805;SRR8256806,NA,SRX5074314,SRP166131,SRS4088126,SAMN10492612,NA,NA,"Incitti et al, PNAS, 2019",NA,https://pubmed.ncbi.nlm.nih.gov/30760602/,Illumina HiSeq 2500,Pluripotent stem cell-derived myogenic progenitors remodel their molecular signature upon in vivo engraftment [RNA-seq],"Optimal cell-based therapies for the treatment of muscle degenerative disorders should not only regenerate fibers, but provide a quiescent satellite cell pool ensuring long-term maintenance and regeneration. Conditional expression of Pax3/Pax7 in differentiating pluripotent stem cells (PSC) allows the generation of myogenic progenitors endowed with satellite cell-like abilities.  To identify the molecular determinants underlying their regenerative potential, we performed transcriptome analyses of these cells along with primary myogenic cells from several developmental stages. Here we show that in vitro generated PSC-derived myogenic progenitors possess a molecular signature similar to embryonic/fetal myoblasts. However, compared to fetal myoblasts, following transplantation they show superior myofiber engraftment and ability to seed the satellite cell niche, respond to multiple re-injuries and contribute to long-term regeneration. Upon engraftment, the transcriptome of Pax3/Pax7-induced PSC-derived myogenic progenitors changes dramatically, acquiring similarity to that of satellite cells, particularly in genes involved in extracellular matrix remodeling. Single cell profiling reveals that these changes are induced, not selected, by the in vivo environment.  These findings demonstrate that Pax3/Pax7-induced PSC-derived myogenic progenitors possess proliferative and migratory abilities characteristic of earlier developmental stages, and an intrinsic ability to respond to environmental cues upon skeletal muscle regeneration. Overall design: Three replicates of each sample (iPax3 and iPax7 myogenic progenitors) were analyzed and compared to reference developmental samples embryonic and fetal myoblasts, and neonatal satellite cells (three rep each). Transcriptome profiling of iPax3/7 cells injected in vivo and re-isolated was then compared to adult satellite cells (3 reps each); finally, iPax3 cells were subjected to single-cell RNA-Seq and compared to single-cell RNA-Seq of adult satellite cells."
van den Heuvel 2019,FSHD1.1,FSHD1 patient-derived primary myocytes,muscle,NA,NA,NA,NA,NA,download pipeline cant handle v1 data (yet!)_fastq provided,FALSE,TRUE,Homo sapiens,GSE122873,GSM3487556,3p_v1,NA,SRR8239853,NA,SRX5058117,SRP170544,SRS4074307,SAMN10473098,NA,NA,"van den Heuvel et al, Hum Mol Genet, 2019",10.1093/hmg/ddy400,https://pubmed.ncbi.nlm.nih.gov/30445587/,NextSeq 500,single-cell RNA sequencing in patient-derived primary myocytes for facioscapulohumeral muscular dystrophy,"Facioscapulohumeral muscular dystrophy (FSHD) is characterized by sporadic de-repression of the transcription factor DUX4 in skeletal muscle. We employed single-cell RNA-sequencing, combined with pseudotime trajectory modeling, to study FSHD disease etiology and cellular progression in human primary myocytes. We identified a small FSHD-specific cell population in all tested patient-derived cultures and detected new genes associated with DUX4 de-repression. We furthermore generated an FSHD cellular progression model, reflecting both the early burst-like DUX4 expression as well as the downstream activation of various FSHD-associated pathways, which allowed us to correlate DUX4 expression signature dynamics with that of regulatory complexes, thereby facilitating the prioritization of epigenetic targets for DUX4 silencing. Overall design: This dataset includes data from muscle biopsy-derived myocyte cultures from 2 FSHD1 patients, 2 FSHD2 patients and 2 healthy control individuals"
van den Heuvel 2019,FSHD1.2,FSHD1 patient-derived primary myocytes,muscle,NA,NA,NA,NA,NA,download pipeline cant handle v1 data (yet!)_fastq provided,FALSE,TRUE,Homo sapiens,GSE122873,GSM3487557,3p_v1,NA,SRR8239854,NA,SRX5058118,SRP170544,SRS4074308,SAMN10473103,NA,NA,"van den Heuvel et al, Hum Mol Genet, 2019",10.1093/hmg/ddy400,https://pubmed.ncbi.nlm.nih.gov/30445587/,NextSeq 500,single-cell RNA sequencing in patient-derived primary myocytes for facioscapulohumeral muscular dystrophy,"Facioscapulohumeral muscular dystrophy (FSHD) is characterized by sporadic de-repression of the transcription factor DUX4 in skeletal muscle. We employed single-cell RNA-sequencing, combined with pseudotime trajectory modeling, to study FSHD disease etiology and cellular progression in human primary myocytes. We identified a small FSHD-specific cell population in all tested patient-derived cultures and detected new genes associated with DUX4 de-repression. We furthermore generated an FSHD cellular progression model, reflecting both the early burst-like DUX4 expression as well as the downstream activation of various FSHD-associated pathways, which allowed us to correlate DUX4 expression signature dynamics with that of regulatory complexes, thereby facilitating the prioritization of epigenetic targets for DUX4 silencing. Overall design: This dataset includes data from muscle biopsy-derived myocyte cultures from 2 FSHD1 patients, 2 FSHD2 patients and 2 healthy control individuals"
van den Heuvel 2019,FSHD2.1,FSHD2 patient-derived primary myocytes,muscle,NA,NA,NA,NA,NA,download pipeline cant handle v1 data (yet!)_fastq provided,FALSE,TRUE,Homo sapiens,GSE122873,GSM3487558,3p_v1,NA,SRR8239855,NA,SRX5058119,SRP170544,SRS4074309,SAMN10473102,NA,NA,"van den Heuvel et al, Hum Mol Genet, 2019",10.1093/hmg/ddy400,https://pubmed.ncbi.nlm.nih.gov/30445587/,NextSeq 500,single-cell RNA sequencing in patient-derived primary myocytes for facioscapulohumeral muscular dystrophy,"Facioscapulohumeral muscular dystrophy (FSHD) is characterized by sporadic de-repression of the transcription factor DUX4 in skeletal muscle. We employed single-cell RNA-sequencing, combined with pseudotime trajectory modeling, to study FSHD disease etiology and cellular progression in human primary myocytes. We identified a small FSHD-specific cell population in all tested patient-derived cultures and detected new genes associated with DUX4 de-repression. We furthermore generated an FSHD cellular progression model, reflecting both the early burst-like DUX4 expression as well as the downstream activation of various FSHD-associated pathways, which allowed us to correlate DUX4 expression signature dynamics with that of regulatory complexes, thereby facilitating the prioritization of epigenetic targets for DUX4 silencing. Overall design: This dataset includes data from muscle biopsy-derived myocyte cultures from 2 FSHD1 patients, 2 FSHD2 patients and 2 healthy control individuals"
van den Heuvel 2019,FSHD2.2,FSHD2 patient-derived primary myocytes,muscle,NA,NA,NA,NA,NA,download pipeline cant handle v1 data (yet!)_fastq provided,FALSE,TRUE,Homo sapiens,GSE122873,GSM3487559,3p_v1,NA,SRR8239856,NA,SRX5058120,SRP170544,SRS4074310,SAMN10473101,NA,NA,"van den Heuvel et al, Hum Mol Genet, 2019",10.1093/hmg/ddy400,https://pubmed.ncbi.nlm.nih.gov/30445587/,NextSeq 500,single-cell RNA sequencing in patient-derived primary myocytes for facioscapulohumeral muscular dystrophy,"Facioscapulohumeral muscular dystrophy (FSHD) is characterized by sporadic de-repression of the transcription factor DUX4 in skeletal muscle. We employed single-cell RNA-sequencing, combined with pseudotime trajectory modeling, to study FSHD disease etiology and cellular progression in human primary myocytes. We identified a small FSHD-specific cell population in all tested patient-derived cultures and detected new genes associated with DUX4 de-repression. We furthermore generated an FSHD cellular progression model, reflecting both the early burst-like DUX4 expression as well as the downstream activation of various FSHD-associated pathways, which allowed us to correlate DUX4 expression signature dynamics with that of regulatory complexes, thereby facilitating the prioritization of epigenetic targets for DUX4 silencing. Overall design: This dataset includes data from muscle biopsy-derived myocyte cultures from 2 FSHD1 patients, 2 FSHD2 patients and 2 healthy control individuals"
van den Heuvel 2019,CTRL.1,Healthy control individual-derived primary myocytes,muscle,NA,NA,NA,NA,NA,download pipeline cant handle v1 data (yet!)_fastq provided,FALSE,TRUE,Homo sapiens,GSE122873,GSM3487560,3p_v1,NA,SRR8239857,NA,SRX5058121,SRP170544,SRS4074311,SAMN10473100,NA,NA,"van den Heuvel et al, Hum Mol Genet, 2019",10.1093/hmg/ddy400,https://pubmed.ncbi.nlm.nih.gov/30445587/,NextSeq 500,single-cell RNA sequencing in patient-derived primary myocytes for facioscapulohumeral muscular dystrophy,"Facioscapulohumeral muscular dystrophy (FSHD) is characterized by sporadic de-repression of the transcription factor DUX4 in skeletal muscle. We employed single-cell RNA-sequencing, combined with pseudotime trajectory modeling, to study FSHD disease etiology and cellular progression in human primary myocytes. We identified a small FSHD-specific cell population in all tested patient-derived cultures and detected new genes associated with DUX4 de-repression. We furthermore generated an FSHD cellular progression model, reflecting both the early burst-like DUX4 expression as well as the downstream activation of various FSHD-associated pathways, which allowed us to correlate DUX4 expression signature dynamics with that of regulatory complexes, thereby facilitating the prioritization of epigenetic targets for DUX4 silencing. Overall design: This dataset includes data from muscle biopsy-derived myocyte cultures from 2 FSHD1 patients, 2 FSHD2 patients and 2 healthy control individuals"
van den Heuvel 2019,CTRL.2,Healthy control individual-derived primary myocytes,muscle,NA,NA,NA,NA,NA,download pipeline cant handle v1 data (yet!)_fastq provided,FALSE,TRUE,Homo sapiens,GSE122873,GSM3487561,3p_v1,NA,SRR8239858,NA,SRX5058122,SRP170544,SRS4074312,SAMN10473099,NA,NA,"van den Heuvel et al, Hum Mol Genet, 2019",10.1093/hmg/ddy400,https://pubmed.ncbi.nlm.nih.gov/30445587/,NextSeq 500,single-cell RNA sequencing in patient-derived primary myocytes for facioscapulohumeral muscular dystrophy,"Facioscapulohumeral muscular dystrophy (FSHD) is characterized by sporadic de-repression of the transcription factor DUX4 in skeletal muscle. We employed single-cell RNA-sequencing, combined with pseudotime trajectory modeling, to study FSHD disease etiology and cellular progression in human primary myocytes. We identified a small FSHD-specific cell population in all tested patient-derived cultures and detected new genes associated with DUX4 de-repression. We furthermore generated an FSHD cellular progression model, reflecting both the early burst-like DUX4 expression as well as the downstream activation of various FSHD-associated pathways, which allowed us to correlate DUX4 expression signature dynamics with that of regulatory complexes, thereby facilitating the prioritization of epigenetic targets for DUX4 silencing. Overall design: This dataset includes data from muscle biopsy-derived myocyte cultures from 2 FSHD1 patients, 2 FSHD2 patients and 2 healthy control individuals"
Penaloza 2019,Penaloza_Mesp1,Single-Cell RNA-seq of Skeletal Progenitors derived from Mesp1,muscle,muscle,NA,NA,NA,NA,ONT,FALSE,TRUE,Mus musculus,GSE131734,GSM3814860,ONT,fastq,SRR9117286,NA,SRX5891346,SRP199390,SRS4813060,SAMN11843118,NA,NA,"Penaloza et al, Biochem Biophys Res Commun, 2019",NA,https://pubmed.ncbi.nlm.nih.gov/31590918/,Illumina HiSeq 2500,Single-Cell RNA-seq of Skeletal Progenitors derived from Mesp1,We developed a differentiation protocol to create skeletal myogenic progenitors in vitro by the induction of Mesp1. The goal of this study is to study the heterogenity of Mesp1 derivatives. Overall design: The Chromium Single Cell 3' technology was used to create library contructs for single cells. This was performed as recommended by 10X Genomics platform.
De Micheli 2020a,D0_Cv3,NA,muscle,tibialis anterior,cell,NA,C57BL/6J,NA,low quality data,FALSE,TRUE,Mus musculus,GSE143437,GSM4259475,3p_v3,fastq,SRR10870298,NA,NA,NA,NA,NA,NA,NA,"De Micheli et al, unpublished",NA,unpublished,NA,NA,NA
Williams 2020,NA,NA,muscle,tibialis anterior,NA,NA,NA,NA,NA,FALSE,TRUE,Homo sapiens,GSE143493,NA,Fluidigm,NA,,,,,,,,,,,,,,
Robinson 2021,Nelfb-KO_3,NA,muscle,NA,NA,NA,NA,NA,Reads are improperly paired; R1 contains multiple read lengths (25 and 26bp),FALSE,TRUE,Mus musculus,GSE150278,GSM4544638,3p_v2,fastq,SRR11768423;SRR11768424;SRR11768425;SRR11768426,NA,SRX8321672,SRP261108,SRS6640987,SAMN14888052,NA,NA,"Robinson et al, Developmental Cell, 2021",NA,https://pubmed.ncbi.nlm.nih.gov/33735618/,NextSeq 500,Negative Elongation Factor (NELF) regulates muscle progenitor expansion for efficient myofiber repair and stem cell pool repopulation [single-cell RNA],"Negative elongation factor (NELF) is a critical transcriptional regulator that stabilizes paused RNA polymerase to permit rapid gene expression changes in response to environmental cues. Although NELF is essential for embryonic development, its role in adult stem cells remains unclear. In this study, through a muscle-stem-cell-specific deletion, we showed that NELF is required for efficient muscle regeneration and stem cell pool replenishment. In mechanistic studies using PRO-seq, single-cell trajectory analyses and myofiber cultures revealed that NELF works at a specific stage of regeneration whereby it modulates p53 signaling to permit massive expansion of muscle progenitors. Strikingly, transplantation experiments indicated that these progenitors are also necessary for stem cell pool repopulation, implying that they are able to return to quiescence. Thus, we identified a critical role for NELF in the expansion of muscle progenitors in response to injury and revealed that progenitors returning to quiescence are major contributors to the stem cell pool repopulation. Overall design: RNA-seq performed on myogenic precursors which were isolated from regenerating skeletal muscle (mouse) at 5 days post-injury for wild type and NELF-B knockout populations."
Robinson 2021,Nelfb-KO_B,NA,muscle,NA,NA,NA,NA,NA,Reads are improperly paired; R1 contains multiple read lengths (25 and 26bp),FALSE,TRUE,Mus musculus,GSE150278,GSM4544639,3p_v2,fastq,SRR11768409;SRR11768410;SRR11768428;SRR11768427,NA,SRX8321673,SRP261108,SRS6640988,SAMN14888051,NA,NA,"Robinson et al, Developmental Cell, 2021",NA,https://pubmed.ncbi.nlm.nih.gov/33735618/,NextSeq 500,Negative Elongation Factor (NELF) regulates muscle progenitor expansion for efficient myofiber repair and stem cell pool repopulation [single-cell RNA],"Negative elongation factor (NELF) is a critical transcriptional regulator that stabilizes paused RNA polymerase to permit rapid gene expression changes in response to environmental cues. Although NELF is essential for embryonic development, its role in adult stem cells remains unclear. In this study, through a muscle-stem-cell-specific deletion, we showed that NELF is required for efficient muscle regeneration and stem cell pool replenishment. In mechanistic studies using PRO-seq, single-cell trajectory analyses and myofiber cultures revealed that NELF works at a specific stage of regeneration whereby it modulates p53 signaling to permit massive expansion of muscle progenitors. Strikingly, transplantation experiments indicated that these progenitors are also necessary for stem cell pool repopulation, implying that they are able to return to quiescence. Thus, we identified a critical role for NELF in the expansion of muscle progenitors in response to injury and revealed that progenitors returning to quiescence are major contributors to the stem cell pool repopulation. Overall design: RNA-seq performed on myogenic precursors which were isolated from regenerating skeletal muscle (mouse) at 5 days post-injury for wild type and NELF-B knockout populations."
Robinson 2021,Nelfb-WT_1,NA,muscle,NA,NA,NA,NA,NA,Reads are improperly paired; R1 contains multiple read lengths (25 and 26bp),FALSE,TRUE,Mus musculus,GSE150278,GSM4544640,3p_v2,fastq,SRR11768411;SRR11768412;SRR11768413;SRR11768414,NA,SRX8321674,SRP261108,SRS6640989,NA,NA,NA,"Robinson et al, Developmental Cell, 2021",NA,https://pubmed.ncbi.nlm.nih.gov/33735618/,NextSeq 500,Negative Elongation Factor (NELF) regulates muscle progenitor expansion for efficient myofiber repair and stem cell pool repopulation [single-cell RNA],"Negative elongation factor (NELF) is a critical transcriptional regulator that stabilizes paused RNA polymerase to permit rapid gene expression changes in response to environmental cues. Although NELF is essential for embryonic development, its role in adult stem cells remains unclear. In this study, through a muscle-stem-cell-specific deletion, we showed that NELF is required for efficient muscle regeneration and stem cell pool replenishment. In mechanistic studies using PRO-seq, single-cell trajectory analyses and myofiber cultures revealed that NELF works at a specific stage of regeneration whereby it modulates p53 signaling to permit massive expansion of muscle progenitors. Strikingly, transplantation experiments indicated that these progenitors are also necessary for stem cell pool repopulation, implying that they are able to return to quiescence. Thus, we identified a critical role for NELF in the expansion of muscle progenitors in response to injury and revealed that progenitors returning to quiescence are major contributors to the stem cell pool repopulation. Overall design: RNA-seq performed on myogenic precursors which were isolated from regenerating skeletal muscle (mouse) at 5 days post-injury for wild type and NELF-B knockout populations."
Robinson 2021,Nelfb-WT_A,NA,muscle,NA,NA,NA,NA,NA,Reads are improperly paired; R1 contains multiple read lengths (25 and 26bp),FALSE,TRUE,Mus musculus,GSE150278,GSM4544641,3p_v2,fastq,SRR11768415;SRR11768416;SRR11768417;SRR11768418,NA,SRX8321675,SRP261108,SRS6640990,NA,NA,NA,"Robinson et al, Developmental Cell, 2021",NA,https://pubmed.ncbi.nlm.nih.gov/33735618/,NextSeq 500,Negative Elongation Factor (NELF) regulates muscle progenitor expansion for efficient myofiber repair and stem cell pool repopulation [single-cell RNA],"Negative elongation factor (NELF) is a critical transcriptional regulator that stabilizes paused RNA polymerase to permit rapid gene expression changes in response to environmental cues. Although NELF is essential for embryonic development, its role in adult stem cells remains unclear. In this study, through a muscle-stem-cell-specific deletion, we showed that NELF is required for efficient muscle regeneration and stem cell pool replenishment. In mechanistic studies using PRO-seq, single-cell trajectory analyses and myofiber cultures revealed that NELF works at a specific stage of regeneration whereby it modulates p53 signaling to permit massive expansion of muscle progenitors. Strikingly, transplantation experiments indicated that these progenitors are also necessary for stem cell pool repopulation, implying that they are able to return to quiescence. Thus, we identified a critical role for NELF in the expansion of muscle progenitors in response to injury and revealed that progenitors returning to quiescence are major contributors to the stem cell pool repopulation. Overall design: RNA-seq performed on myogenic precursors which were isolated from regenerating skeletal muscle (mouse) at 5 days post-injury for wild type and NELF-B knockout populations."
Robinson 2021,Nelfb-WT_B,NA,muscle,NA,NA,NA,NA,NA,Reads are improperly paired; R1 contains multiple read lengths (25 and 26bp),FALSE,TRUE,Mus musculus,GSE150278,GSM4544642,3p_v2,fastq,SRR11768419;SRR11768420;SRR11768421;SRR11768422,NA,SRX8321676,SRP261108,SRS6640991,NA,NA,NA,"Robinson et al, Developmental Cell, 2021",NA,https://pubmed.ncbi.nlm.nih.gov/33735618/,NextSeq 500,Negative Elongation Factor (NELF) regulates muscle progenitor expansion for efficient myofiber repair and stem cell pool repopulation [single-cell RNA],"Negative elongation factor (NELF) is a critical transcriptional regulator that stabilizes paused RNA polymerase to permit rapid gene expression changes in response to environmental cues. Although NELF is essential for embryonic development, its role in adult stem cells remains unclear. In this study, through a muscle-stem-cell-specific deletion, we showed that NELF is required for efficient muscle regeneration and stem cell pool replenishment. In mechanistic studies using PRO-seq, single-cell trajectory analyses and myofiber cultures revealed that NELF works at a specific stage of regeneration whereby it modulates p53 signaling to permit massive expansion of muscle progenitors. Strikingly, transplantation experiments indicated that these progenitors are also necessary for stem cell pool repopulation, implying that they are able to return to quiescence. Thus, we identified a critical role for NELF in the expansion of muscle progenitors in response to injury and revealed that progenitors returning to quiescence are major contributors to the stem cell pool repopulation. Overall design: RNA-seq performed on myogenic precursors which were isolated from regenerating skeletal muscle (mouse) at 5 days post-injury for wild type and NELF-B knockout populations."
Ritchie 2020,MuSC 10 percent library,illumina & nanopore sequencing,muscle,NA,NA,NA,NA,NA,no long read data for now,FALSE,TRUE,Mus musculus,GSE154868,GSM4681738,3p_v2,fastq,SRR12282454;SRR12282455,NA,SRX8785879,SRP273166,SRS7054506,SAMN15594467,NA,NA,unpublished,NA,unpublished,Illumina HiSeq 2500,Long and short-read single cell RNA-seq profiling of mouse muscle stem cells,Single cell RNA-seq was used to identify the gene expression signatures and transcript isoforms that distinguish quiescent and activated muscle stem cells in mouse. Overall design: Quiescent skeletal muscle stem cells isolated from uninjured muscles and activated muscle stem cells isolated post injury were profiled using the Chromium platform (10x Genomics) with sequencing from both short-read (Illumina) and long-read (Nanopore) technologies.
Larouche 2021,Young Uninjured MuSCs [d0_Young_v2],3-4 months; C57BL6J,muscle,muscle stem cell,NA,NA,NA,NA,Not enough cells passing QC,FALSE,FALSE,Mus musculus,GSE165978,GSM5059693,3p_v2,bam,SRR13610667,NA,SRX10004699,SRP304270,SRS8173897,SAMN17761244,NA,NA,"Larouche et al, eLife, 2021",NA,https://pubmed.ncbi.nlm.nih.gov/34323217/,Illumina NovaSeq 6000,Muscle Stem Cell Response to Perturbations of the Neuromuscular Junction Are Attenuated With Aging,"During aging and neuromuscular diseases, there is a progressive loss of skeletal muscle volume and function, which is often associated with denervation and a loss of muscle stem cells (MuSCs). A relationship between MuSCs and innervation has not been established however. Herein, we administered neuromuscular trauma to a MuSC lineage tracing model and observed a subset of MuSCs specifically engraft in a position proximal to the neuromuscular junction (NMJ). In aging and in a model of neuromuscular degeneration (Sod1-/-), this localized engraftment behavior was reduced. Genetic rescue of motor neurons in Sod1-/- mice reestablished integrity of the NMJ and partially restored MuSC ability to engraft into NMJ proximal positions. Using single cell RNA-sequencing of MuSCs, we demonstrate that a subset of MuSCs are molecularly distinguishable from MuSCs responding to myofiber injury. These data reveal unique features of MuSCs that respond to synaptic perturbations caused by aging and other stressors. Overall design: C57BL/6J wild-type female mice were obtained from Charles River Breeding Laboratories, the National Institute on Aging, or from a breeding colony at the University of Michigan (UM). All mice were fed normal chow ad libitum and housed on a 12:12 hour light-dark cycle under UM veterinary staff supervision. All procedures were approved by the University Committee on the Use and Care of Animals at UM and were in accordance with the U.S. National Institute of Health (NIH). Young female mice (4-6 months) and aged female mice (20-24 months) were randomly assigned to one of five groups: uninjured, day 3, and day 7 injured (n=4 per group). To induce skeletal muscle injury, mice were first anesthetized with 2% isoflurane and administered a 1.2% barium chloride (BaCl2) solution injected intramuscularly into several points of the tibialis anterior and gastrocnemius muscles for a total of 80 L per hindlimb."
Dyer 2022,SJRHB030680_R1,A single-cell/nucleus atlas of pediatric rhabdomyosarcoma,muscle,tumor,NA,NA,NA,NA,Patient tumor,FALSE,TRUE,Homo sapiens,GSE174376,GSM5293229,NA,fastq,SRR14520828;SRR14520829;SRR14520830;SRR14520831;SRR14520832;SRR14520833;SRR14520834;SRR14520835,NA,SRX10866309,SRP319643,NA,SAMN19159611,NA,NA,NA,NA,NA,Illumina NovaSeq 6000,NA,NA
Dyer 2022,SJRHB000026_R3,A single-cell/nucleus atlas of pediatric rhabdomyosarcoma,muscle,tumor,NA,NA,NA,NA,some samples are human+mouse,FALSE,TRUE,Homo sapiens,GSE174376,GSM5390457,3p_v3,fastq,SRR14854527;SRR14854528,NA,SRX11173039,SRP319643,NA,SAMN19763857,NA,NA,"Dyer et al, Dev Cell, 2022",10.1016/j.devcel.2022.04.003,https://pubmed.ncbi.nlm.nih.gov/35483358/,Illumina NovaSeq 6000,NA,NA
Dyer 2022,SJRHB000026_R3,A single-cell/nucleus atlas of pediatric rhabdomyosarcoma,muscle,tumor,NA,NA,NA,NA,some samples are human+mouse,FALSE,TRUE,Homo sapiens,GSE174376,GSM5390458,3p_v3,fastq,SRR14854529;SRR14854530,NA,SRX11173040,SRP319643,NA,SAMN19763856,NA,NA,"Dyer et al, Dev Cell, 2022",10.1016/j.devcel.2022.04.003,https://pubmed.ncbi.nlm.nih.gov/35483358/,Illumina NovaSeq 6000,NA,NA
Dyer 2022,SJRHB010927_D1,A single-cell/nucleus atlas of pediatric rhabdomyosarcoma,muscle,tumor,NA,NA,NA,NA,some samples are human+mouse,FALSE,TRUE,Homo sapiens,GSE174376,GSM5390459,3p_v3,fastq,SRR14854531;SRR14854532,NA,SRX11173041,SRP319643,NA,SAMN19763855,NA,NA,"Dyer et al, Dev Cell, 2022",10.1016/j.devcel.2022.04.003,https://pubmed.ncbi.nlm.nih.gov/35483358/,Illumina NovaSeq 6000,NA,NA
Dyer 2022,SJRHB011_D,A single-cell/nucleus atlas of pediatric rhabdomyosarcoma,muscle,tumor,NA,NA,NA,NA,some samples are human+mouse,FALSE,TRUE,Homo sapiens,GSE174376,GSM5390461,3p_v3,fastq,SRR14854535;SRR14854536;SRR14854537;SRR14854538,NA,SRX11173044,SRP319643,NA,SAMN19763853,NA,NA,"Dyer et al, Dev Cell, 2022",10.1016/j.devcel.2022.04.003,https://pubmed.ncbi.nlm.nih.gov/35483358/,Illumina NovaSeq 6000,NA,NA
Dyer 2022,SJRHB012_R,A single-cell/nucleus atlas of pediatric rhabdomyosarcoma,muscle,tumor,NA,NA,NA,NA,some samples are human+mouse,FALSE,TRUE,Homo sapiens,GSE174376,GSM5390462,3p_v3,fastq,SRR14854539;SRR14854540;SRR14854541;SRR14854542,NA,SRX11173045,SRP319643,NA,SAMN19763852,NA,NA,"Dyer et al, Dev Cell, 2022",10.1016/j.devcel.2022.04.003,https://pubmed.ncbi.nlm.nih.gov/35483358/,Illumina NovaSeq 6000,NA,NA
Dyer 2022,SJRHB012405_D1,A single-cell/nucleus atlas of pediatric rhabdomyosarcoma,muscle,tumor,NA,NA,NA,NA,some samples are human+mouse,FALSE,TRUE,Homo sapiens,GSE174376,GSM5390464,3p_v3,fastq,SRR14854554;SRR14854555,NA,SRX11173047,SRP319643,NA,SAMN19763875,NA,NA,"Dyer et al, Dev Cell, 2022",10.1016/j.devcel.2022.04.003,https://pubmed.ncbi.nlm.nih.gov/35483358/,Illumina NovaSeq 6000,NA,NA
Dyer 2022,SJRHB013758_D1,A single-cell/nucleus atlas of pediatric rhabdomyosarcoma,muscle,tumor,NA,NA,NA,NA,some samples are human+mouse,FALSE,TRUE,Homo sapiens,GSE174376,GSM5390465,3p_v3,fastq,SRR14854556;SRR14854557,NA,SRX11173048,SRP319643,NA,SAMN19763867,NA,NA,"Dyer et al, Dev Cell, 2022",10.1016/j.devcel.2022.04.003,https://pubmed.ncbi.nlm.nih.gov/35483358/,Illumina NovaSeq 6000,NA,NA
Dyer 2022,SJRHB013758_D2,A single-cell/nucleus atlas of pediatric rhabdomyosarcoma,muscle,tumor,NA,NA,NA,NA,some samples are human+mouse,FALSE,TRUE,Homo sapiens,GSE174376,GSM5390466,3p_v3,fastq,SRR14854558;SRR14854559,NA,SRX11173049,SRP319643,NA,SAMN19763874,NA,NA,"Dyer et al, Dev Cell, 2022",10.1016/j.devcel.2022.04.003,https://pubmed.ncbi.nlm.nih.gov/35483358/,Illumina NovaSeq 6000,NA,NA
Dyer 2022,SJRHB049189_D1,A single-cell/nucleus atlas of pediatric rhabdomyosarcoma,muscle,tumor,NA,NA,NA,NA,some samples are human+mouse,FALSE,TRUE,Homo sapiens,GSE174376,GSM5390467,3p_v3,fastq,SRR14854560;SRR14854561,NA,SRX11173050,SRP319643,NA,SAMN19763873,NA,NA,"Dyer et al, Dev Cell, 2022",10.1016/j.devcel.2022.04.003,https://pubmed.ncbi.nlm.nih.gov/35483358/,Illumina NovaSeq 6000,NA,NA
Dyer 2022,SJRHB030680_R1_sn,A single-cell/nucleus atlas of pediatric rhabdomyosarcoma,muscle,tumor,NA,NA,NA,NA,some samples are human+mouse,FALSE,TRUE,Homo sapiens,GSE174376,GSM5390468,3p_v2,fastq,SRR14854562;SRR14854563,NA,SRX11173051,SRP319643,NA,SAMN19763872,NA,NA,"Dyer et al, Dev Cell, 2022",10.1016/j.devcel.2022.04.003,https://pubmed.ncbi.nlm.nih.gov/35483358/,Illumina NovaSeq 6000,NA,NA
Dyer 2022,SJRHB010468_D1,A single-cell/nucleus atlas of pediatric rhabdomyosarcoma,muscle,tumor,NA,NA,NA,NA,some samples are human+mouse,FALSE,TRUE,Homo sapiens,GSE174376,GSM5390469,3p_v2,fastq,SRR14854564;SRR14854565;SRR14854566;SRR14854567,NA,SRX11173052,SRP319643,NA,SAMN19763871,NA,NA,"Dyer et al, Dev Cell, 2022",10.1016/j.devcel.2022.04.003,https://pubmed.ncbi.nlm.nih.gov/35483358/,Illumina NovaSeq 6000,NA,NA
Dyer 2022,SJRHB013757_D2,A single-cell/nucleus atlas of pediatric rhabdomyosarcoma,muscle,tumor,NA,NA,NA,NA,some samples are human+mouse,FALSE,TRUE,Homo sapiens,GSE174376,GSM5390470,3p_v3,fastq,SRR14854568;SRR14854569,NA,SRX11173053,SRP319643,NA,SAMN19763870,NA,NA,"Dyer et al, Dev Cell, 2022",10.1016/j.devcel.2022.04.003,https://pubmed.ncbi.nlm.nih.gov/35483358/,Illumina NovaSeq 6000,NA,NA
Dyer 2022,SJRHB013759_A1,A single-cell/nucleus atlas of pediatric rhabdomyosarcoma,muscle,tumor,NA,NA,NA,NA,some samples are human+mouse,FALSE,TRUE,Homo sapiens,GSE174376,GSM5390471,3p_v3,fastq,SRR14854570;SRR14854571,NA,SRX11173054,SRP319643,NA,SAMN19763869,NA,NA,"Dyer et al, Dev Cell, 2022",10.1016/j.devcel.2022.04.003,https://pubmed.ncbi.nlm.nih.gov/35483358/,Illumina NovaSeq 6000,NA,NA
Dyer 2022,SJRHB013759_A2,A single-cell/nucleus atlas of pediatric rhabdomyosarcoma,muscle,tumor,NA,NA,NA,NA,some samples are human+mouse,FALSE,TRUE,Homo sapiens,GSE174376,GSM5390472,3p_v3,fastq,SRR14854572;SRR14854573,NA,SRX11173055,SRP319643,NA,SAMN19763868,NA,NA,"Dyer et al, Dev Cell, 2022",10.1016/j.devcel.2022.04.003,https://pubmed.ncbi.nlm.nih.gov/35483358/,Illumina NovaSeq 6000,NA,NA
Dyer 2022,SJRHB046156_A1,A single-cell/nucleus atlas of pediatric rhabdomyosarcoma,muscle,tumor,NA,NA,NA,NA,some samples are human+mouse,FALSE,TRUE,Homo sapiens,GSE174376,GSM5390473,3p_v3,fastq,SRR14854574;SRR14854575,NA,SRX11173056,SRP319643,NA,SAMN19763866,NA,NA,"Dyer et al, Dev Cell, 2022",10.1016/j.devcel.2022.04.003,https://pubmed.ncbi.nlm.nih.gov/35483358/,Illumina NovaSeq 6000,NA,NA
Cherry 2021,CD45e_old_1wk_ECM,NA,muscle,NA,cell,NA,NA,NA,download issue,FALSE,TRUE,Mus musculus,GSE175889,GSM5350798,3p_v1,bam,SRR14699878,NA,SRX11037932,SRP322118,SRS9107346,SAMN19487622,NA,NA,"Cherry et al, Nature Biomedical Engineering, 2021",10.1038/s41551-021-00770-5,https://pubmed.ncbi.nlm.nih.gov/34341534/,Illumina NovaSeq 6000,A single-cell atlas of the microenvironment of implanted biomaterials and computational analysis of the transcriptional signalling networks [single-cell RNA-seq],"The understanding of the foreign-body responses to implanted biomaterials would benefit from the reconstruction of intracellular and intercellular signalling networks in the microenvironment surrounding the implant. Here, by leveraging single-cell RNA-sequencing data from 42,156 cells harvested from the site of implantation of either polycaprolactone or an extracellular-matrix-derived scaffold in a mouse model of volumetric muscle loss, we report a computational analysis of intercellular-signalling networks reconstructed from data of transcription-factor activation. We found that intercellular signalling networks can be clustered into modules associated with specific cell subsets, and that biomaterial-specific responses can be characterized by interactions between signalling modules for immune, fibroblast and tissue-specific cells. In a Il17ra/ knockout mouse model, we validated that predicted IL-17-linked transcriptional targets led to concomitant changes in gene expression. Moreover, we identified cell subsets that had not been implicated in the responses to implanted biomaterials. Single-cell atlases of the cellular responses to implanted biomaterials will facilitate the design of implantable biomaterials and the understanding of the ensuing cellular responses. Overall design: To generate the scRNAseq data sets we created single cell suspensions from the muscle tissue with and without biomaterials for application to 10X and Drop-seq. Single cell suspensions from whole tissue preparations were enriched for CD45+ cells to enable capture of less frequent cell populations and processed with Drop-seq. Fluorescence activated cell sorting (FACS) was used to apply mesenchymal/fibroblasts (CD45-CD19-CD31-CD29+) to Drop-seq. Finally, a previously published data set of sorted macrophages (CD45+F4/80hi+Ly6c+CD64+) was included. Most samples collected were from young mice (6 week old at time of surgery) during the acute phase of injury one week after surgery. A detailed description of age, time of harvest, treatment, and sorting methodology for each of the samples in the atlas is provided in Supplementary Table 2. The resulting dataset includes 42,156 cells with an average of 198,000 reads and 1,167 genes per cell after filtering low-quality cells and genes across multiple time points and ages."
Cherry 2021,CD45e_old_1wk_PCL,NA,muscle,NA,cell,NA,NA,NA,download issue,FALSE,TRUE,Mus musculus,GSE175889,GSM5350799,3p_v1,bam,SRR14699879,NA,SRX11037935,SRP322118,SRS9107349,SAMN19487613,NA,NA,"Cherry et al, Nature Biomedical Engineering, 2021",10.1038/s41551-021-00770-5,https://pubmed.ncbi.nlm.nih.gov/34341534/,Illumina NovaSeq 6000,A single-cell atlas of the microenvironment of implanted biomaterials and computational analysis of the transcriptional signalling networks [single-cell RNA-seq],"The understanding of the foreign-body responses to implanted biomaterials would benefit from the reconstruction of intracellular and intercellular signalling networks in the microenvironment surrounding the implant. Here, by leveraging single-cell RNA-sequencing data from 42,156 cells harvested from the site of implantation of either polycaprolactone or an extracellular-matrix-derived scaffold in a mouse model of volumetric muscle loss, we report a computational analysis of intercellular-signalling networks reconstructed from data of transcription-factor activation. We found that intercellular signalling networks can be clustered into modules associated with specific cell subsets, and that biomaterial-specific responses can be characterized by interactions between signalling modules for immune, fibroblast and tissue-specific cells. In a Il17ra/ knockout mouse model, we validated that predicted IL-17-linked transcriptional targets led to concomitant changes in gene expression. Moreover, we identified cell subsets that had not been implicated in the responses to implanted biomaterials. Single-cell atlases of the cellular responses to implanted biomaterials will facilitate the design of implantable biomaterials and the understanding of the ensuing cellular responses. Overall design: To generate the scRNAseq data sets we created single cell suspensions from the muscle tissue with and without biomaterials for application to 10X and Drop-seq. Single cell suspensions from whole tissue preparations were enriched for CD45+ cells to enable capture of less frequent cell populations and processed with Drop-seq. Fluorescence activated cell sorting (FACS) was used to apply mesenchymal/fibroblasts (CD45-CD19-CD31-CD29+) to Drop-seq. Finally, a previously published data set of sorted macrophages (CD45+F4/80hi+Ly6c+CD64+) was included. Most samples collected were from young mice (6 week old at time of surgery) during the acute phase of injury one week after surgery. A detailed description of age, time of harvest, treatment, and sorting methodology for each of the samples in the atlas is provided in Supplementary Table 2. The resulting dataset includes 42,156 cells with an average of 198,000 reads and 1,167 genes per cell after filtering low-quality cells and genes across multiple time points and ages."
Cherry 2021,CD45e_old_1wk_Saline,NA,muscle,NA,cell,NA,NA,NA,download issue,FALSE,TRUE,Mus musculus,GSE175889,GSM5350800,3p_v1,bam,SRR14699880,NA,SRX11037936,SRP322118,SRS9107350,SAMN19487612,NA,NA,"Cherry et al, Nature Biomedical Engineering, 2021",10.1038/s41551-021-00770-5,https://pubmed.ncbi.nlm.nih.gov/34341534/,Illumina NovaSeq 6000,A single-cell atlas of the microenvironment of implanted biomaterials and computational analysis of the transcriptional signalling networks [single-cell RNA-seq],"The understanding of the foreign-body responses to implanted biomaterials would benefit from the reconstruction of intracellular and intercellular signalling networks in the microenvironment surrounding the implant. Here, by leveraging single-cell RNA-sequencing data from 42,156 cells harvested from the site of implantation of either polycaprolactone or an extracellular-matrix-derived scaffold in a mouse model of volumetric muscle loss, we report a computational analysis of intercellular-signalling networks reconstructed from data of transcription-factor activation. We found that intercellular signalling networks can be clustered into modules associated with specific cell subsets, and that biomaterial-specific responses can be characterized by interactions between signalling modules for immune, fibroblast and tissue-specific cells. In a Il17ra/ knockout mouse model, we validated that predicted IL-17-linked transcriptional targets led to concomitant changes in gene expression. Moreover, we identified cell subsets that had not been implicated in the responses to implanted biomaterials. Single-cell atlases of the cellular responses to implanted biomaterials will facilitate the design of implantable biomaterials and the understanding of the ensuing cellular responses. Overall design: To generate the scRNAseq data sets we created single cell suspensions from the muscle tissue with and without biomaterials for application to 10X and Drop-seq. Single cell suspensions from whole tissue preparations were enriched for CD45+ cells to enable capture of less frequent cell populations and processed with Drop-seq. Fluorescence activated cell sorting (FACS) was used to apply mesenchymal/fibroblasts (CD45-CD19-CD31-CD29+) to Drop-seq. Finally, a previously published data set of sorted macrophages (CD45+F4/80hi+Ly6c+CD64+) was included. Most samples collected were from young mice (6 week old at time of surgery) during the acute phase of injury one week after surgery. A detailed description of age, time of harvest, treatment, and sorting methodology for each of the samples in the atlas is provided in Supplementary Table 2. The resulting dataset includes 42,156 cells with an average of 198,000 reads and 1,167 genes per cell after filtering low-quality cells and genes across multiple time points and ages."
Cherry 2021,CD45e_old_1wk_Naive,NA,muscle,NA,cell,NA,NA,NA,download issue,FALSE,TRUE,Mus musculus,GSE175889,GSM5350801,3p_v1,bam,SRR14699881,NA,SRX11037937,SRP322118,SRS9107351,SAMN19487621,NA,NA,"Cherry et al, Nature Biomedical Engineering, 2021",10.1038/s41551-021-00770-5,https://pubmed.ncbi.nlm.nih.gov/34341534/,Illumina NovaSeq 6000,A single-cell atlas of the microenvironment of implanted biomaterials and computational analysis of the transcriptional signalling networks [single-cell RNA-seq],"The understanding of the foreign-body responses to implanted biomaterials would benefit from the reconstruction of intracellular and intercellular signalling networks in the microenvironment surrounding the implant. Here, by leveraging single-cell RNA-sequencing data from 42,156 cells harvested from the site of implantation of either polycaprolactone or an extracellular-matrix-derived scaffold in a mouse model of volumetric muscle loss, we report a computational analysis of intercellular-signalling networks reconstructed from data of transcription-factor activation. We found that intercellular signalling networks can be clustered into modules associated with specific cell subsets, and that biomaterial-specific responses can be characterized by interactions between signalling modules for immune, fibroblast and tissue-specific cells. In a Il17ra/ knockout mouse model, we validated that predicted IL-17-linked transcriptional targets led to concomitant changes in gene expression. Moreover, we identified cell subsets that had not been implicated in the responses to implanted biomaterials. Single-cell atlases of the cellular responses to implanted biomaterials will facilitate the design of implantable biomaterials and the understanding of the ensuing cellular responses. Overall design: To generate the scRNAseq data sets we created single cell suspensions from the muscle tissue with and without biomaterials for application to 10X and Drop-seq. Single cell suspensions from whole tissue preparations were enriched for CD45+ cells to enable capture of less frequent cell populations and processed with Drop-seq. Fluorescence activated cell sorting (FACS) was used to apply mesenchymal/fibroblasts (CD45-CD19-CD31-CD29+) to Drop-seq. Finally, a previously published data set of sorted macrophages (CD45+F4/80hi+Ly6c+CD64+) was included. Most samples collected were from young mice (6 week old at time of surgery) during the acute phase of injury one week after surgery. A detailed description of age, time of harvest, treatment, and sorting methodology for each of the samples in the atlas is provided in Supplementary Table 2. The resulting dataset includes 42,156 cells with an average of 198,000 reads and 1,167 genes per cell after filtering low-quality cells and genes across multiple time points and ages."
Cherry 2021,CD45e_young_1wk_ECM,NA,muscle,NA,cell,NA,NA,NA,download issue,FALSE,TRUE,Mus musculus,GSE175889,GSM5350802,3p_v1,bam,SRR14699882,NA,SRX11037938,SRP322118,SRS9107352,SAMN19487620,NA,NA,"Cherry et al, Nature Biomedical Engineering, 2021",10.1038/s41551-021-00770-5,https://pubmed.ncbi.nlm.nih.gov/34341534/,Illumina NovaSeq 6000,A single-cell atlas of the microenvironment of implanted biomaterials and computational analysis of the transcriptional signalling networks [single-cell RNA-seq],"The understanding of the foreign-body responses to implanted biomaterials would benefit from the reconstruction of intracellular and intercellular signalling networks in the microenvironment surrounding the implant. Here, by leveraging single-cell RNA-sequencing data from 42,156 cells harvested from the site of implantation of either polycaprolactone or an extracellular-matrix-derived scaffold in a mouse model of volumetric muscle loss, we report a computational analysis of intercellular-signalling networks reconstructed from data of transcription-factor activation. We found that intercellular signalling networks can be clustered into modules associated with specific cell subsets, and that biomaterial-specific responses can be characterized by interactions between signalling modules for immune, fibroblast and tissue-specific cells. In a Il17ra/ knockout mouse model, we validated that predicted IL-17-linked transcriptional targets led to concomitant changes in gene expression. Moreover, we identified cell subsets that had not been implicated in the responses to implanted biomaterials. Single-cell atlases of the cellular responses to implanted biomaterials will facilitate the design of implantable biomaterials and the understanding of the ensuing cellular responses. Overall design: To generate the scRNAseq data sets we created single cell suspensions from the muscle tissue with and without biomaterials for application to 10X and Drop-seq. Single cell suspensions from whole tissue preparations were enriched for CD45+ cells to enable capture of less frequent cell populations and processed with Drop-seq. Fluorescence activated cell sorting (FACS) was used to apply mesenchymal/fibroblasts (CD45-CD19-CD31-CD29+) to Drop-seq. Finally, a previously published data set of sorted macrophages (CD45+F4/80hi+Ly6c+CD64+) was included. Most samples collected were from young mice (6 week old at time of surgery) during the acute phase of injury one week after surgery. A detailed description of age, time of harvest, treatment, and sorting methodology for each of the samples in the atlas is provided in Supplementary Table 2. The resulting dataset includes 42,156 cells with an average of 198,000 reads and 1,167 genes per cell after filtering low-quality cells and genes across multiple time points and ages."
Cherry 2021,CD45e_young_1wk_PCL,NA,muscle,NA,cell,NA,NA,NA,download issue,FALSE,TRUE,Mus musculus,GSE175889,GSM5350803,3p_v1,bam,SRR14699883,NA,SRX11037939,SRP322118,SRS9107353,SAMN19487619,NA,NA,"Cherry et al, Nature Biomedical Engineering, 2021",10.1038/s41551-021-00770-5,https://pubmed.ncbi.nlm.nih.gov/34341534/,Illumina NovaSeq 6000,A single-cell atlas of the microenvironment of implanted biomaterials and computational analysis of the transcriptional signalling networks [single-cell RNA-seq],"The understanding of the foreign-body responses to implanted biomaterials would benefit from the reconstruction of intracellular and intercellular signalling networks in the microenvironment surrounding the implant. Here, by leveraging single-cell RNA-sequencing data from 42,156 cells harvested from the site of implantation of either polycaprolactone or an extracellular-matrix-derived scaffold in a mouse model of volumetric muscle loss, we report a computational analysis of intercellular-signalling networks reconstructed from data of transcription-factor activation. We found that intercellular signalling networks can be clustered into modules associated with specific cell subsets, and that biomaterial-specific responses can be characterized by interactions between signalling modules for immune, fibroblast and tissue-specific cells. In a Il17ra/ knockout mouse model, we validated that predicted IL-17-linked transcriptional targets led to concomitant changes in gene expression. Moreover, we identified cell subsets that had not been implicated in the responses to implanted biomaterials. Single-cell atlases of the cellular responses to implanted biomaterials will facilitate the design of implantable biomaterials and the understanding of the ensuing cellular responses. Overall design: To generate the scRNAseq data sets we created single cell suspensions from the muscle tissue with and without biomaterials for application to 10X and Drop-seq. Single cell suspensions from whole tissue preparations were enriched for CD45+ cells to enable capture of less frequent cell populations and processed with Drop-seq. Fluorescence activated cell sorting (FACS) was used to apply mesenchymal/fibroblasts (CD45-CD19-CD31-CD29+) to Drop-seq. Finally, a previously published data set of sorted macrophages (CD45+F4/80hi+Ly6c+CD64+) was included. Most samples collected were from young mice (6 week old at time of surgery) during the acute phase of injury one week after surgery. A detailed description of age, time of harvest, treatment, and sorting methodology for each of the samples in the atlas is provided in Supplementary Table 2. The resulting dataset includes 42,156 cells with an average of 198,000 reads and 1,167 genes per cell after filtering low-quality cells and genes across multiple time points and ages."
Cherry 2021,CD45e_young_1wk_Saline,NA,muscle,NA,cell,NA,NA,NA,download issue,FALSE,TRUE,Mus musculus,GSE175889,GSM5350804,3p_v1,bam,SRR14699884,NA,SRX11037940,SRP322118,SRS9107354,SAMN19487618,NA,NA,"Cherry et al, Nature Biomedical Engineering, 2021",10.1038/s41551-021-00770-5,https://pubmed.ncbi.nlm.nih.gov/34341534/,Illumina NovaSeq 6000,A single-cell atlas of the microenvironment of implanted biomaterials and computational analysis of the transcriptional signalling networks [single-cell RNA-seq],"The understanding of the foreign-body responses to implanted biomaterials would benefit from the reconstruction of intracellular and intercellular signalling networks in the microenvironment surrounding the implant. Here, by leveraging single-cell RNA-sequencing data from 42,156 cells harvested from the site of implantation of either polycaprolactone or an extracellular-matrix-derived scaffold in a mouse model of volumetric muscle loss, we report a computational analysis of intercellular-signalling networks reconstructed from data of transcription-factor activation. We found that intercellular signalling networks can be clustered into modules associated with specific cell subsets, and that biomaterial-specific responses can be characterized by interactions between signalling modules for immune, fibroblast and tissue-specific cells. In a Il17ra/ knockout mouse model, we validated that predicted IL-17-linked transcriptional targets led to concomitant changes in gene expression. Moreover, we identified cell subsets that had not been implicated in the responses to implanted biomaterials. Single-cell atlases of the cellular responses to implanted biomaterials will facilitate the design of implantable biomaterials and the understanding of the ensuing cellular responses. Overall design: To generate the scRNAseq data sets we created single cell suspensions from the muscle tissue with and without biomaterials for application to 10X and Drop-seq. Single cell suspensions from whole tissue preparations were enriched for CD45+ cells to enable capture of less frequent cell populations and processed with Drop-seq. Fluorescence activated cell sorting (FACS) was used to apply mesenchymal/fibroblasts (CD45-CD19-CD31-CD29+) to Drop-seq. Finally, a previously published data set of sorted macrophages (CD45+F4/80hi+Ly6c+CD64+) was included. Most samples collected were from young mice (6 week old at time of surgery) during the acute phase of injury one week after surgery. A detailed description of age, time of harvest, treatment, and sorting methodology for each of the samples in the atlas is provided in Supplementary Table 2. The resulting dataset includes 42,156 cells with an average of 198,000 reads and 1,167 genes per cell after filtering low-quality cells and genes across multiple time points and ages."
Cherry 2021,CD45e_young_1wk_Naive,NA,muscle,NA,cell,NA,NA,NA,download issue,FALSE,TRUE,Mus musculus,GSE175889,GSM5350805,3p_v1,bam,SRR14699885,NA,SRX11037941,SRP322118,SRS9107355,SAMN19487617,NA,NA,"Cherry et al, Nature Biomedical Engineering, 2021",10.1038/s41551-021-00770-5,https://pubmed.ncbi.nlm.nih.gov/34341534/,Illumina NovaSeq 6000,A single-cell atlas of the microenvironment of implanted biomaterials and computational analysis of the transcriptional signalling networks [single-cell RNA-seq],"The understanding of the foreign-body responses to implanted biomaterials would benefit from the reconstruction of intracellular and intercellular signalling networks in the microenvironment surrounding the implant. Here, by leveraging single-cell RNA-sequencing data from 42,156 cells harvested from the site of implantation of either polycaprolactone or an extracellular-matrix-derived scaffold in a mouse model of volumetric muscle loss, we report a computational analysis of intercellular-signalling networks reconstructed from data of transcription-factor activation. We found that intercellular signalling networks can be clustered into modules associated with specific cell subsets, and that biomaterial-specific responses can be characterized by interactions between signalling modules for immune, fibroblast and tissue-specific cells. In a Il17ra/ knockout mouse model, we validated that predicted IL-17-linked transcriptional targets led to concomitant changes in gene expression. Moreover, we identified cell subsets that had not been implicated in the responses to implanted biomaterials. Single-cell atlases of the cellular responses to implanted biomaterials will facilitate the design of implantable biomaterials and the understanding of the ensuing cellular responses. Overall design: To generate the scRNAseq data sets we created single cell suspensions from the muscle tissue with and without biomaterials for application to 10X and Drop-seq. Single cell suspensions from whole tissue preparations were enriched for CD45+ cells to enable capture of less frequent cell populations and processed with Drop-seq. Fluorescence activated cell sorting (FACS) was used to apply mesenchymal/fibroblasts (CD45-CD19-CD31-CD29+) to Drop-seq. Finally, a previously published data set of sorted macrophages (CD45+F4/80hi+Ly6c+CD64+) was included. Most samples collected were from young mice (6 week old at time of surgery) during the acute phase of injury one week after surgery. A detailed description of age, time of harvest, treatment, and sorting methodology for each of the samples in the atlas is provided in Supplementary Table 2. The resulting dataset includes 42,156 cells with an average of 198,000 reads and 1,167 genes per cell after filtering low-quality cells and genes across multiple time points and ages."
Cherry 2021,Fibroblast_young_1wk_ECM,NA,muscle,NA,cell,NA,NA,NA,download issue,FALSE,TRUE,Mus musculus,GSE175889,GSM5350806,3p_v1,bam,SRR14699886,NA,SRX11037942,SRP322118,SRS9107356,SAMN19487616,NA,NA,"Cherry et al, Nature Biomedical Engineering, 2021",10.1038/s41551-021-00770-5,https://pubmed.ncbi.nlm.nih.gov/34341534/,Illumina NovaSeq 6000,A single-cell atlas of the microenvironment of implanted biomaterials and computational analysis of the transcriptional signalling networks [single-cell RNA-seq],"The understanding of the foreign-body responses to implanted biomaterials would benefit from the reconstruction of intracellular and intercellular signalling networks in the microenvironment surrounding the implant. Here, by leveraging single-cell RNA-sequencing data from 42,156 cells harvested from the site of implantation of either polycaprolactone or an extracellular-matrix-derived scaffold in a mouse model of volumetric muscle loss, we report a computational analysis of intercellular-signalling networks reconstructed from data of transcription-factor activation. We found that intercellular signalling networks can be clustered into modules associated with specific cell subsets, and that biomaterial-specific responses can be characterized by interactions between signalling modules for immune, fibroblast and tissue-specific cells. In a Il17ra/ knockout mouse model, we validated that predicted IL-17-linked transcriptional targets led to concomitant changes in gene expression. Moreover, we identified cell subsets that had not been implicated in the responses to implanted biomaterials. Single-cell atlases of the cellular responses to implanted biomaterials will facilitate the design of implantable biomaterials and the understanding of the ensuing cellular responses. Overall design: To generate the scRNAseq data sets we created single cell suspensions from the muscle tissue with and without biomaterials for application to 10X and Drop-seq. Single cell suspensions from whole tissue preparations were enriched for CD45+ cells to enable capture of less frequent cell populations and processed with Drop-seq. Fluorescence activated cell sorting (FACS) was used to apply mesenchymal/fibroblasts (CD45-CD19-CD31-CD29+) to Drop-seq. Finally, a previously published data set of sorted macrophages (CD45+F4/80hi+Ly6c+CD64+) was included. Most samples collected were from young mice (6 week old at time of surgery) during the acute phase of injury one week after surgery. A detailed description of age, time of harvest, treatment, and sorting methodology for each of the samples in the atlas is provided in Supplementary Table 2. The resulting dataset includes 42,156 cells with an average of 198,000 reads and 1,167 genes per cell after filtering low-quality cells and genes across multiple time points and ages."
Cherry 2021,Fibroblast_young_1wk_PCL,NA,muscle,NA,cell,NA,NA,NA,download issue,FALSE,TRUE,Mus musculus,GSE175889,GSM5350807,3p_v1,bam,SRR14699887,NA,SRX11037924,SRP322118,SRS9107338,SAMN19487615,NA,NA,"Cherry et al, Nature Biomedical Engineering, 2021",10.1038/s41551-021-00770-5,https://pubmed.ncbi.nlm.nih.gov/34341534/,Illumina NovaSeq 6000,A single-cell atlas of the microenvironment of implanted biomaterials and computational analysis of the transcriptional signalling networks [single-cell RNA-seq],"The understanding of the foreign-body responses to implanted biomaterials would benefit from the reconstruction of intracellular and intercellular signalling networks in the microenvironment surrounding the implant. Here, by leveraging single-cell RNA-sequencing data from 42,156 cells harvested from the site of implantation of either polycaprolactone or an extracellular-matrix-derived scaffold in a mouse model of volumetric muscle loss, we report a computational analysis of intercellular-signalling networks reconstructed from data of transcription-factor activation. We found that intercellular signalling networks can be clustered into modules associated with specific cell subsets, and that biomaterial-specific responses can be characterized by interactions between signalling modules for immune, fibroblast and tissue-specific cells. In a Il17ra/ knockout mouse model, we validated that predicted IL-17-linked transcriptional targets led to concomitant changes in gene expression. Moreover, we identified cell subsets that had not been implicated in the responses to implanted biomaterials. Single-cell atlases of the cellular responses to implanted biomaterials will facilitate the design of implantable biomaterials and the understanding of the ensuing cellular responses. Overall design: To generate the scRNAseq data sets we created single cell suspensions from the muscle tissue with and without biomaterials for application to 10X and Drop-seq. Single cell suspensions from whole tissue preparations were enriched for CD45+ cells to enable capture of less frequent cell populations and processed with Drop-seq. Fluorescence activated cell sorting (FACS) was used to apply mesenchymal/fibroblasts (CD45-CD19-CD31-CD29+) to Drop-seq. Finally, a previously published data set of sorted macrophages (CD45+F4/80hi+Ly6c+CD64+) was included. Most samples collected were from young mice (6 week old at time of surgery) during the acute phase of injury one week after surgery. A detailed description of age, time of harvest, treatment, and sorting methodology for each of the samples in the atlas is provided in Supplementary Table 2. The resulting dataset includes 42,156 cells with an average of 198,000 reads and 1,167 genes per cell after filtering low-quality cells and genes across multiple time points and ages."
Cherry 2021,Fibroblast_young_1wk_Saline,NA,muscle,NA,cell,NA,NA,NA,download issue,FALSE,TRUE,Mus musculus,GSE175889,GSM5350808,3p_v1,bam,SRR14699888,NA,SRX11037925,SRP322118,SRS9107339,SAMN19487614,NA,NA,"Cherry et al, Nature Biomedical Engineering, 2021",10.1038/s41551-021-00770-5,https://pubmed.ncbi.nlm.nih.gov/34341534/,Illumina NovaSeq 6000,A single-cell atlas of the microenvironment of implanted biomaterials and computational analysis of the transcriptional signalling networks [single-cell RNA-seq],"The understanding of the foreign-body responses to implanted biomaterials would benefit from the reconstruction of intracellular and intercellular signalling networks in the microenvironment surrounding the implant. Here, by leveraging single-cell RNA-sequencing data from 42,156 cells harvested from the site of implantation of either polycaprolactone or an extracellular-matrix-derived scaffold in a mouse model of volumetric muscle loss, we report a computational analysis of intercellular-signalling networks reconstructed from data of transcription-factor activation. We found that intercellular signalling networks can be clustered into modules associated with specific cell subsets, and that biomaterial-specific responses can be characterized by interactions between signalling modules for immune, fibroblast and tissue-specific cells. In a Il17ra/ knockout mouse model, we validated that predicted IL-17-linked transcriptional targets led to concomitant changes in gene expression. Moreover, we identified cell subsets that had not been implicated in the responses to implanted biomaterials. Single-cell atlases of the cellular responses to implanted biomaterials will facilitate the design of implantable biomaterials and the understanding of the ensuing cellular responses. Overall design: To generate the scRNAseq data sets we created single cell suspensions from the muscle tissue with and without biomaterials for application to 10X and Drop-seq. Single cell suspensions from whole tissue preparations were enriched for CD45+ cells to enable capture of less frequent cell populations and processed with Drop-seq. Fluorescence activated cell sorting (FACS) was used to apply mesenchymal/fibroblasts (CD45-CD19-CD31-CD29+) to Drop-seq. Finally, a previously published data set of sorted macrophages (CD45+F4/80hi+Ly6c+CD64+) was included. Most samples collected were from young mice (6 week old at time of surgery) during the acute phase of injury one week after surgery. A detailed description of age, time of harvest, treatment, and sorting methodology for each of the samples in the atlas is provided in Supplementary Table 2. The resulting dataset includes 42,156 cells with an average of 198,000 reads and 1,167 genes per cell after filtering low-quality cells and genes across multiple time points and ages."
Cherry 2021,Fibroblast_young_1wk_Naive,NA,muscle,NA,cell,NA,NA,NA,download issue,FALSE,TRUE,Mus musculus,GSE175889,GSM5350809,3p_v1,bam,SRR14699889,NA,SRX11037926,SRP322118,SRS9107340,SAMN19487611,NA,NA,"Cherry et al, Nature Biomedical Engineering, 2021",10.1038/s41551-021-00770-5,https://pubmed.ncbi.nlm.nih.gov/34341534/,Illumina NovaSeq 6000,A single-cell atlas of the microenvironment of implanted biomaterials and computational analysis of the transcriptional signalling networks [single-cell RNA-seq],"The understanding of the foreign-body responses to implanted biomaterials would benefit from the reconstruction of intracellular and intercellular signalling networks in the microenvironment surrounding the implant. Here, by leveraging single-cell RNA-sequencing data from 42,156 cells harvested from the site of implantation of either polycaprolactone or an extracellular-matrix-derived scaffold in a mouse model of volumetric muscle loss, we report a computational analysis of intercellular-signalling networks reconstructed from data of transcription-factor activation. We found that intercellular signalling networks can be clustered into modules associated with specific cell subsets, and that biomaterial-specific responses can be characterized by interactions between signalling modules for immune, fibroblast and tissue-specific cells. In a Il17ra/ knockout mouse model, we validated that predicted IL-17-linked transcriptional targets led to concomitant changes in gene expression. Moreover, we identified cell subsets that had not been implicated in the responses to implanted biomaterials. Single-cell atlases of the cellular responses to implanted biomaterials will facilitate the design of implantable biomaterials and the understanding of the ensuing cellular responses. Overall design: To generate the scRNAseq data sets we created single cell suspensions from the muscle tissue with and without biomaterials for application to 10X and Drop-seq. Single cell suspensions from whole tissue preparations were enriched for CD45+ cells to enable capture of less frequent cell populations and processed with Drop-seq. Fluorescence activated cell sorting (FACS) was used to apply mesenchymal/fibroblasts (CD45-CD19-CD31-CD29+) to Drop-seq. Finally, a previously published data set of sorted macrophages (CD45+F4/80hi+Ly6c+CD64+) was included. Most samples collected were from young mice (6 week old at time of surgery) during the acute phase of injury one week after surgery. A detailed description of age, time of harvest, treatment, and sorting methodology for each of the samples in the atlas is provided in Supplementary Table 2. The resulting dataset includes 42,156 cells with an average of 198,000 reads and 1,167 genes per cell after filtering low-quality cells and genes across multiple time points and ages."
Cherry 2021,Fibroblast_young_6wk_ECM,NA,muscle,NA,cell,NA,NA,NA,download issue,FALSE,TRUE,Mus musculus,GSE175889,GSM5350810,3p_v1,bam,SRR14699890,NA,SRX11037927,SRP322118,SRS9107342,SAMN19487610,NA,NA,"Cherry et al, Nature Biomedical Engineering, 2021",10.1038/s41551-021-00770-5,https://pubmed.ncbi.nlm.nih.gov/34341534/,Illumina NovaSeq 6000,A single-cell atlas of the microenvironment of implanted biomaterials and computational analysis of the transcriptional signalling networks [single-cell RNA-seq],"The understanding of the foreign-body responses to implanted biomaterials would benefit from the reconstruction of intracellular and intercellular signalling networks in the microenvironment surrounding the implant. Here, by leveraging single-cell RNA-sequencing data from 42,156 cells harvested from the site of implantation of either polycaprolactone or an extracellular-matrix-derived scaffold in a mouse model of volumetric muscle loss, we report a computational analysis of intercellular-signalling networks reconstructed from data of transcription-factor activation. We found that intercellular signalling networks can be clustered into modules associated with specific cell subsets, and that biomaterial-specific responses can be characterized by interactions between signalling modules for immune, fibroblast and tissue-specific cells. In a Il17ra/ knockout mouse model, we validated that predicted IL-17-linked transcriptional targets led to concomitant changes in gene expression. Moreover, we identified cell subsets that had not been implicated in the responses to implanted biomaterials. Single-cell atlases of the cellular responses to implanted biomaterials will facilitate the design of implantable biomaterials and the understanding of the ensuing cellular responses. Overall design: To generate the scRNAseq data sets we created single cell suspensions from the muscle tissue with and without biomaterials for application to 10X and Drop-seq. Single cell suspensions from whole tissue preparations were enriched for CD45+ cells to enable capture of less frequent cell populations and processed with Drop-seq. Fluorescence activated cell sorting (FACS) was used to apply mesenchymal/fibroblasts (CD45-CD19-CD31-CD29+) to Drop-seq. Finally, a previously published data set of sorted macrophages (CD45+F4/80hi+Ly6c+CD64+) was included. Most samples collected were from young mice (6 week old at time of surgery) during the acute phase of injury one week after surgery. A detailed description of age, time of harvest, treatment, and sorting methodology for each of the samples in the atlas is provided in Supplementary Table 2. The resulting dataset includes 42,156 cells with an average of 198,000 reads and 1,167 genes per cell after filtering low-quality cells and genes across multiple time points and ages."
Cherry 2021,Fibroblast_young_6wk_PCL,NA,muscle,NA,cell,NA,NA,NA,download issue,FALSE,TRUE,Mus musculus,GSE175889,GSM5350811,3p_v1,bam,SRR14699891,NA,SRX11037928,SRP322118,SRS9107341,SAMN19487609,NA,NA,"Cherry et al, Nature Biomedical Engineering, 2021",10.1038/s41551-021-00770-5,https://pubmed.ncbi.nlm.nih.gov/34341534/,Illumina NovaSeq 6000,A single-cell atlas of the microenvironment of implanted biomaterials and computational analysis of the transcriptional signalling networks [single-cell RNA-seq],"The understanding of the foreign-body responses to implanted biomaterials would benefit from the reconstruction of intracellular and intercellular signalling networks in the microenvironment surrounding the implant. Here, by leveraging single-cell RNA-sequencing data from 42,156 cells harvested from the site of implantation of either polycaprolactone or an extracellular-matrix-derived scaffold in a mouse model of volumetric muscle loss, we report a computational analysis of intercellular-signalling networks reconstructed from data of transcription-factor activation. We found that intercellular signalling networks can be clustered into modules associated with specific cell subsets, and that biomaterial-specific responses can be characterized by interactions between signalling modules for immune, fibroblast and tissue-specific cells. In a Il17ra/ knockout mouse model, we validated that predicted IL-17-linked transcriptional targets led to concomitant changes in gene expression. Moreover, we identified cell subsets that had not been implicated in the responses to implanted biomaterials. Single-cell atlases of the cellular responses to implanted biomaterials will facilitate the design of implantable biomaterials and the understanding of the ensuing cellular responses. Overall design: To generate the scRNAseq data sets we created single cell suspensions from the muscle tissue with and without biomaterials for application to 10X and Drop-seq. Single cell suspensions from whole tissue preparations were enriched for CD45+ cells to enable capture of less frequent cell populations and processed with Drop-seq. Fluorescence activated cell sorting (FACS) was used to apply mesenchymal/fibroblasts (CD45-CD19-CD31-CD29+) to Drop-seq. Finally, a previously published data set of sorted macrophages (CD45+F4/80hi+Ly6c+CD64+) was included. Most samples collected were from young mice (6 week old at time of surgery) during the acute phase of injury one week after surgery. A detailed description of age, time of harvest, treatment, and sorting methodology for each of the samples in the atlas is provided in Supplementary Table 2. The resulting dataset includes 42,156 cells with an average of 198,000 reads and 1,167 genes per cell after filtering low-quality cells and genes across multiple time points and ages."
Cherry 2021,Fibroblast_young_6wk_Saline,NA,muscle,NA,cell,NA,NA,NA,download issue,FALSE,TRUE,Mus musculus,GSE175889,GSM5350812,3p_v1,bam,SRR14699892,NA,SRX11037929,SRP322118,SRS9107343,SAMN19487521,NA,NA,"Cherry et al, Nature Biomedical Engineering, 2021",10.1038/s41551-021-00770-5,https://pubmed.ncbi.nlm.nih.gov/34341534/,Illumina NovaSeq 6000,A single-cell atlas of the microenvironment of implanted biomaterials and computational analysis of the transcriptional signalling networks [single-cell RNA-seq],"The understanding of the foreign-body responses to implanted biomaterials would benefit from the reconstruction of intracellular and intercellular signalling networks in the microenvironment surrounding the implant. Here, by leveraging single-cell RNA-sequencing data from 42,156 cells harvested from the site of implantation of either polycaprolactone or an extracellular-matrix-derived scaffold in a mouse model of volumetric muscle loss, we report a computational analysis of intercellular-signalling networks reconstructed from data of transcription-factor activation. We found that intercellular signalling networks can be clustered into modules associated with specific cell subsets, and that biomaterial-specific responses can be characterized by interactions between signalling modules for immune, fibroblast and tissue-specific cells. In a Il17ra/ knockout mouse model, we validated that predicted IL-17-linked transcriptional targets led to concomitant changes in gene expression. Moreover, we identified cell subsets that had not been implicated in the responses to implanted biomaterials. Single-cell atlases of the cellular responses to implanted biomaterials will facilitate the design of implantable biomaterials and the understanding of the ensuing cellular responses. Overall design: To generate the scRNAseq data sets we created single cell suspensions from the muscle tissue with and without biomaterials for application to 10X and Drop-seq. Single cell suspensions from whole tissue preparations were enriched for CD45+ cells to enable capture of less frequent cell populations and processed with Drop-seq. Fluorescence activated cell sorting (FACS) was used to apply mesenchymal/fibroblasts (CD45-CD19-CD31-CD29+) to Drop-seq. Finally, a previously published data set of sorted macrophages (CD45+F4/80hi+Ly6c+CD64+) was included. Most samples collected were from young mice (6 week old at time of surgery) during the acute phase of injury one week after surgery. A detailed description of age, time of harvest, treatment, and sorting methodology for each of the samples in the atlas is provided in Supplementary Table 2. The resulting dataset includes 42,156 cells with an average of 198,000 reads and 1,167 genes per cell after filtering low-quality cells and genes across multiple time points and ages."
Cherry 2021,Fibroblast_young_6wk_Naive,NA,muscle,NA,cell,NA,NA,NA,download issue,FALSE,TRUE,Mus musculus,GSE175889,GSM5350813,3p_v1,bam,SRR14699893,NA,SRX11037930,SRP322118,SRS9107344,SAMN19487520,NA,NA,"Cherry et al, Nature Biomedical Engineering, 2021",10.1038/s41551-021-00770-5,https://pubmed.ncbi.nlm.nih.gov/34341534/,Illumina NovaSeq 6000,A single-cell atlas of the microenvironment of implanted biomaterials and computational analysis of the transcriptional signalling networks [single-cell RNA-seq],"The understanding of the foreign-body responses to implanted biomaterials would benefit from the reconstruction of intracellular and intercellular signalling networks in the microenvironment surrounding the implant. Here, by leveraging single-cell RNA-sequencing data from 42,156 cells harvested from the site of implantation of either polycaprolactone or an extracellular-matrix-derived scaffold in a mouse model of volumetric muscle loss, we report a computational analysis of intercellular-signalling networks reconstructed from data of transcription-factor activation. We found that intercellular signalling networks can be clustered into modules associated with specific cell subsets, and that biomaterial-specific responses can be characterized by interactions between signalling modules for immune, fibroblast and tissue-specific cells. In a Il17ra/ knockout mouse model, we validated that predicted IL-17-linked transcriptional targets led to concomitant changes in gene expression. Moreover, we identified cell subsets that had not been implicated in the responses to implanted biomaterials. Single-cell atlases of the cellular responses to implanted biomaterials will facilitate the design of implantable biomaterials and the understanding of the ensuing cellular responses. Overall design: To generate the scRNAseq data sets we created single cell suspensions from the muscle tissue with and without biomaterials for application to 10X and Drop-seq. Single cell suspensions from whole tissue preparations were enriched for CD45+ cells to enable capture of less frequent cell populations and processed with Drop-seq. Fluorescence activated cell sorting (FACS) was used to apply mesenchymal/fibroblasts (CD45-CD19-CD31-CD29+) to Drop-seq. Finally, a previously published data set of sorted macrophages (CD45+F4/80hi+Ly6c+CD64+) was included. Most samples collected were from young mice (6 week old at time of surgery) during the acute phase of injury one week after surgery. A detailed description of age, time of harvest, treatment, and sorting methodology for each of the samples in the atlas is provided in Supplementary Table 2. The resulting dataset includes 42,156 cells with an average of 198,000 reads and 1,167 genes per cell after filtering low-quality cells and genes across multiple time points and ages."
Cherry 2021,Macrophage_young_1wk_ECM,NA,muscle,NA,cell,NA,NA,NA,download issue,FALSE,TRUE,Mus musculus,GSE175889,GSM5350814,3p_v1,bam,SRR14699894,NA,SRX11037931,SRP322118,SRS9107345,SAMN19487519,NA,NA,"Cherry et al, Nature Biomedical Engineering, 2021",10.1038/s41551-021-00770-5,https://pubmed.ncbi.nlm.nih.gov/34341534/,Illumina NovaSeq 6000,A single-cell atlas of the microenvironment of implanted biomaterials and computational analysis of the transcriptional signalling networks [single-cell RNA-seq],"The understanding of the foreign-body responses to implanted biomaterials would benefit from the reconstruction of intracellular and intercellular signalling networks in the microenvironment surrounding the implant. Here, by leveraging single-cell RNA-sequencing data from 42,156 cells harvested from the site of implantation of either polycaprolactone or an extracellular-matrix-derived scaffold in a mouse model of volumetric muscle loss, we report a computational analysis of intercellular-signalling networks reconstructed from data of transcription-factor activation. We found that intercellular signalling networks can be clustered into modules associated with specific cell subsets, and that biomaterial-specific responses can be characterized by interactions between signalling modules for immune, fibroblast and tissue-specific cells. In a Il17ra/ knockout mouse model, we validated that predicted IL-17-linked transcriptional targets led to concomitant changes in gene expression. Moreover, we identified cell subsets that had not been implicated in the responses to implanted biomaterials. Single-cell atlases of the cellular responses to implanted biomaterials will facilitate the design of implantable biomaterials and the understanding of the ensuing cellular responses. Overall design: To generate the scRNAseq data sets we created single cell suspensions from the muscle tissue with and without biomaterials for application to 10X and Drop-seq. Single cell suspensions from whole tissue preparations were enriched for CD45+ cells to enable capture of less frequent cell populations and processed with Drop-seq. Fluorescence activated cell sorting (FACS) was used to apply mesenchymal/fibroblasts (CD45-CD19-CD31-CD29+) to Drop-seq. Finally, a previously published data set of sorted macrophages (CD45+F4/80hi+Ly6c+CD64+) was included. Most samples collected were from young mice (6 week old at time of surgery) during the acute phase of injury one week after surgery. A detailed description of age, time of harvest, treatment, and sorting methodology for each of the samples in the atlas is provided in Supplementary Table 2. The resulting dataset includes 42,156 cells with an average of 198,000 reads and 1,167 genes per cell after filtering low-quality cells and genes across multiple time points and ages."
Cherry 2021,Macrophage_young_1wk_PCL,NA,muscle,NA,cell,NA,NA,NA,download issue,FALSE,TRUE,Mus musculus,GSE175889,GSM5350815,3p_v1,bam,SRR14699895,NA,SRX11037933,SRP322118,SRS9107347,SAMN19487518,NA,NA,"Cherry et al, Nature Biomedical Engineering, 2021",10.1038/s41551-021-00770-5,https://pubmed.ncbi.nlm.nih.gov/34341534/,Illumina NovaSeq 6000,A single-cell atlas of the microenvironment of implanted biomaterials and computational analysis of the transcriptional signalling networks [single-cell RNA-seq],"The understanding of the foreign-body responses to implanted biomaterials would benefit from the reconstruction of intracellular and intercellular signalling networks in the microenvironment surrounding the implant. Here, by leveraging single-cell RNA-sequencing data from 42,156 cells harvested from the site of implantation of either polycaprolactone or an extracellular-matrix-derived scaffold in a mouse model of volumetric muscle loss, we report a computational analysis of intercellular-signalling networks reconstructed from data of transcription-factor activation. We found that intercellular signalling networks can be clustered into modules associated with specific cell subsets, and that biomaterial-specific responses can be characterized by interactions between signalling modules for immune, fibroblast and tissue-specific cells. In a Il17ra/ knockout mouse model, we validated that predicted IL-17-linked transcriptional targets led to concomitant changes in gene expression. Moreover, we identified cell subsets that had not been implicated in the responses to implanted biomaterials. Single-cell atlases of the cellular responses to implanted biomaterials will facilitate the design of implantable biomaterials and the understanding of the ensuing cellular responses. Overall design: To generate the scRNAseq data sets we created single cell suspensions from the muscle tissue with and without biomaterials for application to 10X and Drop-seq. Single cell suspensions from whole tissue preparations were enriched for CD45+ cells to enable capture of less frequent cell populations and processed with Drop-seq. Fluorescence activated cell sorting (FACS) was used to apply mesenchymal/fibroblasts (CD45-CD19-CD31-CD29+) to Drop-seq. Finally, a previously published data set of sorted macrophages (CD45+F4/80hi+Ly6c+CD64+) was included. Most samples collected were from young mice (6 week old at time of surgery) during the acute phase of injury one week after surgery. A detailed description of age, time of harvest, treatment, and sorting methodology for each of the samples in the atlas is provided in Supplementary Table 2. The resulting dataset includes 42,156 cells with an average of 198,000 reads and 1,167 genes per cell after filtering low-quality cells and genes across multiple time points and ages."
Cherry 2021,Macrophage_young_1wk_Saline,NA,muscle,NA,cell,NA,NA,NA,download issue,FALSE,TRUE,Mus musculus,GSE175889,GSM5350816,3p_v1,bam,SRR14699896,NA,SRX11037934,SRP322118,SRS9107348,SAMN19487517,NA,NA,"Cherry et al, Nature Biomedical Engineering, 2021",10.1038/s41551-021-00770-5,https://pubmed.ncbi.nlm.nih.gov/34341534/,Illumina NovaSeq 6000,A single-cell atlas of the microenvironment of implanted biomaterials and computational analysis of the transcriptional signalling networks [single-cell RNA-seq],"The understanding of the foreign-body responses to implanted biomaterials would benefit from the reconstruction of intracellular and intercellular signalling networks in the microenvironment surrounding the implant. Here, by leveraging single-cell RNA-sequencing data from 42,156 cells harvested from the site of implantation of either polycaprolactone or an extracellular-matrix-derived scaffold in a mouse model of volumetric muscle loss, we report a computational analysis of intercellular-signalling networks reconstructed from data of transcription-factor activation. We found that intercellular signalling networks can be clustered into modules associated with specific cell subsets, and that biomaterial-specific responses can be characterized by interactions between signalling modules for immune, fibroblast and tissue-specific cells. In a Il17ra/ knockout mouse model, we validated that predicted IL-17-linked transcriptional targets led to concomitant changes in gene expression. Moreover, we identified cell subsets that had not been implicated in the responses to implanted biomaterials. Single-cell atlases of the cellular responses to implanted biomaterials will facilitate the design of implantable biomaterials and the understanding of the ensuing cellular responses. Overall design: To generate the scRNAseq data sets we created single cell suspensions from the muscle tissue with and without biomaterials for application to 10X and Drop-seq. Single cell suspensions from whole tissue preparations were enriched for CD45+ cells to enable capture of less frequent cell populations and processed with Drop-seq. Fluorescence activated cell sorting (FACS) was used to apply mesenchymal/fibroblasts (CD45-CD19-CD31-CD29+) to Drop-seq. Finally, a previously published data set of sorted macrophages (CD45+F4/80hi+Ly6c+CD64+) was included. Most samples collected were from young mice (6 week old at time of surgery) during the acute phase of injury one week after surgery. A detailed description of age, time of harvest, treatment, and sorting methodology for each of the samples in the atlas is provided in Supplementary Table 2. The resulting dataset includes 42,156 cells with an average of 198,000 reads and 1,167 genes per cell after filtering low-quality cells and genes across multiple time points and ages."
Chow 2021,noFANS_1,133155-hg19: Human snRNA no FANS rep 1,muscle,NA,NA,NA,NA,NA,***Raw data are unavailable due to patient privacy concerns***,FALSE,TRUE,Homo sapiens,GSE178734,GSM5396679,NA,NA,NOT_PUBLIC,NA,NA,NA,NA,NA,NA,NA,NO_LINKED_PUBLICATION,NA,NA,NA,NA,NA
Chow 2021,FANS_1,133156-hg19: Human snRNA FANS rep 1,muscle,NA,NA,NA,NA,NA,***Raw data are unavailable due to patient privacy concerns***,FALSE,TRUE,Homo sapiens,GSE178734,GSM5396680,NA,NA,NOT_PUBLIC,NA,NA,NA,NA,NA,NA,NA,NO_LINKED_PUBLICATION,NA,NA,NA,NA,NA
Chow 2021,noFANS_2,133157-hg19: Human snRNA no FANS rep 2,muscle,NA,NA,NA,NA,NA,***Raw data are unavailable due to patient privacy concerns***,FALSE,TRUE,Homo sapiens,GSE178734,GSM5396681,NA,NA,NOT_PUBLIC,NA,NA,NA,NA,NA,NA,NA,NO_LINKED_PUBLICATION,NA,NA,NA,NA,NA
Chow 2021,FANS_2,133158-hg19: Human snRNA FANS rep 2,muscle,NA,NA,NA,NA,NA,***Raw data are unavailable due to patient privacy concerns***,FALSE,TRUE,Homo sapiens,GSE178734,GSM5396682,NA,NA,NOT_PUBLIC,NA,NA,NA,NA,NA,NA,NA,NO_LINKED_PUBLICATION,NA,NA,NA,NA,NA
Chow 2021,human_20k_nuc,63_20_rna-hg19: Human snRNA 20k nuclei,muscle,NA,NA,NA,NA,NA,***Raw data are unavailable due to patient privacy concerns***,FALSE,TRUE,Homo sapiens,GSE178734,GSM5396684,NA,NA,NOT_PUBLIC,NA,NA,NA,NA,NA,NA,NA,NO_LINKED_PUBLICATION,NA,NA,NA,NA,NA
Chow 2021,human_40k_nuc,63_40_rna-hg19: Human snRNA 40k nuclei,muscle,NA,NA,NA,NA,NA,***Raw data are unavailable due to patient privacy concerns***,FALSE,TRUE,Homo sapiens,GSE178734,GSM5396685,NA,NA,NOT_PUBLIC,NA,NA,NA,NA,NA,NA,NA,NO_LINKED_PUBLICATION,NA,NA,NA,NA,NA
Hettinger 2022,Adult WB,NA,muscle,NA,NA,NA,NA,NA,ffq says this sample doesnt exist,FALSE,TRUE,Rattus norvegicus,GSE184413,GSM5588467,3p_v3,fastq,SRR15967539,NA,NA,NA,NA,NA,NA,NA,NA,NA,https://pubmed.ncbi.nlm.nih.gov/35434632/,NA,NA,NA
Hettinger 2022,Adult RE,NA,muscle,NA,NA,NA,NA,NA,NA,FALSE,TRUE,Rattus norvegicus,GSE184413,GSM5588468,3p_v3,fastq,SRR15967540,NA,NA,NA,NA,NA,NA,NA,NA,NA,https://pubmed.ncbi.nlm.nih.gov/35434632/,NA,NA,NA
Hettinger 2022,Adult RE + M,NA,muscle,NA,NA,NA,NA,NA,ffq says this sample doesnt exist,FALSE,TRUE,Rattus norvegicus,GSE184413,GSM5588469,3p_v3,fastq,SRR15967541,NA,NA,NA,NA,NA,NA,NA,NA,NA,https://pubmed.ncbi.nlm.nih.gov/35434632/,NA,NA,NA
Hettinger 2022,Old WB,NA,muscle,NA,NA,NA,NA,NA,ffq says this sample doesnt exist,FALSE,TRUE,Rattus norvegicus,GSE184413,GSM5588470,3p_v3,fastq,SRR15967542,NA,NA,NA,NA,NA,NA,NA,NA,NA,https://pubmed.ncbi.nlm.nih.gov/35434632/,NA,NA,NA
Hettinger 2022,Old RE,NA,muscle,NA,NA,NA,NA,NA,NA,FALSE,TRUE,Rattus norvegicus,GSE184413,GSM5588471,3p_v3,fastq,SRR15967543,NA,NA,NA,NA,NA,NA,NA,NA,NA,https://pubmed.ncbi.nlm.nih.gov/35434632/,NA,NA,NA
Hettinger 2022,Old RE + M,NA,muscle,NA,NA,NA,NA,NA,NA,FALSE,TRUE,Rattus norvegicus,GSE184413,GSM5588472,3p_v3,fastq,SRR15967544,NA,NA,NA,NA,NA,NA,NA,NA,NA,https://pubmed.ncbi.nlm.nih.gov/35434632/,NA,NA,NA
Moiseeva 2023,CD45NegNSen_1,NA,muscle,hindlimb,NA,NA,NA,NA,"fastqs missing read IDs, breaking at cutadapt",FALSE,FALSE,Mus musculus,GSE197017,GSM5906888,3p_v3.1,fastq,SRR18072766;SRR18072767;SRR18072768;SRR18072769;SRR18072770;SRR18072771;SRR18072772;SRR18072773,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Moiseeva 2023,CD45NegNSen_2,NA,muscle,hindlimb,NA,NA,NA,NA,"fastqs missing read IDs, breaking at cutadapt",FALSE,FALSE,Mus musculus,GSE197017,GSM5906889,3p_v3.1,fastq,SRR18072774;SRR18072775;SRR18072776;SRR18072777;SRR18072778;SRR18072779;SRR18072780;SRR18072781,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Moiseeva 2023,CD45PosNSen_1,NA,muscle,hindlimb,NA,NA,NA,NA,"fastqs missing read IDs, breaking at cutadapt",FALSE,FALSE,Mus musculus,GSE197017,GSM5906890,3p_v3.1,fastq,SRR18072782;SRR18072783;SRR18072784;SRR18072785;SRR18072786;SRR18072787;SRR18072788;SRR18072789,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Moiseeva 2023,CD45PosNSen_2,NA,muscle,hindlimb,NA,NA,NA,NA,"fastqs missing read IDs, breaking at cutadapt",FALSE,FALSE,Mus musculus,GSE197017,GSM5906891,3p_v3.1,fastq,SRR18072790;SRR18072791;SRR18072792;SRR18072793;SRR18072794;SRR18072795;SRR18072796;SRR18072797,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Moiseeva 2023,CD45NegSen_1,NA,muscle,hindlimb,NA,NA,NA,NA,"fastqs missing read IDs, breaking at cutadapt",FALSE,FALSE,Mus musculus,GSE197017,GSM5906892,3p_v3.1,fastq,SRR18072798;SRR18072799;SRR18072800;SRR18072801;SRR18072802;SRR18072803;SRR18072804;SRR18072805,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Moiseeva 2023,CD45NegSen_2,NA,muscle,hindlimb,NA,NA,NA,NA,"fastqs missing read IDs, breaking at cutadapt",FALSE,FALSE,Mus musculus,GSE197017,GSM5906893,3p_v3.1,fastq,SRR18072806;SRR18072807;SRR18072808;SRR18072809;SRR18072810;SRR18072811;SRR18072812;SRR18072813,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Moiseeva 2023,CD45PosSen_1,NA,muscle,hindlimb,NA,NA,NA,NA,"fastqs missing read IDs, breaking at cutadapt",FALSE,FALSE,Mus musculus,GSE197017,GSM5906894,3p_v3.1,fastq,SRR18072814;SRR18072815;SRR18072816;SRR18072817;SRR18072818;SRR18072819;SRR18072820;SRR18072821,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Moiseeva 2023,CD45PosSen_2,NA,muscle,hindlimb,NA,NA,NA,NA,"fastqs missing read IDs, breaking at cutadapt",FALSE,FALSE,Mus musculus,GSE197017,GSM5906895,3p_v3.1,fastq,SRR18072822;SRR18072823;SRR18072824;SRR18072825;SRR18072826;SRR18072827;SRR18072828;SRR18072829,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Fahrner 2023,Pax7Cre_Run1,NA,muscle,tibialis anterior – muscle stem cell,NA,NA,NA,NA,metadata not available yet,FALSE,FALSE,Mus musculus,GSE200501,GSM6035241,3p_v3.1,fastq,SRR24093561;SRR24093562,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Fahrner 2023,Pax7Cre_Run2,NA,muscle,tibialis anterior – muscle stem cell,NA,NA,NA,NA,metadata not available yet,FALSE,FALSE,Mus musculus,GSE200501,GSM6035242,3p_v3.1,fastq,SRR24093560,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Fahrner 2023,Pax7CremiR501flox_Run1,NA,muscle,tibialis anterior – muscle stem cell,NA,NA,NA,NA,metadata not available yet,FALSE,FALSE,Mus musculus,GSE200501,GSM6035243,3p_v3.1,fastq,SRR24093558;SRR24093559,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Fahrner 2023,Pax7CremiR501flox_Run2,NA,muscle,tibialis anterior – muscle stem cell,NA,NA,NA,NA,metadata not available yet,FALSE,FALSE,Mus musculus,GSE200501,GSM6035244,3p_v3.1,fastq,SRR24093557,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Yang BA 2022,"Young, Injured Day 5, replicate 2",NA,muscle,NA,NA,NA,NA,NA,Not enough cells passing QC,FALSE,TRUE,Mus musculus,GSE205395,GSM6211370,3p_v3,bam,SRR19524911,NA,SRX15577167,NA,NA,SAMN28843024,NA,NA,NA,NA,NA,NA,NA,NA
Yang BA 2022,"Aged, Injured Day 5, replicate 2",NA,muscle,NA,NA,NA,NA,NA,Not enough cells passing QC,FALSE,TRUE,Mus musculus,GSE205395,GSM6211372,3p_v3,bam,SRR19524913,NA,SRX15577165,NA,NA,SAMN28843026,NA,NA,NA,NA,NA,NA,NA,NA
Cutler 2022,"Adult, 4 days post-injury rep1_2",NA,muscle,NA,NA,NA,NA,NA,Not enough reads to include (only ~300k),FALSE,TRUE,Mus musculus,GSE205690,GSM6217409,3p_v2,fastq,SRR19581906,NA,SRX15633725,NA,NA,SAMN28922315,NA,NA,NA,10.1016/j.isci.2022.104444,https://pubmed.ncbi.nlm.nih.gov/35733848/,NA,NA,NA
Cutler 2022,"Adult, uninjured, rep2_3",NA,muscle,NA,NA,NA,NA,NA,Not enough reads to include (only ~300k),FALSE,TRUE,Mus musculus,GSE205690,GSM6217430,3p_v2,fastq,SRR19581927,NA,SRX15633704,NA,NA,SAMN28922336,NA,NA,NA,10.1016/j.isci.2022.104444,https://pubmed.ncbi.nlm.nih.gov/35733848/,NA,NA,NA
Yaghi 2022,"MmSCs from 2.5-, 5- , 12.5-wk-old Dmdmdx; 2.5- , 12.5-wk-old DBA/2J mice",NA,muscle,MSCs,cell,NA,NA,NA,hashed,FALSE,FALSE,Mus musculus,GSE205737,GSM6222439,3p_v3,fastq,SRR19591782;SRR19591783,NA,SRX15643451,NA,NA,SAMN28928454,NA,NA,NA,NA,NA,NA,NA,NA
Babaeijandaghi 2022,FR121_macrophages HTO,NA,muscle,tibialis anterior,NA,NA,NA,NA,R2 contains two constant sequences – pretty sure this isn’t scRNAseq data (GEO methods not clear),FALSE,FALSE,Mus musculus,GSE212371,GSM6528918,3p_v3,fastq,SRR21356437;SRR21356438;SRR21356439;SRR21356440,NA,SRX17362183,NA,NA,SAMN30603394,NA,NA,NA,NA,NA,NA,NA,NA
Young 2022,mmusculus_GASTROC_mdx,NA,muscle,gastrocnemius,NA,NA,NA,NA,NA,FALSE,TRUE,Mus musculus,GSE215305,GSM6631766,3p_visium,bam,SRR21871734,NA,SRX17858859,SRP402129,NA,SAMN31252343,NA,NA,"Young et al, The FASEB Journal, 2022",10.1096/fj.202200289RR,https://pubmed.ncbi.nlm.nih.gov/36190443/,NA,NA,NA
Wang X 2023,"mononuclear cells, WT quadriceps 14 weeks [QW]",NA,muscle,quadricep,NA,NA,NA,NA,fastqs missing read IDs,FALSE,TRUE,Mus musculus,GSE218201,GSM6736410,3p_v3,fastq,SRR22321625;SRR22321626;SRR22321627;SRR22321628,NA,SRX18294854,NA,NA,SAMN31772143,NA,NA,NA,NA,NA,NA,NA,NA
Wang X 2023,"mononuclear cells, WT diaphragm 14 weeks [DW]",NA,muscle,diaphragm,NA,NA,NA,NA,fastqs missing read IDs,FALSE,TRUE,Mus musculus,GSE218201,GSM6736411,3p_v3,fastq,SRR22321621;SRR22321622;SRR22321623;SRR22321624,NA,SRX18294855,NA,NA,SAMN31772142,NA,NA,NA,NA,NA,NA,NA,NA
Wang X 2023,"mononuclear cells, mdx5cv quadriceps 14 weeks [Q5CV]",NA,muscle,quadricep,NA,NA,NA,NA,fastqs missing read IDs,FALSE,TRUE,Mus musculus,GSE218201,GSM6736412,3p_v3,fastq,SRR22321617;SRR22321618;SRR22321619;SRR22321620,NA,SRX18294856,NA,NA,SAMN31772141,NA,NA,NA,NA,NA,NA,NA,NA
Wang X 2023,"mononuclear cells, mdx5cv diaphragm 14 weeks [D5CV]",NA,muscle,diaphragm,NA,NA,NA,NA,fastqs missing read IDs,FALSE,TRUE,Mus musculus,GSE218201,GSM6736413,3p_v3,fastq,SRR22321613;SRR22321614; SRR22321615; SRR22321616,NA,SRX18294857,NA,NA,SAMN31772140,NA,NA,NA,NA,NA,NA,NA,NA
Danielli 2022,RH4/KFR shSCR/shP3F1,NA,muscle,tumor,NA,NA,NA,NA,hashed,FALSE,TRUE,Homo sapiens,GSE218974,GSM6761397,3p_v3,fastq,SRR22672254;SRR22672255,NA,SRX18635140,NA,NA,SAMN31927033,NA,NA,NA,NA,NA,NA,NA,NA
Danielli 2022,aRMS-1 (IC-pPDX-104) / aRMS-2 (IC-pPDX-29) / aRMS-3 (IC-pPDX-35),NA,muscle,tumor,NA,NA,NA,NA,hashed,FALSE,TRUE,Homo sapiens,GSE218974,GSM6761398,3p_v3,fastq,SRR22672252;SRR22672253,NA,SRX18635141,NA,NA,SAMN31927032,NA,NA,NA,NA,NA,NA,NA,NA
Danielli 2022,aRMS-4 (Mast118) / aRMS-5 (Berlin13304),NA,muscle,tumor,NA,NA,NA,NA,hashed,FALSE,TRUE,Homo sapiens,GSE218974,GSM6761399,3p_v3,fastq,SRR22672250;SRR22672251,NA,SRX18635142,NA,NA,SAMN31927031,NA,NA,NA,NA,NA,NA,NA,NA
Danielli 2022,eRMS-2.1 (Rh71) / eRMS-2.2 (Rh74) / eRMS-3.2 (Mast139),NA,muscle,tumor,NA,NA,NA,NA,hashed,FALSE,TRUE,Homo sapiens,GSE218974,GSM6761400,3p_v3,fastq,SRR22672248;SRR22672249,NA,SRX18635143,NA,NA,SAMN31927030,NA,NA,NA,NA,NA,NA,NA,NA
Danielli 2022,eRMS-8.1 (Berlin 13454) / eRMS-8.2 (Berlin 13870) / eRMS-8.3 (Berlin 13933),NA,muscle,tumor,NA,NA,NA,NA,hashed,FALSE,TRUE,Homo sapiens,GSE218974,GSM6761401,3p_v3,fastq,SRR22672246;SRR22672247,NA,SRX18635144,NA,NA,SAMN31927029,NA,NA,NA,NA,NA,NA,NA,NA
Danielli 2022,eRMS-1.1 (Rh70) / eRMS-1.2 (Rh73) / eRMS-4 (IC-pPDX-82),NA,muscle,tumor,NA,NA,NA,NA,hashed,FALSE,TRUE,Homo sapiens,GSE218974,GSM6761402,3p_v3,fastq,SRR22672244;SRR22672245,NA,SRX18635145,NA,NA,SAMN31927028,NA,NA,NA,NA,NA,NA,NA,NA
Danielli 2022,KFR / Rh4 / RMS,NA,muscle,cell line,NA,NA,NA,NA,hashed,FALSE,FALSE,Homo sapiens,GSE218974,GSM6761403,3p_v3,fastq,SRR22672242;SRR22672243,NA,SRX18635146,NA,NA,SAMN31927027,NA,NA,NA,NA,NA,NA,NA,NA
Kalucka 2020,kalucka_soleus,#TODO: add ENA download info,muscle,NA,cell,NA,NA,NA,NA,FALSE,TRUE,Mus musculus,NA,NA,NA,fastq,NA,NA,NA,NA,NA,NA,NA,NA,"Kalucka et al, Cell, 2020",NA,https://pubmed.ncbi.nlm.nih.gov/32059779/,NA,NA,NA
Kalucka 2020,kalucka_edl,#TODO: add ENA download info,muscle,NA,cell,NA,NA,NA,NA,FALSE,TRUE,Mus musculus,NA,NA,NA,fastq,NA,NA,NA,NA,NA,NA,NA,NA,"Kalucka et al, Cell, 2020",NA,https://pubmed.ncbi.nlm.nih.gov/32059779/,NA,NA,NA
Chinese Academy of Agricultural Sciences,NA,NA,muscle,NA,NA,NA,NA,NA,R1 longer than R2?,FALSE,TRUE,Mus musculus,NA,NA,NA,fastq,SRR12364842,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Mournetas 2021,D17_Healthy Cell 03_p,NA,muscle,iPSC,NA,NA,NA,NA,https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-9510/files/,FALSE,FALSE,Homo sapiens,NA,NA,NA,bam,ERR4567596,NA,NA,NA,NA,NA,NA,NA,NA,NA,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7890274/,NA,NA,NA
Chinese Academy of Agricultural Sciences,NA,NA,muscle,NA,NA,NA,NA,NA,R1 longer than R2?,FALSE,TRUE,Mus musculus,NA,NA,NA,fastq,SRR12364843,NA,SRX8864048,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Tabula Microcebus 2022,NA,NA,muscle,hindlimb,cell,NA,NA,NA,Data not yet public,FALSE,TRUE,Microcebus murinus,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,https://registry.opendata.aws/tabula-sapiens/,"Tabula Sapiens Consortium et al, bioRxiv, 2021",NA,https://www.biorxiv.org/content/10.1101/2021.07.19.452956v2,NA,NA,NA
Tabula Microcebus 2022,NA,NA,muscle,diaphragm,cell,NA,NA,NA,Data not yet public,FALSE,TRUE,Microcebus murinus,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,https://registry.opendata.aws/tabula-sapiens/,"Tabula Sapiens Consortium et al, bioRxiv, 2021",NA,https://www.biorxiv.org/content/10.1101/2021.07.19.452956v2,NA,NA,NA
Tabula Microcebus 2022,NA,NA,muscle,tongue,cell,NA,NA,NA,Data not yet public,FALSE,TRUE,Microcebus murinus,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,https://registry.opendata.aws/tabula-sapiens/,"Tabula Sapiens Consortium et al, bioRxiv, 2021",NA,https://www.biorxiv.org/content/10.1101/2021.07.19.452956v2,NA,NA,NA
Qiu 2020,Qiu 2020,NA,muscle,NA,NA,NA,NA,NA,NA,FALSE,TRUE,Sus domesticus,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,"Qiu et al, Cells, 2020",NA,https://pubmed.ncbi.nlm.nih.gov/32331484/,NA,NA,NA
Tabula Muris 2018,10X_P4_0,NA,muscle,tongue,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE109774,GSM3040890,3p_v2,bam,SRR6835844,NA,NA,NA,NA,NA,NA,NA,"Tabula Muris, Nature, 2018",10.1038/s41586-018-0590-4,https://pubmed.ncbi.nlm.nih.gov/30283141/,Illumina NovaSeq 6000,Tabula Muris: Transcriptomic characterization of 20 organs and tissues from Mus musculus at single cell resolution,We have created a resource of single cell transcriptome data from the model organism Mus musculus. Contributor: The Tabula Muris Consortium The full list of contributors to this dataset can be found in the corresponding publication. Overall design: Single cell RNA sequencing of single cells across 20 tissues of 3 month aged mice
Tabula Muris 2018,10X_P4_1,NA,muscle,tongue,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE109774,GSM3040891,3p_v2,bam,SRR6835845,NA,NA,NA,NA,NA,NA,NA,"Tabula Muris, Nature, 2018",10.1038/s41586-018-0590-4,https://pubmed.ncbi.nlm.nih.gov/30283141/,Illumina NovaSeq 6000,Tabula Muris: Transcriptomic characterization of 20 organs and tissues from Mus musculus at single cell resolution,We have created a resource of single cell transcriptome data from the model organism Mus musculus. Contributor: The Tabula Muris Consortium The full list of contributors to this dataset can be found in the corresponding publication. Overall design: Single cell RNA sequencing of single cells across 20 tissues of 3 month aged mice
Tabula Muris 2018,10X_P7_10,NA,muscle,tongue,cell,female,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE109774,GSM3040908,3p_v2,bam,SRR6835862,NA,NA,NA,NA,NA,NA,NA,"Tabula Muris, Nature, 2018",10.1038/s41586-018-0590-4,https://pubmed.ncbi.nlm.nih.gov/30283141/,Illumina NovaSeq 6000,Tabula Muris: Transcriptomic characterization of 20 organs and tissues from Mus musculus at single cell resolution,We have created a resource of single cell transcriptome data from the model organism Mus musculus. Contributor: The Tabula Muris Consortium The full list of contributors to this dataset can be found in the corresponding publication. Overall design: Single cell RNA sequencing of single cells across 20 tissues of 3 month aged mice
Tabula Muris 2018,10X_P7_14,NA,muscle,hindlimb,cell,female,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE109774,GSM3040912,3p_v2,bam,SRR6835866,NA,SRX3791785,SRP131661,SRS3044258,NA,ftp://ftp.sra.ebi.ac.uk/vol1/SRA653/SRA653146/bam/10X_P7_14.bam,NA,"Tabula Muris, Nature, 2018",10.1038/s41586-018-0590-4,https://pubmed.ncbi.nlm.nih.gov/30283141/,Illumina NovaSeq 6000,Tabula Muris: Transcriptomic characterization of 20 organs and tissues from Mus musculus at single cell resolution,We have created a resource of single cell transcriptome data from the model organism Mus musculus. Contributor: The Tabula Muris Consortium The full list of contributors to this dataset can be found in the corresponding publication. Overall design: Single cell RNA sequencing of single cells across 20 tissues of 3 month aged mice
Tabula Muris 2018,10X_P7_15,NA,muscle,hindlimb,cell,female,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE109774,GSM3040913,3p_v2,bam,SRR6835867,NA,SRX3791786,SRP131661,SRS3044259,NA,ftp://ftp.sra.ebi.ac.uk/vol1/SRA653/SRA653146/bam/10X_P7_15.bam,NA,"Tabula Muris, Nature, 2018",10.1038/s41586-018-0590-4,https://pubmed.ncbi.nlm.nih.gov/30283141/,Illumina NovaSeq 6000,Tabula Muris: Transcriptomic characterization of 20 organs and tissues from Mus musculus at single cell resolution,We have created a resource of single cell transcriptome data from the model organism Mus musculus. Contributor: The Tabula Muris Consortium The full list of contributors to this dataset can be found in the corresponding publication. Overall design: Single cell RNA sequencing of single cells across 20 tissues of 3 month aged mice
Scott 2019,Scott_qsnt,Single cell RNA-seq tdTomato MPs quiescent,muscle,NA,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE110037,GSM2976778,3p_v2,bam,SRR6664634,NA,SRX3641495,SRP132021,SRS2907691,SAMN08455725,https://sra-download.ncbi.nlm.nih.gov/traces/sra59/SRZ/006664/SRR6664634/qsnt.bam,NA,"Scott et al, Cell Stem Cell, 2019",10.1016/j.stem.2019.11.004,https://pubmed.ncbi.nlm.nih.gov/31809738/,NextSeq 500,Single cell RNA sequencing time-course of mesenchymal progenitors during regeneration after notexin induced muscle injury,"After tissue injury mesenchymal progenitors undergo a transient proliferative expansion, morphological transition and migration from their perivascular niche. To gain transcriptomic insights into the MP function in regeneration, a muscle-injury model was employed to activate MPs and follow their contribution to tissue regeneration. To compliment the population RNA seq profile previously obtained and to uncover the suspected heterogeneity of MPs in this context, tdTomato positive cells from selected timepoints were profiled by single cell RNA sequencing. Overall design: Single cell RNA-seq analyes of enriched mesenchymal progenitors at selected timepoints during skeletal muscle regeneration."
Scott 2019,Scott_d1,Single cell RNA-seq tdTomato MPs 1 day post notexin injury,muscle,NA,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE110037,GSM2976779,3p_v2,bam,SRR6664635,NA,SRX3641496,SRP132021,SRS2907692,SAMN08455724,https://sra-download.ncbi.nlm.nih.gov/traces/sra59/SRZ/006664/SRR6664635/d1.bam,NA,"Scott et al, Cell Stem Cell, 2019",10.1016/j.stem.2019.11.004,https://pubmed.ncbi.nlm.nih.gov/31809738/,NextSeq 500,Single cell RNA sequencing time-course of mesenchymal progenitors during regeneration after notexin induced muscle injury,"After tissue injury mesenchymal progenitors undergo a transient proliferative expansion, morphological transition and migration from their perivascular niche. To gain transcriptomic insights into the MP function in regeneration, a muscle-injury model was employed to activate MPs and follow their contribution to tissue regeneration. To compliment the population RNA seq profile previously obtained and to uncover the suspected heterogeneity of MPs in this context, tdTomato positive cells from selected timepoints were profiled by single cell RNA sequencing. Overall design: Single cell RNA-seq analyes of enriched mesenchymal progenitors at selected timepoints during skeletal muscle regeneration."
Scott 2019,Scott_d2,Single cell RNA-seq tdTomato MPs 2 day post notexin injury,muscle,NA,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE110037,GSM2976780,3p_v2,bam,SRR6664636,NA,SRX3641497,SRP132021,SRS2907693,SAMN08455723,https://sra-download.ncbi.nlm.nih.gov/traces/sra59/SRZ/006664/SRR6664636/d2.bam,NA,"Scott et al, Cell Stem Cell, 2019",10.1016/j.stem.2019.11.004,https://pubmed.ncbi.nlm.nih.gov/31809738/,NextSeq 500,Single cell RNA sequencing time-course of mesenchymal progenitors during regeneration after notexin induced muscle injury,"After tissue injury mesenchymal progenitors undergo a transient proliferative expansion, morphological transition and migration from their perivascular niche. To gain transcriptomic insights into the MP function in regeneration, a muscle-injury model was employed to activate MPs and follow their contribution to tissue regeneration. To compliment the population RNA seq profile previously obtained and to uncover the suspected heterogeneity of MPs in this context, tdTomato positive cells from selected timepoints were profiled by single cell RNA sequencing. Overall design: Single cell RNA-seq analyes of enriched mesenchymal progenitors at selected timepoints during skeletal muscle regeneration."
Scott 2019,Scott_d4,Single cell RNA-seq tdTomato MPs 4 day post notexin injury,muscle,NA,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE110037,GSM2976781,3p_v2,bam,SRR6664637,NA,SRX3641498,SRP132021,SRS2907694,SAMN08455726,https://sra-download.ncbi.nlm.nih.gov/traces/sra59/SRZ/006664/SRR6664637/d4.bam,NA,"Scott et al, Cell Stem Cell, 2019",10.1016/j.stem.2019.11.004,https://pubmed.ncbi.nlm.nih.gov/31809738/,NextSeq 500,Single cell RNA sequencing time-course of mesenchymal progenitors during regeneration after notexin induced muscle injury,"After tissue injury mesenchymal progenitors undergo a transient proliferative expansion, morphological transition and migration from their perivascular niche. To gain transcriptomic insights into the MP function in regeneration, a muscle-injury model was employed to activate MPs and follow their contribution to tissue regeneration. To compliment the population RNA seq profile previously obtained and to uncover the suspected heterogeneity of MPs in this context, tdTomato positive cells from selected timepoints were profiled by single cell RNA sequencing. Overall design: Single cell RNA-seq analyes of enriched mesenchymal progenitors at selected timepoints during skeletal muscle regeneration."
Scott 2019,Scott_d14,Single cell RNA-seq tdTomato MPs 14 day post notexin injury,muscle,NA,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE110037,GSM2976782,3p_v2,bam,SRR6664638,NA,SRX3641499,SRP132021,SRS2907695,SAMN08455722,https://sra-download.ncbi.nlm.nih.gov/traces/sra59/SRZ/006664/SRR6664638/d14.bam,NA,"Scott et al, Cell Stem Cell, 2019",10.1016/j.stem.2019.11.004,https://pubmed.ncbi.nlm.nih.gov/31809738/,NextSeq 500,Single cell RNA sequencing time-course of mesenchymal progenitors during regeneration after notexin induced muscle injury,"After tissue injury mesenchymal progenitors undergo a transient proliferative expansion, morphological transition and migration from their perivascular niche. To gain transcriptomic insights into the MP function in regeneration, a muscle-injury model was employed to activate MPs and follow their contribution to tissue regeneration. To compliment the population RNA seq profile previously obtained and to uncover the suspected heterogeneity of MPs in this context, tdTomato positive cells from selected timepoints were profiled by single cell RNA sequencing. Overall design: Single cell RNA-seq analyes of enriched mesenchymal progenitors at selected timepoints during skeletal muscle regeneration."
Giordani 2019,Uninjured_WT_1,NA,muscle,hindlimb,cell,male,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE110878,GSM3520458,3p_v2,bam,SRR8352705,NA,SRX5163634,SRP133163,SRS4172659,SAMN10614781,NA,NA,"Giordani et al, Molc Cell, 2019",10.1016/j.molcel.2019.02.026,https://pubmed.ncbi.nlm.nih.gov/30922843/,NextSeq 500,Combination of high-dimensional approaches for skeletal muscle tissue cartography,"The regenerative capacity of skeletal muscle relies on muscle stem cells (MuSCs, or satellite cells) and its niche interactions with different neighboring cells. To understand the cellular diversity within adult skeletal muscle tissue, we harvested mononuclear cells from hindlimb skeletal muscles, sorted into single cells and profiled them by single-cell RNA-seq. To further understand and compare the expression profile between MuSCs and a novel smooth-muscle/mesenchymal-like cells (SMMCs) population,  we isolated the two cell types by FACS and profiled them respectively by bulk RNA-seq. Overall design: (scRNA-seq) Mononuclear cells from hindlimb skeletal muscle from wild type mouse were profiled by taking advantage of 10X Chromium platform. (bulk RNA-seq) MuSCs and SMMCs cell population were isolated from hindlimb skeletal muscle from wild type mouse. Their polyA+ RNA were profiled using Smart-seq2."
Giordani 2019,Uninjured_WT_2,NA,muscle,hindlimb,cell,male,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE110878,GSM3520459,3p_v2,bam,SRR8352706,NA,SRX5163635,SRP133163,SRS4172660,SAMN10614780,NA,NA,"Giordani et al, Molc Cell, 2019",10.1016/j.molcel.2019.02.026,https://pubmed.ncbi.nlm.nih.gov/30922843/,NextSeq 500,Combination of high-dimensional approaches for skeletal muscle tissue cartography,"The regenerative capacity of skeletal muscle relies on muscle stem cells (MuSCs, or satellite cells) and its niche interactions with different neighboring cells. To understand the cellular diversity within adult skeletal muscle tissue, we harvested mononuclear cells from hindlimb skeletal muscles, sorted into single cells and profiled them by single-cell RNA-seq. To further understand and compare the expression profile between MuSCs and a novel smooth-muscle/mesenchymal-like cells (SMMCs) population,  we isolated the two cell types by FACS and profiled them respectively by bulk RNA-seq. Overall design: (scRNA-seq) Mononuclear cells from hindlimb skeletal muscle from wild type mouse were profiled by taking advantage of 10X Chromium platform. (bulk RNA-seq) MuSCs and SMMCs cell population were isolated from hindlimb skeletal muscle from wild type mouse. Their polyA+ RNA were profiled using Smart-seq2."
Jin 2018,N_plus_CTX_rep1,4 days post-CTX; not infected; 7AAD-CD45+CD64+MerTK+,muscle,hindlimb,cell,female,C57BL/6,7AAD-CD45+CD64+MerTK+,NA,TRUE,FALSE,Mus musculus,GSE113111,GSM3097061,3p_v2,bam,SRR6998056,NA,SRX3932538,SRP139922,SRS3165512,SAMN08928280,ftp://ftp.sra.ebi.ac.uk/vol1/SRA688/SRA688834/bam/N_plus_CTX_rep1_possorted_genome_bam.bam,NA,"Jin et al, JCI Insights, 2018",10.1172/jci.insight.121549,https://pubmed.ncbi.nlm.nih.gov/30232283/,Illumina HiSeq 2500,sc-RNA sequencing of skeletal muscle macrophages during T. gondii infection and injury,"The proper coordination of macrophages is essential for skeletal muscle repair. However, the full heterogenity of macrophages responding to injury has yet to be elucidated on the single-cell level. Furthermore, chronic inflammation may shift macrophage heterogeneity at steady-state and affect the generation of heterogeneity necessary for tissue repair. We use scRNA-sequencing to determine the heterogeneity of skeletal muscle macrophages during infection and wound repair (uninfected and infected). We identify multiple transcriptionally distinct macrophage subsets during injury in uninfected mice as well as during infection at steady-state. Interestingly, in response to injury, infected skeletal muscle macrophages fail to generate certain subsets of reparative macrophages in a timely fashion. Overall design: 8-12 week old C57BL/6 mice were orally infected with 5 ME49 T.gondii cysts and allowed to reach d24 post-infection to establish chronicity. Age and sex-matched uninfected and infected mice were given cardiotoxin naja pallida i.m. in one leg at 24 days post-infection. Contralateral leg was used as an uninjured control. Muscles were harvested at 4 days-post injury and prepared into a single cell suspension. Single cell suspensions were bulk sorted for macrophages by 7AAD-CD45+CD64+MerTK+ cells. Sorted cells from each group was individually assessed for and loaded onto the 10X Genomics Chromium platform for single-cell capture. cDNA libraries were constructed and subsequently sequenced on the Illumina platform. Experimental groups were performed in duplicate."
Jin 2018,N_plus_CTX_rep2,4 days post-CTX; not infected; 7AAD-CD45+CD64+MerTK+,muscle,hindlimb,cell,female,C57BL/6,7AAD-CD45+CD64+MerTK+,NA,TRUE,FALSE,Mus musculus,GSE113111,GSM3097062,3p_v2,bam,SRR6998057,NA,SRX3932539,SRP139922,SRS3165514,SAMN08928279,ftp://ftp.sra.ebi.ac.uk/vol1/SRA688/SRA688834/bam/N_plus_CTX_rep2_possorted_genome_bam.bam,NA,"Jin et al, JCI Insights, 2018",10.1172/jci.insight.121549,https://pubmed.ncbi.nlm.nih.gov/30232283/,Illumina HiSeq 2500,sc-RNA sequencing of skeletal muscle macrophages during T. gondii infection and injury,"The proper coordination of macrophages is essential for skeletal muscle repair. However, the full heterogenity of macrophages responding to injury has yet to be elucidated on the single-cell level. Furthermore, chronic inflammation may shift macrophage heterogeneity at steady-state and affect the generation of heterogeneity necessary for tissue repair. We use scRNA-sequencing to determine the heterogeneity of skeletal muscle macrophages during infection and wound repair (uninfected and infected). We identify multiple transcriptionally distinct macrophage subsets during injury in uninfected mice as well as during infection at steady-state. Interestingly, in response to injury, infected skeletal muscle macrophages fail to generate certain subsets of reparative macrophages in a timely fashion. Overall design: 8-12 week old C57BL/6 mice were orally infected with 5 ME49 T.gondii cysts and allowed to reach d24 post-infection to establish chronicity. Age and sex-matched uninfected and infected mice were given cardiotoxin naja pallida i.m. in one leg at 24 days post-infection. Contralateral leg was used as an uninjured control. Muscles were harvested at 4 days-post injury and prepared into a single cell suspension. Single cell suspensions were bulk sorted for macrophages by 7AAD-CD45+CD64+MerTK+ cells. Sorted cells from each group was individually assessed for and loaded onto the 10X Genomics Chromium platform for single-cell capture. cDNA libraries were constructed and subsequently sequenced on the Illumina platform. Experimental groups were performed in duplicate."
Jin 2018,Inf_rep1,No CTX; T. gondii infected; 7AAD-CD45+CD64+MerTK+,muscle,hindlimb,cell,female,C57BL/6,7AAD-CD45+CD64+MerTK+,NA,TRUE,FALSE,Mus musculus,GSE113111,GSM3097063,3p_v2,bam,SRR6998058,NA,SRX3932540,SRP139922,SRS3165513,SAMN08928278,NA,NA,"Jin et al, JCI Insights, 2018",10.1172/jci.insight.121549,https://pubmed.ncbi.nlm.nih.gov/30232283/,Illumina HiSeq 2500,sc-RNA sequencing of skeletal muscle macrophages during T. gondii infection and injury,"The proper coordination of macrophages is essential for skeletal muscle repair. However, the full heterogenity of macrophages responding to injury has yet to be elucidated on the single-cell level. Furthermore, chronic inflammation may shift macrophage heterogeneity at steady-state and affect the generation of heterogeneity necessary for tissue repair. We use scRNA-sequencing to determine the heterogeneity of skeletal muscle macrophages during infection and wound repair (uninfected and infected). We identify multiple transcriptionally distinct macrophage subsets during injury in uninfected mice as well as during infection at steady-state. Interestingly, in response to injury, infected skeletal muscle macrophages fail to generate certain subsets of reparative macrophages in a timely fashion. Overall design: 8-12 week old C57BL/6 mice were orally infected with 5 ME49 T.gondii cysts and allowed to reach d24 post-infection to establish chronicity. Age and sex-matched uninfected and infected mice were given cardiotoxin naja pallida i.m. in one leg at 24 days post-infection. Contralateral leg was used as an uninjured control. Muscles were harvested at 4 days-post injury and prepared into a single cell suspension. Single cell suspensions were bulk sorted for macrophages by 7AAD-CD45+CD64+MerTK+ cells. Sorted cells from each group was individually assessed for and loaded onto the 10X Genomics Chromium platform for single-cell capture. cDNA libraries were constructed and subsequently sequenced on the Illumina platform. Experimental groups were performed in duplicate."
Jin 2018,Inf_rep2,No CTX; T. gondii infected; 7AAD-CD45+CD64+MerTK+,muscle,hindlimb,cell,female,C57BL/6,7AAD-CD45+CD64+MerTK+,NA,TRUE,FALSE,Mus musculus,GSE113111,GSM3097064,3p_v2,bam,SRR6998059,NA,SRX3932541,SRP139922,SRS3165515,SAMN08928283,NA,NA,"Jin et al, JCI Insights, 2018",10.1172/jci.insight.121549,https://pubmed.ncbi.nlm.nih.gov/30232283/,Illumina HiSeq 2500,sc-RNA sequencing of skeletal muscle macrophages during T. gondii infection and injury,"The proper coordination of macrophages is essential for skeletal muscle repair. However, the full heterogenity of macrophages responding to injury has yet to be elucidated on the single-cell level. Furthermore, chronic inflammation may shift macrophage heterogeneity at steady-state and affect the generation of heterogeneity necessary for tissue repair. We use scRNA-sequencing to determine the heterogeneity of skeletal muscle macrophages during infection and wound repair (uninfected and infected). We identify multiple transcriptionally distinct macrophage subsets during injury in uninfected mice as well as during infection at steady-state. Interestingly, in response to injury, infected skeletal muscle macrophages fail to generate certain subsets of reparative macrophages in a timely fashion. Overall design: 8-12 week old C57BL/6 mice were orally infected with 5 ME49 T.gondii cysts and allowed to reach d24 post-infection to establish chronicity. Age and sex-matched uninfected and infected mice were given cardiotoxin naja pallida i.m. in one leg at 24 days post-infection. Contralateral leg was used as an uninjured control. Muscles were harvested at 4 days-post injury and prepared into a single cell suspension. Single cell suspensions were bulk sorted for macrophages by 7AAD-CD45+CD64+MerTK+ cells. Sorted cells from each group was individually assessed for and loaded onto the 10X Genomics Chromium platform for single-cell capture. cDNA libraries were constructed and subsequently sequenced on the Illumina platform. Experimental groups were performed in duplicate."
Jin 2018,Inf_plus_CTX_rep1,4 days post-CTX; T. gondii infected; 7AAD-CD45+CD64+MerTK+,muscle,hindlimb,cell,female,C57BL/6,7AAD-CD45+CD64+MerTK+,NA,TRUE,FALSE,Mus musculus,GSE113111,GSM3097065,3p_v2,bam,SRR6998060,NA,SRX3932542,SRP139922,SRS3165516,SAMN08928282,NA,NA,"Jin et al, JCI Insights, 2018",10.1172/jci.insight.121549,https://pubmed.ncbi.nlm.nih.gov/30232283/,Illumina HiSeq 2500,sc-RNA sequencing of skeletal muscle macrophages during T. gondii infection and injury,"The proper coordination of macrophages is essential for skeletal muscle repair. However, the full heterogenity of macrophages responding to injury has yet to be elucidated on the single-cell level. Furthermore, chronic inflammation may shift macrophage heterogeneity at steady-state and affect the generation of heterogeneity necessary for tissue repair. We use scRNA-sequencing to determine the heterogeneity of skeletal muscle macrophages during infection and wound repair (uninfected and infected). We identify multiple transcriptionally distinct macrophage subsets during injury in uninfected mice as well as during infection at steady-state. Interestingly, in response to injury, infected skeletal muscle macrophages fail to generate certain subsets of reparative macrophages in a timely fashion. Overall design: 8-12 week old C57BL/6 mice were orally infected with 5 ME49 T.gondii cysts and allowed to reach d24 post-infection to establish chronicity. Age and sex-matched uninfected and infected mice were given cardiotoxin naja pallida i.m. in one leg at 24 days post-infection. Contralateral leg was used as an uninjured control. Muscles were harvested at 4 days-post injury and prepared into a single cell suspension. Single cell suspensions were bulk sorted for macrophages by 7AAD-CD45+CD64+MerTK+ cells. Sorted cells from each group was individually assessed for and loaded onto the 10X Genomics Chromium platform for single-cell capture. cDNA libraries were constructed and subsequently sequenced on the Illumina platform. Experimental groups were performed in duplicate."
Jin 2018,Inf_plus_CTX_rep2,4 days post-CTX; T. gondii infected; 7AAD-CD45+CD64+MerTK+,muscle,hindlimb,cell,female,C57BL/6,7AAD-CD45+CD64+MerTK+,NA,TRUE,FALSE,Mus musculus,GSE113111,GSM3097066,3p_v2,bam,SRR6998061,NA,SRX3932543,SRP139922,SRS3165517,SAMN08928281,NA,NA,"Jin et al, JCI Insights, 2018",10.1172/jci.insight.121549,https://pubmed.ncbi.nlm.nih.gov/30232283/,Illumina HiSeq 2500,sc-RNA sequencing of skeletal muscle macrophages during T. gondii infection and injury,"The proper coordination of macrophages is essential for skeletal muscle repair. However, the full heterogenity of macrophages responding to injury has yet to be elucidated on the single-cell level. Furthermore, chronic inflammation may shift macrophage heterogeneity at steady-state and affect the generation of heterogeneity necessary for tissue repair. We use scRNA-sequencing to determine the heterogeneity of skeletal muscle macrophages during infection and wound repair (uninfected and infected). We identify multiple transcriptionally distinct macrophage subsets during injury in uninfected mice as well as during infection at steady-state. Interestingly, in response to injury, infected skeletal muscle macrophages fail to generate certain subsets of reparative macrophages in a timely fashion. Overall design: 8-12 week old C57BL/6 mice were orally infected with 5 ME49 T.gondii cysts and allowed to reach d24 post-infection to establish chronicity. Age and sex-matched uninfected and infected mice were given cardiotoxin naja pallida i.m. in one leg at 24 days post-infection. Contralateral leg was used as an uninjured control. Muscles were harvested at 4 days-post injury and prepared into a single cell suspension. Single cell suspensions were bulk sorted for macrophages by 7AAD-CD45+CD64+MerTK+ cells. Sorted cells from each group was individually assessed for and loaded onto the 10X Genomics Chromium platform for single-cell capture. cDNA libraries were constructed and subsequently sequenced on the Illumina platform. Experimental groups were performed in duplicate."
Incitti 2019,Adult satellite cells single-cell RNA-Seq,ES-derived myogenic progenitors,muscle,psc-derived,cell,NA,NA,NA,NA,TRUE,FALSE,Mus musculus,GSE121469,GSM3436818,3p_v2,bam,SRR8078715,NA,SRX4905902,SRP166131,SRS3952114,SAMN10258822,NA,NA,"Incitti et al, PNAS, 2019",10.1073/pnas.1808303116,https://pubmed.ncbi.nlm.nih.gov/30760602/,Illumina HiSeq 2500,Pluripotent stem cell-derived myogenic progenitors remodel their molecular signature upon in vivo engraftment [RNA-seq],"Optimal cell-based therapies for the treatment of muscle degenerative disorders should not only regenerate fibers, but provide a quiescent satellite cell pool ensuring long-term maintenance and regeneration. Conditional expression of Pax3/Pax7 in differentiating pluripotent stem cells (PSC) allows the generation of myogenic progenitors endowed with satellite cell-like abilities.  To identify the molecular determinants underlying their regenerative potential, we performed transcriptome analyses of these cells along with primary myogenic cells from several developmental stages. Here we show that in vitro generated PSC-derived myogenic progenitors possess a molecular signature similar to embryonic/fetal myoblasts. However, compared to fetal myoblasts, following transplantation they show superior myofiber engraftment and ability to seed the satellite cell niche, respond to multiple re-injuries and contribute to long-term regeneration. Upon engraftment, the transcriptome of Pax3/Pax7-induced PSC-derived myogenic progenitors changes dramatically, acquiring similarity to that of satellite cells, particularly in genes involved in extracellular matrix remodeling. Single cell profiling reveals that these changes are induced, not selected, by the in vivo environment.  These findings demonstrate that Pax3/Pax7-induced PSC-derived myogenic progenitors possess proliferative and migratory abilities characteristic of earlier developmental stages, and an intrinsic ability to respond to environmental cues upon skeletal muscle regeneration. Overall design: Three replicates of each sample (iPax3 and iPax7 myogenic progenitors) were analyzed and compared to reference developmental samples embryonic and fetal myoblasts, and neonatal satellite cells (three rep each). Transcriptome profiling of iPax3/7 cells injected in vivo and re-isolated was then compared to adult satellite cells (3 reps each); finally, iPax3 cells were subjected to single-cell RNA-Seq and compared to single-cell RNA-Seq of adult satellite cells."
Incitti 2019,iPax3 single-cell RNA-Seq,ES-derived myogenic progenitors,muscle,psc-derived,cell,NA,NA,NA,NA,TRUE,FALSE,Mus musculus,GSE121469,GSM3436819,3p_v2,bam,SRR8078716,NA,SRX4905903,SRP166131,SRS3952115,SAMN10258821,NA,NA,"Incitti et al, PNAS, 2019",10.1073/pnas.1808303116,https://pubmed.ncbi.nlm.nih.gov/30760602/,Illumina HiSeq 2500,Pluripotent stem cell-derived myogenic progenitors remodel their molecular signature upon in vivo engraftment [RNA-seq],"Optimal cell-based therapies for the treatment of muscle degenerative disorders should not only regenerate fibers, but provide a quiescent satellite cell pool ensuring long-term maintenance and regeneration. Conditional expression of Pax3/Pax7 in differentiating pluripotent stem cells (PSC) allows the generation of myogenic progenitors endowed with satellite cell-like abilities.  To identify the molecular determinants underlying their regenerative potential, we performed transcriptome analyses of these cells along with primary myogenic cells from several developmental stages. Here we show that in vitro generated PSC-derived myogenic progenitors possess a molecular signature similar to embryonic/fetal myoblasts. However, compared to fetal myoblasts, following transplantation they show superior myofiber engraftment and ability to seed the satellite cell niche, respond to multiple re-injuries and contribute to long-term regeneration. Upon engraftment, the transcriptome of Pax3/Pax7-induced PSC-derived myogenic progenitors changes dramatically, acquiring similarity to that of satellite cells, particularly in genes involved in extracellular matrix remodeling. Single cell profiling reveals that these changes are induced, not selected, by the in vivo environment.  These findings demonstrate that Pax3/Pax7-induced PSC-derived myogenic progenitors possess proliferative and migratory abilities characteristic of earlier developmental stages, and an intrinsic ability to respond to environmental cues upon skeletal muscle regeneration. Overall design: Three replicates of each sample (iPax3 and iPax7 myogenic progenitors) were analyzed and compared to reference developmental samples embryonic and fetal myoblasts, and neonatal satellite cells (three rep each). Transcriptome profiling of iPax3/7 cells injected in vivo and re-isolated was then compared to adult satellite cells (3 reps each); finally, iPax3 cells were subjected to single-cell RNA-Seq and compared to single-cell RNA-Seq of adult satellite cells."
Dell'Orso 2019,total_muscle_wt_rep1,total muscle,muscle,hindlimb,cell,female,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE126834,GSM3614992,3p_v2,fastq,SRR8602275,NA,SRX5402237,SRP186474,SRS4388158,SAMN10977231,NA,NA,"Dell'Orso et al, Development, 2019",10.1242/dev.174177,https://pubmed.ncbi.nlm.nih.gov/30890574/,Illumina HiSeq 3000,Single-cell analysis of homeostatic and regenerative adult skeletal muscle stem cells,"Skeletal muscle stem cells (MuSCs) ensure the formation and homeostasis of skeletal muscle and are responsible for its growth and repair processes. For repair to occur, MuSCs must exit from quiescence, abandon their niche and asymmetrically and symmetrically divide to reconstitute the stem cell pool and give rise to muscle progenitors, respectively. The transcriptomes of pooled MuSCs have provided a rich source of information for describing the genetic programs underlying distinct static cell states; however, bulk microarray and RNA-seq afford only averaged gene expression profiles, which blur the heterogeneity and developmental dynamics of asynchronous MuSC populations. The granularity required to identify distinct cell types, states, and their dynamics can be provided by single-cell analysis.  We were able to compare the transcriptomes of thousands of MuSCs and primary myoblasts isolated from homeostatic or regenerating muscles by single-cell RNA- sequencing. Using computational approaches, we could reconstruct dynamic trajectories and place, in a pseudotemporal manner, the transcriptomes of individual MuSC within these trajectories. This approach allowed for the identification of distinct clusters of MuSCs and primary myoblasts with partially overlapping but distinct transcriptional signatures, as well as the description of metabolic pathways associated with defined MuSC states. Overall design: Single cells suspentions were loaded into 10X Genomics for single cells transcriptome analysis using 10 X Genomics single cells RNAseq kit v2.2"
Dell'Orso 2019,total_muscle_wt_rep2,total muscle,muscle,hindlimb,cell,female,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE126834,GSM3614993,3p_v2,fastq,SRR8602276,NA,SRX5402238,SRP186474,SRS4388159,SAMN10977225,NA,NA,"Dell'Orso et al, Development, 2019",10.1242/dev.174177,https://pubmed.ncbi.nlm.nih.gov/30890574/,Illumina HiSeq 3000,Single-cell analysis of homeostatic and regenerative adult skeletal muscle stem cells,"Skeletal muscle stem cells (MuSCs) ensure the formation and homeostasis of skeletal muscle and are responsible for its growth and repair processes. For repair to occur, MuSCs must exit from quiescence, abandon their niche and asymmetrically and symmetrically divide to reconstitute the stem cell pool and give rise to muscle progenitors, respectively. The transcriptomes of pooled MuSCs have provided a rich source of information for describing the genetic programs underlying distinct static cell states; however, bulk microarray and RNA-seq afford only averaged gene expression profiles, which blur the heterogeneity and developmental dynamics of asynchronous MuSC populations. The granularity required to identify distinct cell types, states, and their dynamics can be provided by single-cell analysis.  We were able to compare the transcriptomes of thousands of MuSCs and primary myoblasts isolated from homeostatic or regenerating muscles by single-cell RNA- sequencing. Using computational approaches, we could reconstruct dynamic trajectories and place, in a pseudotemporal manner, the transcriptomes of individual MuSC within these trajectories. This approach allowed for the identification of distinct clusters of MuSCs and primary myoblasts with partially overlapping but distinct transcriptional signatures, as well as the description of metabolic pathways associated with defined MuSC states. Overall design: Single cells suspentions were loaded into 10X Genomics for single cells transcriptome analysis using 10 X Genomics single cells RNAseq kit v2.2"
Dell'Orso 2019,homeostatic_MuSCs_rep1,FACS Isolated Muscle satellite cells,muscle,muscle stem cell,cell,male,NA,MuSCs,NA,TRUE,FALSE,Mus musculus,GSE126834,GSM3614994,3p_v2,fastq,SRR8602277,NA,SRX5402239,SRP186474,SRS4388160,SAMN10977221,NA,NA,"Dell'Orso et al, Development, 2019",10.1242/dev.174177,https://pubmed.ncbi.nlm.nih.gov/30890574/,Illumina HiSeq 3000,Single-cell analysis of homeostatic and regenerative adult skeletal muscle stem cells,"Skeletal muscle stem cells (MuSCs) ensure the formation and homeostasis of skeletal muscle and are responsible for its growth and repair processes. For repair to occur, MuSCs must exit from quiescence, abandon their niche and asymmetrically and symmetrically divide to reconstitute the stem cell pool and give rise to muscle progenitors, respectively. The transcriptomes of pooled MuSCs have provided a rich source of information for describing the genetic programs underlying distinct static cell states; however, bulk microarray and RNA-seq afford only averaged gene expression profiles, which blur the heterogeneity and developmental dynamics of asynchronous MuSC populations. The granularity required to identify distinct cell types, states, and their dynamics can be provided by single-cell analysis.  We were able to compare the transcriptomes of thousands of MuSCs and primary myoblasts isolated from homeostatic or regenerating muscles by single-cell RNA- sequencing. Using computational approaches, we could reconstruct dynamic trajectories and place, in a pseudotemporal manner, the transcriptomes of individual MuSC within these trajectories. This approach allowed for the identification of distinct clusters of MuSCs and primary myoblasts with partially overlapping but distinct transcriptional signatures, as well as the description of metabolic pathways associated with defined MuSC states. Overall design: Single cells suspentions were loaded into 10X Genomics for single cells transcriptome analysis using 10 X Genomics single cells RNAseq kit v2.2"
Dell'Orso 2019,homeostatic_MuSCs_rep2,FACS Isolated Muscle satellite cells,muscle,muscle stem cell,cell,male,NA,MuSCs,NA,TRUE,FALSE,Mus musculus,GSE126834,GSM3614995,3p_v2,fastq,SRR8602278,NA,SRX5402240,SRP186474,SRS4388161,SAMN10977220,NA,NA,"Dell'Orso et al, Development, 2019",10.1242/dev.174177,https://pubmed.ncbi.nlm.nih.gov/30890574/,Illumina HiSeq 3000,Single-cell analysis of homeostatic and regenerative adult skeletal muscle stem cells,"Skeletal muscle stem cells (MuSCs) ensure the formation and homeostasis of skeletal muscle and are responsible for its growth and repair processes. For repair to occur, MuSCs must exit from quiescence, abandon their niche and asymmetrically and symmetrically divide to reconstitute the stem cell pool and give rise to muscle progenitors, respectively. The transcriptomes of pooled MuSCs have provided a rich source of information for describing the genetic programs underlying distinct static cell states; however, bulk microarray and RNA-seq afford only averaged gene expression profiles, which blur the heterogeneity and developmental dynamics of asynchronous MuSC populations. The granularity required to identify distinct cell types, states, and their dynamics can be provided by single-cell analysis.  We were able to compare the transcriptomes of thousands of MuSCs and primary myoblasts isolated from homeostatic or regenerating muscles by single-cell RNA- sequencing. Using computational approaches, we could reconstruct dynamic trajectories and place, in a pseudotemporal manner, the transcriptomes of individual MuSC within these trajectories. This approach allowed for the identification of distinct clusters of MuSCs and primary myoblasts with partially overlapping but distinct transcriptional signatures, as well as the description of metabolic pathways associated with defined MuSC states. Overall design: Single cells suspentions were loaded into 10X Genomics for single cells transcriptome analysis using 10 X Genomics single cells RNAseq kit v2.2"
Dell'Orso 2019,inj_60h_MuSCs_rep1,Post injury (60h) FACS Isolated Muscle satellite cells,muscle,muscle stem cell,cell,female,NA,MuSCs,NA,TRUE,FALSE,Mus musculus,GSE126834,GSM3614996,3p_v2,fastq,SRR8602279,NA,SRX5402241,SRP186474,SRS4388162,SAMN10977218,NA,NA,"Dell'Orso et al, Development, 2019",10.1242/dev.174177,https://pubmed.ncbi.nlm.nih.gov/30890574/,Illumina HiSeq 3000,Single-cell analysis of homeostatic and regenerative adult skeletal muscle stem cells,"Skeletal muscle stem cells (MuSCs) ensure the formation and homeostasis of skeletal muscle and are responsible for its growth and repair processes. For repair to occur, MuSCs must exit from quiescence, abandon their niche and asymmetrically and symmetrically divide to reconstitute the stem cell pool and give rise to muscle progenitors, respectively. The transcriptomes of pooled MuSCs have provided a rich source of information for describing the genetic programs underlying distinct static cell states; however, bulk microarray and RNA-seq afford only averaged gene expression profiles, which blur the heterogeneity and developmental dynamics of asynchronous MuSC populations. The granularity required to identify distinct cell types, states, and their dynamics can be provided by single-cell analysis.  We were able to compare the transcriptomes of thousands of MuSCs and primary myoblasts isolated from homeostatic or regenerating muscles by single-cell RNA- sequencing. Using computational approaches, we could reconstruct dynamic trajectories and place, in a pseudotemporal manner, the transcriptomes of individual MuSC within these trajectories. This approach allowed for the identification of distinct clusters of MuSCs and primary myoblasts with partially overlapping but distinct transcriptional signatures, as well as the description of metabolic pathways associated with defined MuSC states. Overall design: Single cells suspentions were loaded into 10X Genomics for single cells transcriptome analysis using 10 X Genomics single cells RNAseq kit v2.2"
Dell'Orso 2019,inj_60h_MuSCs_rep2,Post injury (60h) FACS Isolated Muscle satellite cells,muscle,muscle stem cell,cell,female,NA,MuSCs,NA,TRUE,FALSE,Mus musculus,GSE126834,GSM3614997,3p_v2,fastq,SRR8602280,NA,SRX5402242,SRP186474,SRS4388163,SAMN10977217,NA,NA,"Dell'Orso et al, Development, 2019",10.1242/dev.174177,https://pubmed.ncbi.nlm.nih.gov/30890574/,Illumina HiSeq 3000,Single-cell analysis of homeostatic and regenerative adult skeletal muscle stem cells,"Skeletal muscle stem cells (MuSCs) ensure the formation and homeostasis of skeletal muscle and are responsible for its growth and repair processes. For repair to occur, MuSCs must exit from quiescence, abandon their niche and asymmetrically and symmetrically divide to reconstitute the stem cell pool and give rise to muscle progenitors, respectively. The transcriptomes of pooled MuSCs have provided a rich source of information for describing the genetic programs underlying distinct static cell states; however, bulk microarray and RNA-seq afford only averaged gene expression profiles, which blur the heterogeneity and developmental dynamics of asynchronous MuSC populations. The granularity required to identify distinct cell types, states, and their dynamics can be provided by single-cell analysis.  We were able to compare the transcriptomes of thousands of MuSCs and primary myoblasts isolated from homeostatic or regenerating muscles by single-cell RNA- sequencing. Using computational approaches, we could reconstruct dynamic trajectories and place, in a pseudotemporal manner, the transcriptomes of individual MuSC within these trajectories. This approach allowed for the identification of distinct clusters of MuSCs and primary myoblasts with partially overlapping but distinct transcriptional signatures, as well as the description of metabolic pathways associated with defined MuSC states. Overall design: Single cells suspentions were loaded into 10X Genomics for single cells transcriptome analysis using 10 X Genomics single cells RNAseq kit v2.2"
Dell'Orso 2019,Primary_MB,FACS Isolated Muscle satellite cells cultured for 4-5 passages on collagen coated plates,muscle,myoblasts,cell,NA,NA,MBs,NA,TRUE,TRUE,Mus musculus,GSE126834,GSM3614998,3p_v2,fastq,SRR8602281,NA,SRX5402243,SRP186474,SRS4388164,SAMN10977216,NA,NA,"Dell'Orso et al, Development, 2019",10.1242/dev.174177,https://pubmed.ncbi.nlm.nih.gov/30890574/,Illumina HiSeq 3000,Single-cell analysis of homeostatic and regenerative adult skeletal muscle stem cells,"Skeletal muscle stem cells (MuSCs) ensure the formation and homeostasis of skeletal muscle and are responsible for its growth and repair processes. For repair to occur, MuSCs must exit from quiescence, abandon their niche and asymmetrically and symmetrically divide to reconstitute the stem cell pool and give rise to muscle progenitors, respectively. The transcriptomes of pooled MuSCs have provided a rich source of information for describing the genetic programs underlying distinct static cell states; however, bulk microarray and RNA-seq afford only averaged gene expression profiles, which blur the heterogeneity and developmental dynamics of asynchronous MuSC populations. The granularity required to identify distinct cell types, states, and their dynamics can be provided by single-cell analysis.  We were able to compare the transcriptomes of thousands of MuSCs and primary myoblasts isolated from homeostatic or regenerating muscles by single-cell RNA- sequencing. Using computational approaches, we could reconstruct dynamic trajectories and place, in a pseudotemporal manner, the transcriptomes of individual MuSC within these trajectories. This approach allowed for the identification of distinct clusters of MuSCs and primary myoblasts with partially overlapping but distinct transcriptional signatures, as well as the description of metabolic pathways associated with defined MuSC states. Overall design: Single cells suspentions were loaded into 10X Genomics for single cells transcriptome analysis using 10 X Genomics single cells RNAseq kit v2.2"
Martins 2020,NMorganoids_D50_1-3,Neuromuscular organoid. Time point: 5 days differentiated. 10 Day 5 NM organoids labelled with two indexes (pooled 5+5).,muscle,organoid,cell,NA,NA,NA,NA,TRUE,TRUE,Homo sapiens,GSE128357,GSM3672209,3p_v2,fastq,SRR8734991,NA,SRX5527772,SRP188565,SRS4494325,SAMN11131652,NA,NA,"Martins et al, Cell Stem Cell, 2020",10.1016/j.stem.2019.12.007,https://pubmed.ncbi.nlm.nih.gov/31956040/,Illumina HiSeq 4000,Self-organizing human trunk 3D neuromuscular organoids,"Neuromuscular networks assemble during early human embryonic development and are essential for the control of body movement. Previous neuromuscular junction modeling efforts using human pluripotent stem cells (hPSCs) generated either spinal cord neurons or skeletal muscles in monolayer culture. Here, we use hPSC-derived axial stem cells, the building blocks of the posterior body, to simultaneously generate spinal cord neurons and skeletal muscle cells that self-organize to generate human neuromuscular organoids (NMOs) that can be maintained in 3D for several months. Single-cell RNA-sequencing of individual organoids revealed reproducibility across experiments and enabled the tracking of the neural and mesodermal differentiation trajectories as organoids developed and matured. NMOs contain functional neuromuscular junctions supported by terminal Schwann cells. They contract and develop central pattern generator-like neuronal circuits. Finally, we successfully use NMOs to recapitulate key aspects of myasthenia gravis pathology, thus highlighting the significant potential of NMOs for modeling neuromuscular diseases in the future. Overall design: We have analyzed single cells from 10 organoids at Day 5. The organoids were separated in two samples (5 pooled organoids each) and labelled with different indexes. In total 5,135 cells were analyzed with a median of 3,333 genes per cell. For Day 50 we analyzed 4 organoids. One sample consisted of one organoid analyzed independently, and the other Day 50 sample consisted of 3 organoids tagged with different indexes. In total 17,294 cells were analyzed with a median of 2,343 genes per cell."
Martins 2020,NMorganoids_D50_4,"Neuromuscular organoid. Time point: 50 days differentiated. Day 50 NM organoids 1, 2 and 3, labelled with different indexes.",muscle,organoid,cell,NA,NA,NA,NA,TRUE,TRUE,Homo sapiens,GSE128357,GSM3672210,3p_v2,fastq,SRR10914868,NA,SRX7582270,SRP188565,SRS6015922,SAMN11131649,NA,NA,"Martins et al, Cell Stem Cell, 2020",10.1016/j.stem.2019.12.007,https://pubmed.ncbi.nlm.nih.gov/31956040/,Illumina HiSeq 4000,Self-organizing human trunk 3D neuromuscular organoids,"Neuromuscular networks assemble during early human embryonic development and are essential for the control of body movement. Previous neuromuscular junction modeling efforts using human pluripotent stem cells (hPSCs) generated either spinal cord neurons or skeletal muscles in monolayer culture. Here, we use hPSC-derived axial stem cells, the building blocks of the posterior body, to simultaneously generate spinal cord neurons and skeletal muscle cells that self-organize to generate human neuromuscular organoids (NMOs) that can be maintained in 3D for several months. Single-cell RNA-sequencing of individual organoids revealed reproducibility across experiments and enabled the tracking of the neural and mesodermal differentiation trajectories as organoids developed and matured. NMOs contain functional neuromuscular junctions supported by terminal Schwann cells. They contract and develop central pattern generator-like neuronal circuits. Finally, we successfully use NMOs to recapitulate key aspects of myasthenia gravis pathology, thus highlighting the significant potential of NMOs for modeling neuromuscular diseases in the future. Overall design: We have analyzed single cells from 10 organoids at Day 5. The organoids were separated in two samples (5 pooled organoids each) and labelled with different indexes. In total 5,135 cells were analyzed with a median of 3,333 genes per cell. For Day 50 we analyzed 4 organoids. One sample consisted of one organoid analyzed independently, and the other Day 50 sample consisted of 3 organoids tagged with different indexes. In total 17,294 cells were analyzed with a median of 2,343 genes per cell."
Martins 2020,NMorganoids_D5,Neuromuscular organoid. Time point: 50 days differentiated.,muscle,organoid,cell,NA,NA,NA,NA,TRUE,TRUE,Homo sapiens,GSE128357,GSM4276650,3p_v2,fastq,SRR8734990,NA,SRX5527771,SRP188565,SRS4494324,SAMN13884430,NA,NA,"Martins et al, Cell Stem Cell, 2020",10.1016/j.stem.2019.12.007,https://pubmed.ncbi.nlm.nih.gov/31956040/,Illumina HiSeq 4000,Self-organizing human trunk 3D neuromuscular organoids,"Neuromuscular networks assemble during early human embryonic development and are essential for the control of body movement. Previous neuromuscular junction modeling efforts using human pluripotent stem cells (hPSCs) generated either spinal cord neurons or skeletal muscles in monolayer culture. Here, we use hPSC-derived axial stem cells, the building blocks of the posterior body, to simultaneously generate spinal cord neurons and skeletal muscle cells that self-organize to generate human neuromuscular organoids (NMOs) that can be maintained in 3D for several months. Single-cell RNA-sequencing of individual organoids revealed reproducibility across experiments and enabled the tracking of the neural and mesodermal differentiation trajectories as organoids developed and matured. NMOs contain functional neuromuscular junctions supported by terminal Schwann cells. They contract and develop central pattern generator-like neuronal circuits. Finally, we successfully use NMOs to recapitulate key aspects of myasthenia gravis pathology, thus highlighting the significant potential of NMOs for modeling neuromuscular diseases in the future. Overall design: We have analyzed single cells from 10 organoids at Day 5. The organoids were separated in two samples (5 pooled organoids each) and labelled with different indexes. In total 5,135 cells were analyzed with a median of 3,333 genes per cell. For Day 50 we analyzed 4 organoids. One sample consisted of one organoid analyzed independently, and the other Day 50 sample consisted of 3 organoids tagged with different indexes. In total 17,294 cells were analyzed with a median of 2,343 genes per cell."
Verma 2019,NoInjury,NA,muscle,NA,cell,male,Pax7tdT:Flk1GFPPax7tdT:Flk1GFP,NA,NA,TRUE,TRUE,Mus musculus,GSE129057,GSM3692304,3p_v2,fastq,SRR8832578,NA,SRX5620858,SRP190027,SRS4566017,SAMN11288434,NA,NA,"Verma et al, bioRxiv, 2021",NA,https://www.biorxiv.org/content/10.1101/2021.08.28.458037v1,Illumina HiSeq 2500,Single-cell skeletal muscle satellite cells and endothelial cells during homeostasis and regeneration,"We performed single cell RNA sequencing on muscle satellite cells (MuSCs) and endothelial cells (ECs) isolated from mouse hind limb muscle from both basal condition and 3-days post CTX injury to look at both quiescent and activated SCs from mice expressing genetic reporters (Pax7CreERT2:R26RtdT:Flk1GFP) by FACS. We could reliably find injury and activated SC as judged by side and forward scatter. We FACS isolated cells from both days separately and spiked in 20% of the ECs into the SCs, and performed single cell RNA-seq for each time point. We performed extensive sequencing averaging more than 300K read/cell. We were able to align the data and overlap the basal and injured cells and able to deconvolve the quiescent SCs from the activated and more differentiated MuSCs, ECs  and contaminating cell types from gene signatures. Overall design: Cells for single cell sequencing were obtained from Pax7tdT:Flk1GFP mice hind limb muscles following enzymatic digestion as previously described (Liu et al., 2015). Dead cells were excluded from the analysis using ZombieNIR (Biolegends, 423105). TdTomato+ and GFP+ cells were sorted individually and then 20% of GFP+ cells were spiked into 80% TdTomato+. We loaded ~5,000 cells into 1 channel of the Chromium system for each of these samples and prepared libraries according to the manufacturer's protocol using version 2.0 chemistry (10x Genomics). Following capture and lysis, we synthesized cDNA and amplified for 12 cycles as per the manufacturer's protocol (10X Genomics). The amplified cDNA was used to construct Illumina sequencing libraries that were each sequenced on one lane of an Illumina HiSeq 2500 machine. We used Cell Ranger 2.0 (10X Genomics) to process raw sequencing data. This pipeline converted Illumina basecall files to fastq format, aligned sequencing reads to the mm10 transcriptome using the STAR aligner, quantified the expression of transcripts in each cell using Chromium barcodes."
Verma 2019,3dCTX,NA,muscle,NA,cell,male,Pax7tdT:Flk1GFPPax7tdT:Flk1GFP,NA,NA,TRUE,TRUE,Mus musculus,GSE129057,GSM3692305,3p_v2,fastq,SRR8832579,NA,SRX5620859,SRP190027,SRS4566019,SAMN11288433,NA,NA,"Verma et al, bioRxiv, 2021",NA,https://www.biorxiv.org/content/10.1101/2021.08.28.458037v1,Illumina HiSeq 2500,Single-cell skeletal muscle satellite cells and endothelial cells during homeostasis and regeneration,"We performed single cell RNA sequencing on muscle satellite cells (MuSCs) and endothelial cells (ECs) isolated from mouse hind limb muscle from both basal condition and 3-days post CTX injury to look at both quiescent and activated SCs from mice expressing genetic reporters (Pax7CreERT2:R26RtdT:Flk1GFP) by FACS. We could reliably find injury and activated SC as judged by side and forward scatter. We FACS isolated cells from both days separately and spiked in 20% of the ECs into the SCs, and performed single cell RNA-seq for each time point. We performed extensive sequencing averaging more than 300K read/cell. We were able to align the data and overlap the basal and injured cells and able to deconvolve the quiescent SCs from the activated and more differentiated MuSCs, ECs  and contaminating cell types from gene signatures. Overall design: Cells for single cell sequencing were obtained from Pax7tdT:Flk1GFP mice hind limb muscles following enzymatic digestion as previously described (Liu et al., 2015). Dead cells were excluded from the analysis using ZombieNIR (Biolegends, 423105). TdTomato+ and GFP+ cells were sorted individually and then 20% of GFP+ cells were spiked into 80% TdTomato+. We loaded ~5,000 cells into 1 channel of the Chromium system for each of these samples and prepared libraries according to the manufacturer's protocol using version 2.0 chemistry (10x Genomics). Following capture and lysis, we synthesized cDNA and amplified for 12 cycles as per the manufacturer's protocol (10X Genomics). The amplified cDNA was used to construct Illumina sequencing libraries that were each sequenced on one lane of an Illumina HiSeq 2500 machine. We used Cell Ranger 2.0 (10X Genomics) to process raw sequencing data. This pipeline converted Illumina basecall files to fastq format, aligned sequencing reads to the mm10 transcriptome using the STAR aligner, quantified the expression of transcripts in each cell using Chromium barcodes."
Rubenstein 2020,Muscle_1,NA,muscle,vastus lateralis,cell,NA,NA,NA,NA,TRUE,TRUE,Homo sapiens,GSE130646,GSM3746212,3p_v2,fastq,SRR9018531;SRR9018532,NA,SRX5796651,SRP195589,SRS4727851,SAMN11567249,NA,NA,"Rubenstein et al, Sci Rep, 2021",10.1038/s41598-019-57110-6,https://pubmed.ncbi.nlm.nih.gov/31937892/,Illumina HiSeq 2500,Single-cell transcriptional profiles in human skeletal muscle,"Skeletal muscle is a complex heterogeneous tissue comprised of diverse muscle fiber and non-fiber cell types that, in addition to movement, influences other systems such as immunity, metabolism and cognition. We investigated gene expression patterns of resident human skeletal muscle cells using single-cell RNA-seq of dissections from vastus lateralis. We generate transcriptome profiles of 11 mononuclear human skeletal muscle mononuclear cell types, including immune, endothelial, pericyte and satellite cells.  We delineate two fibro-adipogenic progenitor cell subtypes that may contribute to heterotopic ossification and muscular dystrophy fibrosis under pathological conditions. An important application of cell type signatures is for computational deconvolution of cell type specific changes using data from bulk transcriptome experiments. Analysis of transcriptome data from a 12 week resistance training study using the human skeletal muscle cell-type signatures revealed significant changes in specific mononuclear cell-type proportions related to age, sex, acute exercise and training. This characterization of human skeletal muscle cell subtypes will resolve cell type specific changes in large-scale physical activity muscle transcriptome studies and can further the understanding of the diverse effects of exercise and the pathophysiology of muscle disease. Overall design: Single cell RNA sequencing was conducted on four samples of mononuclear muscle cells isolated from a single vastus lateralis biopsy."
Rubenstein 2020,Muscle_2,NA,muscle,vastus lateralis,cell,NA,NA,NA,NA,TRUE,TRUE,Homo sapiens,GSE130646,GSM3746213,3p_v2,fastq,SRR9018533;SRR9018534,NA,SRX5796652,SRP195589,SRS4727852,SAMN11567248,NA,NA,"Rubenstein et al, Sci Rep, 2021",10.1038/s41598-019-57110-6,https://pubmed.ncbi.nlm.nih.gov/31937892/,Illumina HiSeq 2500,Single-cell transcriptional profiles in human skeletal muscle,"Skeletal muscle is a complex heterogeneous tissue comprised of diverse muscle fiber and non-fiber cell types that, in addition to movement, influences other systems such as immunity, metabolism and cognition. We investigated gene expression patterns of resident human skeletal muscle cells using single-cell RNA-seq of dissections from vastus lateralis. We generate transcriptome profiles of 11 mononuclear human skeletal muscle mononuclear cell types, including immune, endothelial, pericyte and satellite cells.  We delineate two fibro-adipogenic progenitor cell subtypes that may contribute to heterotopic ossification and muscular dystrophy fibrosis under pathological conditions. An important application of cell type signatures is for computational deconvolution of cell type specific changes using data from bulk transcriptome experiments. Analysis of transcriptome data from a 12 week resistance training study using the human skeletal muscle cell-type signatures revealed significant changes in specific mononuclear cell-type proportions related to age, sex, acute exercise and training. This characterization of human skeletal muscle cell subtypes will resolve cell type specific changes in large-scale physical activity muscle transcriptome studies and can further the understanding of the diverse effects of exercise and the pathophysiology of muscle disease. Overall design: Single cell RNA sequencing was conducted on four samples of mononuclear muscle cells isolated from a single vastus lateralis biopsy."
Rubenstein 2020,Muscle_3,NA,muscle,vastus lateralis,cell,NA,NA,NA,NA,TRUE,TRUE,Homo sapiens,GSE130646,GSM3746214,3p_v2,fastq,SRR9018527;SRR9018528,NA,SRX5796653,SRP195589,SRS4727853,SAMN11567247,NA,NA,"Rubenstein et al, Sci Rep, 2021",10.1038/s41598-019-57110-6,https://pubmed.ncbi.nlm.nih.gov/31937892/,Illumina HiSeq 2500,Single-cell transcriptional profiles in human skeletal muscle,"Skeletal muscle is a complex heterogeneous tissue comprised of diverse muscle fiber and non-fiber cell types that, in addition to movement, influences other systems such as immunity, metabolism and cognition. We investigated gene expression patterns of resident human skeletal muscle cells using single-cell RNA-seq of dissections from vastus lateralis. We generate transcriptome profiles of 11 mononuclear human skeletal muscle mononuclear cell types, including immune, endothelial, pericyte and satellite cells.  We delineate two fibro-adipogenic progenitor cell subtypes that may contribute to heterotopic ossification and muscular dystrophy fibrosis under pathological conditions. An important application of cell type signatures is for computational deconvolution of cell type specific changes using data from bulk transcriptome experiments. Analysis of transcriptome data from a 12 week resistance training study using the human skeletal muscle cell-type signatures revealed significant changes in specific mononuclear cell-type proportions related to age, sex, acute exercise and training. This characterization of human skeletal muscle cell subtypes will resolve cell type specific changes in large-scale physical activity muscle transcriptome studies and can further the understanding of the diverse effects of exercise and the pathophysiology of muscle disease. Overall design: Single cell RNA sequencing was conducted on four samples of mononuclear muscle cells isolated from a single vastus lateralis biopsy."
Rubenstein 2020,Muscle_4,NA,muscle,vastus lateralis,cell,NA,NA,NA,NA,TRUE,TRUE,Homo sapiens,GSE130646,GSM3746215,3p_v2,fastq,SRR9018529;SRR9018530,NA,SRX5796654,SRP195589,SRS4727854,SAMN11567246,NA,NA,"Rubenstein et al, Sci Rep, 2021",10.1038/s41598-019-57110-6,https://pubmed.ncbi.nlm.nih.gov/31937892/,Illumina HiSeq 2500,Single-cell transcriptional profiles in human skeletal muscle,"Skeletal muscle is a complex heterogeneous tissue comprised of diverse muscle fiber and non-fiber cell types that, in addition to movement, influences other systems such as immunity, metabolism and cognition. We investigated gene expression patterns of resident human skeletal muscle cells using single-cell RNA-seq of dissections from vastus lateralis. We generate transcriptome profiles of 11 mononuclear human skeletal muscle mononuclear cell types, including immune, endothelial, pericyte and satellite cells.  We delineate two fibro-adipogenic progenitor cell subtypes that may contribute to heterotopic ossification and muscular dystrophy fibrosis under pathological conditions. An important application of cell type signatures is for computational deconvolution of cell type specific changes using data from bulk transcriptome experiments. Analysis of transcriptome data from a 12 week resistance training study using the human skeletal muscle cell-type signatures revealed significant changes in specific mononuclear cell-type proportions related to age, sex, acute exercise and training. This characterization of human skeletal muscle cell subtypes will resolve cell type specific changes in large-scale physical activity muscle transcriptome studies and can further the understanding of the diverse effects of exercise and the pathophysiology of muscle disease. Overall design: Single cell RNA sequencing was conducted on four samples of mononuclear muscle cells isolated from a single vastus lateralis biopsy."
Tabula Muris Senis 2020,MACA_18m_F_MUSCLE_50_pre_sort,NA,muscle,hindlimb,cell,female,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE132042,MACA_18m_F_MUSCLE_50_pre_sort,3p_v2,aws,NA,https://czb-tabula-muris-senis.s3.us-west-2.amazonaws.com/10x/FASTQs/MACA_18m_F_MUSCLE_50_pre_sort/MACA_18m_F_MUSCLE_50_pre_sort_S13_L001_R1_001.fastq.gz https://czb-tabula-muris-senis.s3.us-west-2.amazonaws.com/10x/FASTQs/MACA_18m_F_MUSCLE_50_pre_sort/MACA_18m_F_MUSCLE_50_pre_sort_S13_L002_R1_001.fastq.gz https://czb-tabula-muris-senis.s3.us-west-2.amazonaws.com/10x/FASTQs/MACA_18m_F_MUSCLE_50_pre_sort/MACA_18m_F_MUSCLE_50_pre_sort_S13_L001_R2_001.fastq.gz https://czb-tabula-muris-senis.s3.us-west-2.amazonaws.com/10x/FASTQs/MACA_18m_F_MUSCLE_50_pre_sort/MACA_18m_F_MUSCLE_50_pre_sort_S13_L002_R2_001.fastq.gz,NA,NA,NA,NA,NA,NA,"Tabula Muris Senis, Nature, 2020",10.1038/s41586-020-2496-1,https://pubmed.ncbi.nlm.nih.gov/32669714/,NA,NA,NA
Tabula Muris Senis 2020,MACA_18m_F_MUSCLE_51,NA,muscle,hindlimb,cell,female,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE132042,MACA_18m_F_MUSCLE_51,3p_v2,aws,NA,https://czb-tabula-muris-senis.s3.us-west-2.amazonaws.com/10x/FASTQs/MACA_18m_F_MUSCLE_51_pre_sort/MACA_18m_F_MUSCLE_51_pre_sort_S14_L001_R1_001.fastq.gz https://czb-tabula-muris-senis.s3.us-west-2.amazonaws.com/10x/FASTQs/MACA_18m_F_MUSCLE_51_pre_sort/MACA_18m_F_MUSCLE_51_pre_sort_S14_L002_R1_001.fastq.gz https://czb-tabula-muris-senis.s3.us-west-2.amazonaws.com/10x/FASTQs/MACA_18m_F_MUSCLE_51_pre_sort/MACA_18m_F_MUSCLE_51_pre_sort_S14_L001_R2_001.fastq.gz https://czb-tabula-muris-senis.s3.us-west-2.amazonaws.com/10x/FASTQs/MACA_18m_F_MUSCLE_51_pre_sort/MACA_18m_F_MUSCLE_51_pre_sort_S14_L002_R2_001.fastq.gz,NA,NA,NA,NA,NA,NA,"Tabula Muris Senis, Nature, 2020",10.1038/s41586-020-2496-1,https://pubmed.ncbi.nlm.nih.gov/32669714/,NA,NA,NA
Tabula Muris Senis 2020,MACA_18m_M_MUSCLE_52,NA,muscle,hindlimb,cell,male,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE132042,MACA_18m_M_MUSCLE_52,3p_v2,aws,NA,https://czb-tabula-muris-senis.s3.us-west-2.amazonaws.com/10x/FASTQs/MACA_18m_M_MUSCLE_52/MACA_18m_M_MUSCLE_52_S7_L001_R1_001.fastq.gz https://czb-tabula-muris-senis.s3.us-west-2.amazonaws.com/10x/FASTQs/MACA_18m_M_MUSCLE_52/MACA_18m_M_MUSCLE_52_S7_L002_R1_001.fastq.gz https://czb-tabula-muris-senis.s3.us-west-2.amazonaws.com/10x/FASTQs/MACA_18m_M_MUSCLE_52/MACA_18m_M_MUSCLE_52_S7_L001_R2_001.fastq.gz https://czb-tabula-muris-senis.s3.us-west-2.amazonaws.com/10x/FASTQs/MACA_18m_M_MUSCLE_52/MACA_18m_M_MUSCLE_52_S7_L002_R2_001.fastq.gz,NA,NA,NA,NA,NA,NA,"Tabula Muris Senis, Nature, 2020",10.1038/s41586-020-2496-1,https://pubmed.ncbi.nlm.nih.gov/32669714/,NA,NA,NA
Tabula Muris Senis 2020,MACA_18m_M_MUSCLE_53,NA,muscle,hindlimb,cell,male,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE132042,MACA_18m_M_MUSCLE_53,3p_v2,aws,NA,https://czb-tabula-muris-senis.s3.us-west-2.amazonaws.com/10x/FASTQs/MACA_18m_M_MUSCLE_53/MACA_18m_M_MUSCLE_53_S8_L001_R1_001.fastq.gz https://czb-tabula-muris-senis.s3.us-west-2.amazonaws.com/10x/FASTQs/MACA_18m_M_MUSCLE_53/MACA_18m_M_MUSCLE_53_S8_L002_R1_001.fastq.gz https://czb-tabula-muris-senis.s3.us-west-2.amazonaws.com/10x/FASTQs/MACA_18m_M_MUSCLE_53/MACA_18m_M_MUSCLE_53_S8_L001_R2_001.fastq.gz https://czb-tabula-muris-senis.s3.us-west-2.amazonaws.com/10x/FASTQs/MACA_18m_M_MUSCLE_53/MACA_18m_M_MUSCLE_53_S8_L002_R2_001.fastq.gz,NA,NA,NA,NA,NA,NA,"Tabula Muris Senis, Nature, 2020",10.1038/s41586-020-2496-1,https://pubmed.ncbi.nlm.nih.gov/32669714/,NA,NA,NA
Tabula Muris Senis 2020,MACA_21m_F_MUSCLE_54,NA,muscle,hindlimb,cell,female,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE132042,MACA_21m_F_MUSCLE_54,3p_v2,aws,NA,https://czb-tabula-muris-senis.s3.us-west-2.amazonaws.com/10x/FASTQs/MACA_21m_F_MUSCLE_54/MACA_21m_F_MUSCLE_54_S5_L001_R1_001.fastq.gz https://czb-tabula-muris-senis.s3.us-west-2.amazonaws.com/10x/FASTQs/MACA_21m_F_MUSCLE_54/MACA_21m_F_MUSCLE_54_S5_L002_R1_001.fastq.gz https://czb-tabula-muris-senis.s3.us-west-2.amazonaws.com/10x/FASTQs/MACA_21m_F_MUSCLE_54/MACA_21m_F_MUSCLE_54_S5_L001_R2_001.fastq.gz https://czb-tabula-muris-senis.s3.us-west-2.amazonaws.com/10x/FASTQs/MACA_21m_F_MUSCLE_54/MACA_21m_F_MUSCLE_54_S5_L002_R2_001.fastq.gz,NA,NA,NA,NA,NA,NA,"Tabula Muris Senis, Nature, 2020",10.1038/s41586-020-2496-1,https://pubmed.ncbi.nlm.nih.gov/32669714/,NA,NA,NA
Tabula Muris Senis 2020,MACA_21m_F_MUSCLE_55,NA,muscle,hindlimb,cell,female,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE132042,MACA_21m_F_MUSCLE_55,3p_v2,aws,NA,https://czb-tabula-muris-senis.s3.us-west-2.amazonaws.com/10x/FASTQs/MACA_21m_F_MUSCLE_55/MACA_21m_F_MUSCLE_55_S6_L001_R1_001.fastq.gz https://czb-tabula-muris-senis.s3.us-west-2.amazonaws.com/10x/FASTQs/MACA_21m_F_MUSCLE_55/MACA_21m_F_MUSCLE_55_S6_L002_R1_001.fastq.gz https://czb-tabula-muris-senis.s3.us-west-2.amazonaws.com/10x/FASTQs/MACA_21m_F_MUSCLE_55/MACA_21m_F_MUSCLE_55_S6_L001_R2_001.fastq.gz https://czb-tabula-muris-senis.s3.us-west-2.amazonaws.com/10x/FASTQs/MACA_21m_F_MUSCLE_55/MACA_21m_F_MUSCLE_55_S6_L002_R2_001.fastq.gz,NA,NA,NA,NA,NA,NA,"Tabula Muris Senis, Nature, 2020",10.1038/s41586-020-2496-1,https://pubmed.ncbi.nlm.nih.gov/32669714/,NA,NA,NA
Tabula Muris Senis 2020,MACA_24m_M_MUSCLE_58,NA,muscle,hindlimb,cell,male,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE132042,MACA_24m_M_MUSCLE_58,3p_v2,aws,NA,https://czb-tabula-muris-senis.s3.us-west-2.amazonaws.com/10x/FASTQs/MACA_24m_M_MUSCLE_58/MACA_24m_M_MUSCLE_58_S7_L001_R1_001.fastq.gz https://czb-tabula-muris-senis.s3.us-west-2.amazonaws.com/10x/FASTQs/MACA_24m_M_MUSCLE_58/MACA_24m_M_MUSCLE_58_S7_L002_R1_001.fastq.gz https://czb-tabula-muris-senis.s3.us-west-2.amazonaws.com/10x/FASTQs/MACA_24m_M_MUSCLE_58/MACA_24m_M_MUSCLE_58_S7_L001_R2_001.fastq.gz https://czb-tabula-muris-senis.s3.us-west-2.amazonaws.com/10x/FASTQs/MACA_24m_M_MUSCLE_58/MACA_24m_M_MUSCLE_58_S7_L002_R2_001.fastq.gz,NA,NA,NA,NA,NA,NA,"Tabula Muris Senis, Nature, 2020",10.1038/s41586-020-2496-1,https://pubmed.ncbi.nlm.nih.gov/32669714/,NA,NA,NA
Tabula Muris Senis 2020,MACA_24m_M_MUSCLE_59,NA,muscle,hindlimb,cell,male,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE132042,MACA_24m_M_MUSCLE_59,3p_v2,aws,NA,https://czb-tabula-muris-senis.s3.us-west-2.amazonaws.com/10x/FASTQs/MACA_24m_M_MUSCLE_59/MACA_24m_M_MUSCLE_59_S8_L001_R1_001.fastq.gz https://czb-tabula-muris-senis.s3.us-west-2.amazonaws.com/10x/FASTQs/MACA_24m_M_MUSCLE_59/MACA_24m_M_MUSCLE_59_S8_L002_R1_001.fastq.gz https://czb-tabula-muris-senis.s3.us-west-2.amazonaws.com/10x/FASTQs/MACA_24m_M_MUSCLE_59/MACA_24m_M_MUSCLE_59_S8_L001_R2_001.fastq.gz https://czb-tabula-muris-senis.s3.us-west-2.amazonaws.com/10x/FASTQs/MACA_24m_M_MUSCLE_59/MACA_24m_M_MUSCLE_59_S8_L002_R2_001.fastq.gz,NA,NA,NA,NA,NA,NA,"Tabula Muris Senis, Nature, 2020",10.1038/s41586-020-2496-1,https://pubmed.ncbi.nlm.nih.gov/32669714/,NA,NA,NA
Tabula Muris Senis 2020,MACA_24m_M_MUSCLE_60,NA,muscle,hindlimb,cell,male,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE132042,MACA_24m_M_MUSCLE_60,3p_v2,aws,NA,https://czb-tabula-muris-senis.s3.us-west-2.amazonaws.com/10x/FASTQs/MACA_24m_M_MUSCLE_60/MACA_24m_M_MUSCLE_60_S13_L001_R1_001.fastq.gz https://czb-tabula-muris-senis.s3.us-west-2.amazonaws.com/10x/FASTQs/MACA_24m_M_MUSCLE_60/MACA_24m_M_MUSCLE_60_S13_L002_R1_001.fastq.gz https://czb-tabula-muris-senis.s3.us-west-2.amazonaws.com/10x/FASTQs/MACA_24m_M_MUSCLE_60/MACA_24m_M_MUSCLE_60_S13_L001_R2_001.fastq.gz https://czb-tabula-muris-senis.s3.us-west-2.amazonaws.com/10x/FASTQs/MACA_24m_M_MUSCLE_60/MACA_24m_M_MUSCLE_60_S13_L002_R2_001.fastq.gz,NA,NA,NA,NA,NA,NA,"Tabula Muris Senis, Nature, 2020",10.1038/s41586-020-2496-1,https://pubmed.ncbi.nlm.nih.gov/32669714/,NA,NA,NA
Tabula Muris Senis 2020,MACA_24m_M_MUSCLE_61,NA,muscle,hindlimb,cell,male,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE132042,MACA_24m_M_MUSCLE_61,3p_v2,aws,NA,https://czb-tabula-muris-senis.s3.us-west-2.amazonaws.com/10x/FASTQs/MACA_24m_M_MUSCLE_61/MACA_24m_M_MUSCLE_61_S14_L001_R1_001.fastq.gz https://czb-tabula-muris-senis.s3.us-west-2.amazonaws.com/10x/FASTQs/MACA_24m_M_MUSCLE_61/MACA_24m_M_MUSCLE_61_S14_L002_R1_001.fastq.gz https://czb-tabula-muris-senis.s3.us-west-2.amazonaws.com/10x/FASTQs/MACA_24m_M_MUSCLE_61/MACA_24m_M_MUSCLE_61_S14_L001_R2_001.fastq.gz https://czb-tabula-muris-senis.s3.us-west-2.amazonaws.com/10x/FASTQs/MACA_24m_M_MUSCLE_61/MACA_24m_M_MUSCLE_61_S14_L002_R2_001.fastq.gz,NA,NA,NA,NA,NA,NA,"Tabula Muris Senis, Nature, 2020",10.1038/s41586-020-2496-1,https://pubmed.ncbi.nlm.nih.gov/32669714/,NA,NA,NA
Tabula Muris Senis 2020,MACA_24m_M_TONGUE_58,NA,muscle,tongue,cell,male,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE132042,MACA_24m_M_TONGUE_58,3p_v2,aws,NA,https://czb-tabula-muris-senis.s3.us-west-2.amazonaws.com/10x/FASTQs/MACA_24m_M_TONGUE_58/MACA_24m_M_TONGUE_58_S3_L001_R1_001.fastq.gz;https://czb-tabula-muris-senis.s3.us-west-2.amazonaws.com/10x/FASTQs/MACA_24m_M_TONGUE_58/MACA_24m_M_TONGUE_58_S3_L001_R2_001.fastq.gz;https://czb-tabula-muris-senis.s3.us-west-2.amazonaws.com/10x/FASTQs/MACA_24m_M_TONGUE_58/MACA_24m_M_TONGUE_58_S3_L002_R1_001.fastq.gz;https://czb-tabula-muris-senis.s3.us-west-2.amazonaws.com/10x/FASTQs/MACA_24m_M_TONGUE_58/MACA_24m_M_TONGUE_58_S3_L002_R2_001.fastq.gz,NA,NA,NA,NA,NA,NA,"Tabula Muris Senis, Nature, 2020",10.1038/s41586-020-2496-1,https://pubmed.ncbi.nlm.nih.gov/32669714/,NA,NA,NA
Tabula Muris Senis 2020,MACA_24m_M_TONGUE_59,NA,muscle,tongue,cell,male,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE132042,MACA_24m_M_TONGUE_59,3p_v2,aws,NA,https://czb-tabula-muris-senis.s3.us-west-2.amazonaws.com/10x/FASTQs/MACA_24m_M_TONGUE_59/MACA_24m_M_TONGUE_59_S4_L001_R1_001.fastq.gz;https://czb-tabula-muris-senis.s3.us-west-2.amazonaws.com/10x/FASTQs/MACA_24m_M_TONGUE_59/MACA_24m_M_TONGUE_59_S4_L001_R2_001.fastq.gz;https://czb-tabula-muris-senis.s3.us-west-2.amazonaws.com/10x/FASTQs/MACA_24m_M_TONGUE_59/MACA_24m_M_TONGUE_59_S4_L002_R1_001.fastq.gz;https://czb-tabula-muris-senis.s3.us-west-2.amazonaws.com/10x/FASTQs/MACA_24m_M_TONGUE_59/MACA_24m_M_TONGUE_59_S4_L002_R2_001.fastq.gz,NA,NA,NA,NA,NA,NA,"Tabula Muris Senis, Nature, 2020",10.1038/s41586-020-2496-1,https://pubmed.ncbi.nlm.nih.gov/32669714/,NA,NA,NA
Tabula Muris Senis 2020,MACA_24m_M_TONGUE_60,NA,muscle,tongue,cell,male,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE132042,MACA_24m_M_TONGUE_60,3p_v2,aws,NA,https://czb-tabula-muris-senis.s3.us-west-2.amazonaws.com/10x/FASTQs/MACA_24m_M_TONGUE_60/MACA_24m_M_TONGUE_60_S11_L001_R1_001.fastq.gz;https://czb-tabula-muris-senis.s3.us-west-2.amazonaws.com/10x/FASTQs/MACA_24m_M_TONGUE_60/MACA_24m_M_TONGUE_60_S11_L001_R2_001.fastq.gz;https://czb-tabula-muris-senis.s3.us-west-2.amazonaws.com/10x/FASTQs/MACA_24m_M_TONGUE_60/MACA_24m_M_TONGUE_60_S11_L002_R1_001.fastq.gz;https://czb-tabula-muris-senis.s3.us-west-2.amazonaws.com/10x/FASTQs/MACA_24m_M_TONGUE_60/MACA_24m_M_TONGUE_60_S11_L002_R2_001.fastq.gz,NA,NA,NA,NA,NA,NA,"Tabula Muris Senis, Nature, 2020",10.1038/s41586-020-2496-1,https://pubmed.ncbi.nlm.nih.gov/32669714/,NA,NA,NA
Li 2019,Pax7Hi,NA,muscle,hindlimb,cell,female,C56BL/6J:Pax7-nGFP Tg,Pax7-GFP,NA,TRUE,FALSE,Mus musculus,GSE134540,GSM3955372,3p_v2,fastq,SRR9715805;SRR9715806;SRR9715807;SRR9715808,NA,SRX6473682,SRP215427,SRS5122664,NA,NA,NA,"Li et al, The EMBO Journal, 2019",10.15252/embj.2019102154,https://pubmed.ncbi.nlm.nih.gov/31736098/,Illumina NovaSeq 6000,Muscle-secreted G-CSF as a metabolic niche factor ameliorates loss of muscle stem cell in aged mice (scRNA-seq),"Function and number of muscle stem cells (satellite cells, SCs) declines with muscle aging. Although SCs are heterogeneous and different subpopulations have been identified, it remains unknown if a specific subpopulation of muscle SCs selectively decreases during aging. Here, we find Pax7Hi cells are dramatically reduced in aged mice and this aged-dependent loss of Pax7Hi cells is metabolically mediated by myofiber-secreted granulocyte-colony stimulating factor G-CSF as the Pax7Hi SCs are replenished by exercise-induced G-CSF in aged mice. Mechanistically, we show that transcription of G-CSF (Csf3) gene in myofibers is regulated by MyoD in a metabolism-dependent manner and the myofibers-secreted G-CSF acts as a metabolic niche factor required for establishing and maintaining the Pax7Hi SC subpopulation in adult and physiological aged mice by promoting the asymmetric division of Pax7Hi and Pax7Mi SCs. Together, our findings uncover a metabolic niche role of muscle metabolism in regulating Pax7 SC heterogeneity in mice. Overall design: Three subpopulations of satellite cells (Pax7Hi, Pax7Mi and Pax7Lo) were isolated by FACS based on levels of GFP (Pax7) from tibialis anterior muscle of Pax7-nGFP transgenic mice and subjected to single cell RNA sequencing (scRNA-Seq)."
Li 2019,Pax7Mi,NA,muscle,hindlimb,cell,female,C56BL/6J:Pax7-nGFP Tg,Pax7-GFP,NA,TRUE,FALSE,Mus musculus,GSE134540,GSM3955373,3p_v2,fastq,SRR9715810;SRR9715811;SRR9715812;SRR9715813;SRR9715814;SRR9715815;SRR9715816,NA,SRX6473683,SRP215427,SRS5122665,NA,NA,NA,"Li et al, The EMBO Journal, 2019",10.15252/embj.2019102154,https://pubmed.ncbi.nlm.nih.gov/31736098/,Illumina NovaSeq 6000,Muscle-secreted G-CSF as a metabolic niche factor ameliorates loss of muscle stem cell in aged mice (scRNA-seq),"Function and number of muscle stem cells (satellite cells, SCs) declines with muscle aging. Although SCs are heterogeneous and different subpopulations have been identified, it remains unknown if a specific subpopulation of muscle SCs selectively decreases during aging. Here, we find Pax7Hi cells are dramatically reduced in aged mice and this aged-dependent loss of Pax7Hi cells is metabolically mediated by myofiber-secreted granulocyte-colony stimulating factor G-CSF as the Pax7Hi SCs are replenished by exercise-induced G-CSF in aged mice. Mechanistically, we show that transcription of G-CSF (Csf3) gene in myofibers is regulated by MyoD in a metabolism-dependent manner and the myofibers-secreted G-CSF acts as a metabolic niche factor required for establishing and maintaining the Pax7Hi SC subpopulation in adult and physiological aged mice by promoting the asymmetric division of Pax7Hi and Pax7Mi SCs. Together, our findings uncover a metabolic niche role of muscle metabolism in regulating Pax7 SC heterogeneity in mice. Overall design: Three subpopulations of satellite cells (Pax7Hi, Pax7Mi and Pax7Lo) were isolated by FACS based on levels of GFP (Pax7) from tibialis anterior muscle of Pax7-nGFP transgenic mice and subjected to single cell RNA sequencing (scRNA-Seq)."
Li 2019,Pax7Lo,NA,muscle,hindlimb,cell,female,C56BL/6J:Pax7-nGFP Tg,Pax7-GFP,NA,TRUE,FALSE,Mus musculus,GSE134540,GSM3955374,3p_v2,fastq,SRR9715817;SRR9715818;SRR9715819;SRR9715820;SRR9715821;SRR9715822;SRR9715823;SRR9715824,NA,SRX6473684,SRP215427,SRS5122666,NA,NA,NA,"Li et al, The EMBO Journal, 2019",10.15252/embj.2019102154,https://pubmed.ncbi.nlm.nih.gov/31736098/,Illumina NovaSeq 6000,Muscle-secreted G-CSF as a metabolic niche factor ameliorates loss of muscle stem cell in aged mice (scRNA-seq),"Function and number of muscle stem cells (satellite cells, SCs) declines with muscle aging. Although SCs are heterogeneous and different subpopulations have been identified, it remains unknown if a specific subpopulation of muscle SCs selectively decreases during aging. Here, we find Pax7Hi cells are dramatically reduced in aged mice and this aged-dependent loss of Pax7Hi cells is metabolically mediated by myofiber-secreted granulocyte-colony stimulating factor G-CSF as the Pax7Hi SCs are replenished by exercise-induced G-CSF in aged mice. Mechanistically, we show that transcription of G-CSF (Csf3) gene in myofibers is regulated by MyoD in a metabolism-dependent manner and the myofibers-secreted G-CSF acts as a metabolic niche factor required for establishing and maintaining the Pax7Hi SC subpopulation in adult and physiological aged mice by promoting the asymmetric division of Pax7Hi and Pax7Mi SCs. Together, our findings uncover a metabolic niche role of muscle metabolism in regulating Pax7 SC heterogeneity in mice. Overall design: Three subpopulations of satellite cells (Pax7Hi, Pax7Mi and Pax7Lo) were isolated by FACS based on levels of GFP (Pax7) from tibialis anterior muscle of Pax7-nGFP transgenic mice and subjected to single cell RNA sequencing (scRNA-Seq)."
Ma 2020,Muscle-M-Y,NA,muscle,NA,NA,NA,NA,NA,NA,TRUE,TRUE,Rattus norvegicus,GSE137869,GSM4331858,3p_v2,fastq,SRR11143068;SRR11143069;SRR11143070;SRR11143071,NA,SRX7779412,SRP222987,SRS6195952,SAMN14162462,NA,NA,"Ma et al, Cell, 2020",10.1016/j.cell.2020.02.008,https://pubmed.ncbi.nlm.nih.gov/32109414/,Illumina HiSeq 2000,Caloric restriction reprograms the single-cell transcriptional landscape of Rattus norvegicus aging,"Aging causes a functional decline in tissues throughout the body that may be delayed by caloric restriction (CR). However, the cellular profiles and signatures of aging, as well as those ameliorated by CR, remain unclear. Here, we built comprehensive single-cell and single-nucleus transcriptomic atlases across various rat tissues undergoing aging and CR. CR attenuated aging-related changes in cell type composition, gene expression, and core transcriptional regulatory networks. Immune cells were increased during aging, and CR favorably reversed the aging-disturbed immune ecosystem. Computational prediction revealed that the abnormal cell-cell communication patterns observed during aging, including the excessive proinflammatory ligand-receptor interplay, were reversed by CR. Our work provides  multi-tissue single-cell transcriptional landscapes associated with aging and CR in a mammal, enhances our understanding of the robustness of CR as a geroprotective intervention, and uncovers how metabolic intervention can act upon the immune system to modify the process of aging. Overall design: Single-cell and single-nucleus RNA sequencing for 210K cells/nuclei from 9 kinds of tissues of rats"
Ma 2020,Muscle-M-O,NA,muscle,NA,NA,NA,NA,NA,NA,TRUE,TRUE,Rattus norvegicus,GSE137869,GSM4331859,3p_v2,fastq,SRR11143072;SRR11143073;SRR11143074;SRR11143075,NA,SRX7779413,SRP222987,SRS6195954,SAMN14162461,NA,NA,"Ma et al, Cell, 2020",10.1016/j.cell.2020.02.008,https://pubmed.ncbi.nlm.nih.gov/32109414/,Illumina HiSeq 2000,Caloric restriction reprograms the single-cell transcriptional landscape of Rattus norvegicus aging,"Aging causes a functional decline in tissues throughout the body that may be delayed by caloric restriction (CR). However, the cellular profiles and signatures of aging, as well as those ameliorated by CR, remain unclear. Here, we built comprehensive single-cell and single-nucleus transcriptomic atlases across various rat tissues undergoing aging and CR. CR attenuated aging-related changes in cell type composition, gene expression, and core transcriptional regulatory networks. Immune cells were increased during aging, and CR favorably reversed the aging-disturbed immune ecosystem. Computational prediction revealed that the abnormal cell-cell communication patterns observed during aging, including the excessive proinflammatory ligand-receptor interplay, were reversed by CR. Our work provides  multi-tissue single-cell transcriptional landscapes associated with aging and CR in a mammal, enhances our understanding of the robustness of CR as a geroprotective intervention, and uncovers how metabolic intervention can act upon the immune system to modify the process of aging. Overall design: Single-cell and single-nucleus RNA sequencing for 210K cells/nuclei from 9 kinds of tissues of rats"
Ma 2020,Muscle-M-CR,NA,muscle,NA,NA,NA,NA,NA,NA,TRUE,TRUE,Rattus norvegicus,GSE137869,GSM4331860,3p_v2,fastq,SRR11143076;SRR11143077;SRR11143078;SRR11143079,NA,SRX7779414,SRP222987,SRS6195953,SAMN14162460,NA,NA,"Ma et al, Cell, 2020",10.1016/j.cell.2020.02.008,https://pubmed.ncbi.nlm.nih.gov/32109414/,Illumina HiSeq 2000,Caloric restriction reprograms the single-cell transcriptional landscape of Rattus norvegicus aging,"Aging causes a functional decline in tissues throughout the body that may be delayed by caloric restriction (CR). However, the cellular profiles and signatures of aging, as well as those ameliorated by CR, remain unclear. Here, we built comprehensive single-cell and single-nucleus transcriptomic atlases across various rat tissues undergoing aging and CR. CR attenuated aging-related changes in cell type composition, gene expression, and core transcriptional regulatory networks. Immune cells were increased during aging, and CR favorably reversed the aging-disturbed immune ecosystem. Computational prediction revealed that the abnormal cell-cell communication patterns observed during aging, including the excessive proinflammatory ligand-receptor interplay, were reversed by CR. Our work provides  multi-tissue single-cell transcriptional landscapes associated with aging and CR in a mammal, enhances our understanding of the robustness of CR as a geroprotective intervention, and uncovers how metabolic intervention can act upon the immune system to modify the process of aging. Overall design: Single-cell and single-nucleus RNA sequencing for 210K cells/nuclei from 9 kinds of tissues of rats"
Ma 2020,Muscle-F-Y,NA,muscle,NA,NA,NA,NA,NA,NA,TRUE,TRUE,Rattus norvegicus,GSE137869,GSM4331861,3p_v2,fastq,SRR11143080;SRR11143081;SRR11143082;SRR11143083,NA,SRX7779415,SRP222987,SRS6195955,SAMN14162459,NA,NA,"Ma et al, Cell, 2020",10.1016/j.cell.2020.02.008,https://pubmed.ncbi.nlm.nih.gov/32109414/,Illumina HiSeq 2000,Caloric restriction reprograms the single-cell transcriptional landscape of Rattus norvegicus aging,"Aging causes a functional decline in tissues throughout the body that may be delayed by caloric restriction (CR). However, the cellular profiles and signatures of aging, as well as those ameliorated by CR, remain unclear. Here, we built comprehensive single-cell and single-nucleus transcriptomic atlases across various rat tissues undergoing aging and CR. CR attenuated aging-related changes in cell type composition, gene expression, and core transcriptional regulatory networks. Immune cells were increased during aging, and CR favorably reversed the aging-disturbed immune ecosystem. Computational prediction revealed that the abnormal cell-cell communication patterns observed during aging, including the excessive proinflammatory ligand-receptor interplay, were reversed by CR. Our work provides  multi-tissue single-cell transcriptional landscapes associated with aging and CR in a mammal, enhances our understanding of the robustness of CR as a geroprotective intervention, and uncovers how metabolic intervention can act upon the immune system to modify the process of aging. Overall design: Single-cell and single-nucleus RNA sequencing for 210K cells/nuclei from 9 kinds of tissues of rats"
Ma 2020,Muscle-F-O,NA,muscle,NA,NA,NA,NA,NA,NA,TRUE,TRUE,Rattus norvegicus,GSE137869,GSM4331862,3p_v2,fastq,SRR11143084;SRR11143085;SRR11143086;SRR11143087,NA,SRX7779416,SRP222987,SRS6195956,SAMN14162458,NA,NA,"Ma et al, Cell, 2020",10.1016/j.cell.2020.02.008,https://pubmed.ncbi.nlm.nih.gov/32109414/,Illumina HiSeq 2000,Caloric restriction reprograms the single-cell transcriptional landscape of Rattus norvegicus aging,"Aging causes a functional decline in tissues throughout the body that may be delayed by caloric restriction (CR). However, the cellular profiles and signatures of aging, as well as those ameliorated by CR, remain unclear. Here, we built comprehensive single-cell and single-nucleus transcriptomic atlases across various rat tissues undergoing aging and CR. CR attenuated aging-related changes in cell type composition, gene expression, and core transcriptional regulatory networks. Immune cells were increased during aging, and CR favorably reversed the aging-disturbed immune ecosystem. Computational prediction revealed that the abnormal cell-cell communication patterns observed during aging, including the excessive proinflammatory ligand-receptor interplay, were reversed by CR. Our work provides  multi-tissue single-cell transcriptional landscapes associated with aging and CR in a mammal, enhances our understanding of the robustness of CR as a geroprotective intervention, and uncovers how metabolic intervention can act upon the immune system to modify the process of aging. Overall design: Single-cell and single-nucleus RNA sequencing for 210K cells/nuclei from 9 kinds of tissues of rats"
Ma 2020,Muscle-F-CR,NA,muscle,NA,NA,NA,NA,NA,NA,TRUE,TRUE,Rattus norvegicus,GSE137869,GSM4331863,3p_v2,fastq,SRR11143088;SRR11143089;SRR11143090;SRR11143091,NA,SRX7779417,SRP222987,SRS6195957,SAMN14162457,NA,NA,"Ma et al, Cell, 2020",10.1016/j.cell.2020.02.008,https://pubmed.ncbi.nlm.nih.gov/32109414/,Illumina HiSeq 2000,Caloric restriction reprograms the single-cell transcriptional landscape of Rattus norvegicus aging,"Aging causes a functional decline in tissues throughout the body that may be delayed by caloric restriction (CR). However, the cellular profiles and signatures of aging, as well as those ameliorated by CR, remain unclear. Here, we built comprehensive single-cell and single-nucleus transcriptomic atlases across various rat tissues undergoing aging and CR. CR attenuated aging-related changes in cell type composition, gene expression, and core transcriptional regulatory networks. Immune cells were increased during aging, and CR favorably reversed the aging-disturbed immune ecosystem. Computational prediction revealed that the abnormal cell-cell communication patterns observed during aging, including the excessive proinflammatory ligand-receptor interplay, were reversed by CR. Our work provides  multi-tissue single-cell transcriptional landscapes associated with aging and CR in a mammal, enhances our understanding of the robustness of CR as a geroprotective intervention, and uncovers how metabolic intervention can act upon the immune system to modify the process of aging. Overall design: Single-cell and single-nucleus RNA sequencing for 210K cells/nuclei from 9 kinds of tissues of rats"
Sommerfeld 2019,ECM,urinary bladder matrix,muscle,quadriceps femoris,cell,NA,NA,NA,NA,TRUE,FALSE,Mus musculus,GSE138027,GSM4096943,3p_v2,bam,SRR10186720,NA,SRX6907242,SRP223292,SRS5439062,SAMN12851009,NA,NA,"Sommerfeld et al, Scie Immunol, 2019",10.1126/sciimmunol.aax4783,https://pubmed.ncbi.nlm.nih.gov/31604843/,Illumina HiSeq 2000,Interleukin-36y-producing macrophages drive IL-17-mediated fibrosis.,"Biomaterials induce an immune response and mobilization of macrophages, yet identification and phenotypic characterization of functional macrophage subsets in vivo remain limited. We performed single-cell RNA sequencing analysis on macrophages sorted from either a biologic matrix [urinary bladder matrix (UBM)] or synthetic biomaterial [polycaprolactone (PCL)]. Implantation of UBM promotes tissue repair through generation of a tissue environment characterized by a T helper 2 (Th2)/interleukin (IL)4 immune profile, whereas PCL induces a standard foreign body response characterized by Th17/IL-17 and fibrosis. Unbiased clustering and pseudotime analysis revealed distinct macrophage subsets responsible for antigen presentation, chemoattraction, and phagocytosis, as well as a small population with expression profiles of both dendritic cells and skeletal muscle after UBM implantation. In the PCL tissue environment, we identified a CD9 hi+ IL-36y + macrophage subset that expressed Th17-associated molecules. These macrophages were virtually absent in mice lacking the IL-17 receptor, suggesting that they might be involved in IL-17dependent immune and autoimmune responses. Identification and comparison of the unique phenotypical and functional macrophage subsets in mouse and human tissue samples suggest broad relevance of the new classification. These distinct macrophage subsets demonstrate previously unrecognized myeloid phenotypes involved in different tissue responses and provide targets for potential therapeutic modulation in tissue repair and pathology. Overall design: Macrophages were sorted from mice quadriceps 1 week after undergoing volumetric muscle loss surgery with treatment of urinary bladder matrix, polycaprolactone, or saline. After sorting, cells were encapsulated using the 10x Chromium single cell RNA sequencing platform. Library prep followed the 10x 3' v2 protocol and were sequenced using an Illumina HiSeq 2000. Alignment was performed using 10x recommendations with the CellRanger software package to generate a counts matrix. Clusters of cells were determined using Seurat. In particular, data from the three conditions were pooled, normalized, and scaled. PCA was performed and used for clustering with a graph based method (shared nearest neighbor with the Louvaine method for community detection)."
Sommerfeld 2019,saline,saline,muscle,quadriceps femoris,cell,NA,NA,NA,NA,TRUE,FALSE,Mus musculus,GSE138027,GSM4096944,3p_v2,bam,SRR10186721,NA,SRX6907243,SRP223292,SRS5439063,SAMN12851008,NA,NA,"Sommerfeld et al, Scie Immunol, 2019",10.1126/sciimmunol.aax4783,https://pubmed.ncbi.nlm.nih.gov/31604843/,Illumina HiSeq 2000,Interleukin-36y-producing macrophages drive IL-17-mediated fibrosis.,"Biomaterials induce an immune response and mobilization of macrophages, yet identification and phenotypic characterization of functional macrophage subsets in vivo remain limited. We performed single-cell RNA sequencing analysis on macrophages sorted from either a biologic matrix [urinary bladder matrix (UBM)] or synthetic biomaterial [polycaprolactone (PCL)]. Implantation of UBM promotes tissue repair through generation of a tissue environment characterized by a T helper 2 (Th2)/interleukin (IL)4 immune profile, whereas PCL induces a standard foreign body response characterized by Th17/IL-17 and fibrosis. Unbiased clustering and pseudotime analysis revealed distinct macrophage subsets responsible for antigen presentation, chemoattraction, and phagocytosis, as well as a small population with expression profiles of both dendritic cells and skeletal muscle after UBM implantation. In the PCL tissue environment, we identified a CD9 hi+ IL-36y + macrophage subset that expressed Th17-associated molecules. These macrophages were virtually absent in mice lacking the IL-17 receptor, suggesting that they might be involved in IL-17dependent immune and autoimmune responses. Identification and comparison of the unique phenotypical and functional macrophage subsets in mouse and human tissue samples suggest broad relevance of the new classification. These distinct macrophage subsets demonstrate previously unrecognized myeloid phenotypes involved in different tissue responses and provide targets for potential therapeutic modulation in tissue repair and pathology. Overall design: Macrophages were sorted from mice quadriceps 1 week after undergoing volumetric muscle loss surgery with treatment of urinary bladder matrix, polycaprolactone, or saline. After sorting, cells were encapsulated using the 10x Chromium single cell RNA sequencing platform. Library prep followed the 10x 3' v2 protocol and were sequenced using an Illumina HiSeq 2000. Alignment was performed using 10x recommendations with the CellRanger software package to generate a counts matrix. Clusters of cells were determined using Seurat. In particular, data from the three conditions were pooled, normalized, and scaled. PCA was performed and used for clustering with a graph based method (shared nearest neighbor with the Louvaine method for community detection)."
Sommerfeld 2019,PCL,polycaprolactone,muscle,quadriceps femoris,cell,NA,NA,NA,NA,TRUE,FALSE,Mus musculus,GSE138027,GSM4096945,3p_v2,bam,SRR10186722,NA,SRX6907244,SRP223292,SRS5439064,SAMN12851007,NA,NA,"Sommerfeld et al, Scie Immunol, 2019",10.1126/sciimmunol.aax4783,https://pubmed.ncbi.nlm.nih.gov/31604843/,Illumina HiSeq 2000,Interleukin-36y-producing macrophages drive IL-17-mediated fibrosis.,"Biomaterials induce an immune response and mobilization of macrophages, yet identification and phenotypic characterization of functional macrophage subsets in vivo remain limited. We performed single-cell RNA sequencing analysis on macrophages sorted from either a biologic matrix [urinary bladder matrix (UBM)] or synthetic biomaterial [polycaprolactone (PCL)]. Implantation of UBM promotes tissue repair through generation of a tissue environment characterized by a T helper 2 (Th2)/interleukin (IL)4 immune profile, whereas PCL induces a standard foreign body response characterized by Th17/IL-17 and fibrosis. Unbiased clustering and pseudotime analysis revealed distinct macrophage subsets responsible for antigen presentation, chemoattraction, and phagocytosis, as well as a small population with expression profiles of both dendritic cells and skeletal muscle after UBM implantation. In the PCL tissue environment, we identified a CD9 hi+ IL-36y + macrophage subset that expressed Th17-associated molecules. These macrophages were virtually absent in mice lacking the IL-17 receptor, suggesting that they might be involved in IL-17dependent immune and autoimmune responses. Identification and comparison of the unique phenotypical and functional macrophage subsets in mouse and human tissue samples suggest broad relevance of the new classification. These distinct macrophage subsets demonstrate previously unrecognized myeloid phenotypes involved in different tissue responses and provide targets for potential therapeutic modulation in tissue repair and pathology. Overall design: Macrophages were sorted from mice quadriceps 1 week after undergoing volumetric muscle loss surgery with treatment of urinary bladder matrix, polycaprolactone, or saline. After sorting, cells were encapsulated using the 10x Chromium single cell RNA sequencing platform. Library prep followed the 10x 3' v2 protocol and were sequenced using an Illumina HiSeq 2000. Alignment was performed using 10x recommendations with the CellRanger software package to generate a counts matrix. Clusters of cells were determined using Seurat. In particular, data from the three conditions were pooled, normalized, and scaled. PCA was performed and used for clustering with a graph based method (shared nearest neighbor with the Louvaine method for community detection)."
Rubenstein 2020,Rubenstein_quads,NA,muscle,quadricep,cell,male,C57BL/6J,NA,NA,TRUE,TRUE,Mus musculus,GSE138707,GSM4116571,3p_v3,fastq,SRR10257731,NA,SRX6975664,SRP225077,SRS5500994,NA,NA,NA,"Rubenstein et al, Sci Rep, 2020",10.1038/s41598-019-57110-6,https://pubmed.ncbi.nlm.nih.gov/31937892/,NextSeq 500,Single cell sequencing of mouse muscles,Purpose: The goals of this study are to compare the Quadriceps and diaphragm muscles Methods: Library prepared followed by 10X Genomics standard protocol. Transcriptome were generated by high throughput sequencing Overall design: Single cell RNA sequencing was conducted on samples of cells isolated from limb muscle (Quadriceps) and respiratory muscle (Diaphragm) in mouse.
Rubenstein 2020,Rubenstein_diaph,NA,muscle,diaphragm,cell,male,C57BL/6J,NA,NA,TRUE,TRUE,Mus musculus,GSE138707,GSM4116572,3p_v3,fastq,SRR10257732,NA,SRX6975665,SRP225077,SRS5500995,NA,NA,NA,"Rubenstein et al, Sci Rep, 2020",10.1038/s41598-019-57110-6,https://pubmed.ncbi.nlm.nih.gov/31937892/,NextSeq 500,Single cell sequencing of mouse muscles,Purpose: The goals of this study are to compare the Quadriceps and diaphragm muscles Methods: Library prepared followed by 10X Genomics standard protocol. Transcriptome were generated by high throughput sequencing Overall design: Single cell RNA sequencing was conducted on samples of cells isolated from limb muscle (Quadriceps) and respiratory muscle (Diaphragm) in mouse.
Oprescu 2020,oprescu_D0_5,tibialis anterior non-injured SM,muscle,tibialis anterior,cell,male,C5Bl6/N,NA,NA,TRUE,TRUE,Mus musculus,GSE138826,GSM4120117,3p_v3,fastq,SRR10275413,NA,SRX6988624,SRP225546,SRS5511292,SAMN13026775,NA,NA,"Oprescu et al, iScience, 2020",10.1016/j.isci.2020.100993,https://pubmed.ncbi.nlm.nih.gov/32248062/,Illumina NovaSeq 6000,10X skeletal muscle regeneration scRNA-seq,"Single-cell RNA sequencing of cells dissociated from skeletal muscle at discrete regeneration timepoints to reveal transcriptional identities of contributors to skeletal muscle regeneration. Overall design: Tibialis anterior muscle from C5Bl6 WT male mice were injected with cardiotoxin to induce muscle injury and collected at  at 0.5, 2, 3.5, 5, 10, 21 days post injury and a non-injured sample. Muscle was digested with collagenase and dispase to dissociate single cells, stained with a cell viability marker and subjected to FACS to generate single cell suspensions. Single cell suspensions were loaded onto the 10X Genomics Platform and processed according to the manufacturer's instructions. Each sample is an individual time point, n=3 male mice combined per time point. The regen_data.rds file is list of two annotated data frames, of which each item contains the merged dataset with all cells from all timepoints. Item [1] which contains the RNA counts while item [2] contains the SCT normalized values. Columns are the samples, rows and the gene values and the metadata is structures accordingly."
Oprescu 2020,oprescu_D2,tibialis anterior 0.5 days post CTX injury,muscle,tibialis anterior,cell,male,C5Bl6/N,NA,NA,TRUE,TRUE,Mus musculus,GSE138826,GSM4120118,3p_v3,fastq,SRR10275414,NA,SRX6988625,SRP225546,SRS5511293,SAMN13026787,NA,NA,"Oprescu et al, iScience, 2020",10.1016/j.isci.2020.100993,https://pubmed.ncbi.nlm.nih.gov/32248062/,Illumina NovaSeq 6000,10X skeletal muscle regeneration scRNA-seq,"Single-cell RNA sequencing of cells dissociated from skeletal muscle at discrete regeneration timepoints to reveal transcriptional identities of contributors to skeletal muscle regeneration. Overall design: Tibialis anterior muscle from C5Bl6 WT male mice were injected with cardiotoxin to induce muscle injury and collected at  at 0.5, 2, 3.5, 5, 10, 21 days post injury and a non-injured sample. Muscle was digested with collagenase and dispase to dissociate single cells, stained with a cell viability marker and subjected to FACS to generate single cell suspensions. Single cell suspensions were loaded onto the 10X Genomics Platform and processed according to the manufacturer's instructions. Each sample is an individual time point, n=3 male mice combined per time point. The regen_data.rds file is list of two annotated data frames, of which each item contains the merged dataset with all cells from all timepoints. Item [1] which contains the RNA counts while item [2] contains the SCT normalized values. Columns are the samples, rows and the gene values and the metadata is structures accordingly."
Oprescu 2020,oprescu_D3_5,tibialis anterior 2 days post CTX injury,muscle,tibialis anterior,cell,male,C5Bl6/N,NA,NA,TRUE,TRUE,Mus musculus,GSE138826,GSM4120119,3p_v3,fastq,SRR10275415,NA,SRX6988626,SRP225546,SRS5511294,SAMN13026786,NA,NA,"Oprescu et al, iScience, 2020",10.1016/j.isci.2020.100993,https://pubmed.ncbi.nlm.nih.gov/32248062/,Illumina NovaSeq 6000,10X skeletal muscle regeneration scRNA-seq,"Single-cell RNA sequencing of cells dissociated from skeletal muscle at discrete regeneration timepoints to reveal transcriptional identities of contributors to skeletal muscle regeneration. Overall design: Tibialis anterior muscle from C5Bl6 WT male mice were injected with cardiotoxin to induce muscle injury and collected at  at 0.5, 2, 3.5, 5, 10, 21 days post injury and a non-injured sample. Muscle was digested with collagenase and dispase to dissociate single cells, stained with a cell viability marker and subjected to FACS to generate single cell suspensions. Single cell suspensions were loaded onto the 10X Genomics Platform and processed according to the manufacturer's instructions. Each sample is an individual time point, n=3 male mice combined per time point. The regen_data.rds file is list of two annotated data frames, of which each item contains the merged dataset with all cells from all timepoints. Item [1] which contains the RNA counts while item [2] contains the SCT normalized values. Columns are the samples, rows and the gene values and the metadata is structures accordingly."
Oprescu 2020,oprescu_D5,tibialis anterior 3.5 days post CTX injury,muscle,tibialis anterior,cell,male,C5Bl6/N,NA,NA,TRUE,TRUE,Mus musculus,GSE138826,GSM4120120,3p_v3,fastq,SRR10275416,NA,SRX6988627,SRP225546,SRS5511295,SAMN13026785,NA,NA,"Oprescu et al, iScience, 2020",10.1016/j.isci.2020.100993,https://pubmed.ncbi.nlm.nih.gov/32248062/,Illumina NovaSeq 6000,10X skeletal muscle regeneration scRNA-seq,"Single-cell RNA sequencing of cells dissociated from skeletal muscle at discrete regeneration timepoints to reveal transcriptional identities of contributors to skeletal muscle regeneration. Overall design: Tibialis anterior muscle from C5Bl6 WT male mice were injected with cardiotoxin to induce muscle injury and collected at  at 0.5, 2, 3.5, 5, 10, 21 days post injury and a non-injured sample. Muscle was digested with collagenase and dispase to dissociate single cells, stained with a cell viability marker and subjected to FACS to generate single cell suspensions. Single cell suspensions were loaded onto the 10X Genomics Platform and processed according to the manufacturer's instructions. Each sample is an individual time point, n=3 male mice combined per time point. The regen_data.rds file is list of two annotated data frames, of which each item contains the merged dataset with all cells from all timepoints. Item [1] which contains the RNA counts while item [2] contains the SCT normalized values. Columns are the samples, rows and the gene values and the metadata is structures accordingly."
Oprescu 2020,oprescu_D10,tibialis anterior 5 days post CTX injury,muscle,tibialis anterior,cell,male,C5Bl6/N,NA,NA,TRUE,TRUE,Mus musculus,GSE138826,GSM4120121,3p_v3,fastq,SRR10275417,NA,SRX6988628,SRP225546,SRS5511296,SAMN13026784,NA,NA,"Oprescu et al, iScience, 2020",10.1016/j.isci.2020.100993,https://pubmed.ncbi.nlm.nih.gov/32248062/,Illumina NovaSeq 6000,10X skeletal muscle regeneration scRNA-seq,"Single-cell RNA sequencing of cells dissociated from skeletal muscle at discrete regeneration timepoints to reveal transcriptional identities of contributors to skeletal muscle regeneration. Overall design: Tibialis anterior muscle from C5Bl6 WT male mice were injected with cardiotoxin to induce muscle injury and collected at  at 0.5, 2, 3.5, 5, 10, 21 days post injury and a non-injured sample. Muscle was digested with collagenase and dispase to dissociate single cells, stained with a cell viability marker and subjected to FACS to generate single cell suspensions. Single cell suspensions were loaded onto the 10X Genomics Platform and processed according to the manufacturer's instructions. Each sample is an individual time point, n=3 male mice combined per time point. The regen_data.rds file is list of two annotated data frames, of which each item contains the merged dataset with all cells from all timepoints. Item [1] which contains the RNA counts while item [2] contains the SCT normalized values. Columns are the samples, rows and the gene values and the metadata is structures accordingly."
Oprescu 2020,oprescu_D21,tibialis anterior 10 days post CTX injury,muscle,tibialis anterior,cell,male,C5Bl6/N,NA,NA,TRUE,TRUE,Mus musculus,GSE138826,GSM4120122,3p_v3,fastq,SRR10275418,NA,SRX6988629,SRP225546,SRS5511297,SAMN13026783,NA,NA,"Oprescu et al, iScience, 2020",10.1016/j.isci.2020.100993,https://pubmed.ncbi.nlm.nih.gov/32248062/,Illumina NovaSeq 6000,10X skeletal muscle regeneration scRNA-seq,"Single-cell RNA sequencing of cells dissociated from skeletal muscle at discrete regeneration timepoints to reveal transcriptional identities of contributors to skeletal muscle regeneration. Overall design: Tibialis anterior muscle from C5Bl6 WT male mice were injected with cardiotoxin to induce muscle injury and collected at  at 0.5, 2, 3.5, 5, 10, 21 days post injury and a non-injured sample. Muscle was digested with collagenase and dispase to dissociate single cells, stained with a cell viability marker and subjected to FACS to generate single cell suspensions. Single cell suspensions were loaded onto the 10X Genomics Platform and processed according to the manufacturer's instructions. Each sample is an individual time point, n=3 male mice combined per time point. The regen_data.rds file is list of two annotated data frames, of which each item contains the merged dataset with all cells from all timepoints. Item [1] which contains the RNA counts while item [2] contains the SCT normalized values. Columns are the samples, rows and the gene values and the metadata is structures accordingly."
Oprescu 2020,oprescu_D0,tibialis anterior 21 days post CTX injury,muscle,tibialis anterior,cell,male,C5Bl6/N,NA,NA,TRUE,TRUE,Mus musculus,GSE138826,GSM4120123,3p_v3,fastq,SRR10275419,NA,SRX6988630,SRP225546,SRS5511298,SAMN13026782,NA,NA,"Oprescu et al, iScience, 2020",10.1016/j.isci.2020.100993,https://pubmed.ncbi.nlm.nih.gov/32248062/,Illumina NovaSeq 6000,10X skeletal muscle regeneration scRNA-seq,"Single-cell RNA sequencing of cells dissociated from skeletal muscle at discrete regeneration timepoints to reveal transcriptional identities of contributors to skeletal muscle regeneration. Overall design: Tibialis anterior muscle from C5Bl6 WT male mice were injected with cardiotoxin to induce muscle injury and collected at  at 0.5, 2, 3.5, 5, 10, 21 days post injury and a non-injured sample. Muscle was digested with collagenase and dispase to dissociate single cells, stained with a cell viability marker and subjected to FACS to generate single cell suspensions. Single cell suspensions were loaded onto the 10X Genomics Platform and processed according to the manufacturer's instructions. Each sample is an individual time point, n=3 male mice combined per time point. The regen_data.rds file is list of two annotated data frames, of which each item contains the merged dataset with all cells from all timepoints. Item [1] which contains the RNA counts while item [2] contains the SCT normalized values. Columns are the samples, rows and the gene values and the metadata is structures accordingly."
Wang 2020,muscle_D,Mouse Diaphragm Muscle Macrophage,muscle,diaphragm,cell,female,C57BL/6J,NA,NA,TRUE,TRUE,Mus musculus,GSE142480,GSM4230226,3p_v2,fastq,SRR10752709;SRR10752710;SRR10752711,NA,SRX7427501,SRP238469,SRS5873471,SAMN13663852,NA,NA,"Wang et al, PNAS, 2020",10.1073/pnas.1915950117,https://pubmed.ncbi.nlm.nih.gov/32796104/,Illumina HiSeq 2500,Heterogeneous Origins and Functions of Mouse Skeletal Muscle Resident Macrophages,"Tissue resident macrophages can arise from either embryonic or adult hematopoiesis and play important roles in a wide range of biological processes, such as tissue remodeling during organogenesis, tissue homeostasis in the steady state, tissue repair following injury, and immune response to pathogens. Although the origins and tissue-specific functions of resident macrophages have been extensively studied in many other tissues, they are not well characterized in skeletal muscle. In the present study, we have characterized for the first time the ontogeny of skeletal muscle resident macrophages, showing evidence that they arise from both embryonic hematopoietic progenitors, including yolk sac primitive macrophages and fetal liver monocytes, and adult bone marrow hematopoietic stem cells. Single cell-based transcriptome analysis revealed that skeletal muscle resident macrophages were highly distinctive from resident macrophages in other tissues, expressing a specific set of transcription factors and containing functionally diverse subsets correlating to their origins. They appear more active in maintaining tissue homeostasis and promoting muscle growth and regeneration. Overall design: Skeletal muscle resident macrophages from quadriceps and diaphragm, as well as peritoneal macrophages and lung alveolar macrophages, of 8 weeks old C57 BL/6J mice were sorted by flow cytometry and were then subjected to single cell-based RNA sequencing."
Wang 2020,muscle_Q,Mouse Quadriceps Muscle Macrophage,muscle,quadricep,cell,female,C57BL/6J,NA,NA,TRUE,TRUE,Mus musculus,GSE142480,GSM4230229,3p_v2,fastq,SRR10752718;SRR10752719;SRR10752720,NA,SRX7427504,SRP238469,SRS5873474,SAMN13663849,NA,NA,"Wang et al, PNAS, 2020",10.1073/pnas.1915950117,https://pubmed.ncbi.nlm.nih.gov/32796104/,Illumina HiSeq 2500,Heterogeneous Origins and Functions of Mouse Skeletal Muscle Resident Macrophages,"Tissue resident macrophages can arise from either embryonic or adult hematopoiesis and play important roles in a wide range of biological processes, such as tissue remodeling during organogenesis, tissue homeostasis in the steady state, tissue repair following injury, and immune response to pathogens. Although the origins and tissue-specific functions of resident macrophages have been extensively studied in many other tissues, they are not well characterized in skeletal muscle. In the present study, we have characterized for the first time the ontogeny of skeletal muscle resident macrophages, showing evidence that they arise from both embryonic hematopoietic progenitors, including yolk sac primitive macrophages and fetal liver monocytes, and adult bone marrow hematopoietic stem cells. Single cell-based transcriptome analysis revealed that skeletal muscle resident macrophages were highly distinctive from resident macrophages in other tissues, expressing a specific set of transcription factors and containing functionally diverse subsets correlating to their origins. They appear more active in maintaining tissue homeostasis and promoting muscle growth and regeneration. Overall design: Skeletal muscle resident macrophages from quadriceps and diaphragm, as well as peritoneal macrophages and lung alveolar macrophages, of 8 weeks old C57 BL/6J mice were sorted by flow cytometry and were then subjected to single cell-based RNA sequencing."
Yartseva 2020,Yartseva_0dpi,NA,muscle,muscle stem cell,cell,male,PAX7.IRES.Cre. ki_Rosa26.LSL.tdTomato,NA,NA,TRUE,FALSE,Mus musculus,GSE142581,GSM4232371,3p_v2,fastq,SRR10764954;SRR10764955,NA,SRX7438905,SRP238712,SRS5883559,SAMN13677038,NA,NA,"Yartseva et al, Cell Reports, 2020",10.1016/j.celrep.2019.12.100,https://pubmed.ncbi.nlm.nih.gov/32023464/,Illumina HiSeq 4000,DELTA1/NOTCH2-mediated signaling regulates muscle stem cell self-renewal,"How satellite cells and their progenitors balance differentiation and self-renewal to achieve sustainable tissue regeneration is not well understood. A major roadblock to understanding satellite cell fate decisions has been the difficulty to study this process in vivo. By visualizing expression dynamics of myogenic transcription factors during early regeneration in vivo, we identified the time point at which cells undergo decisions to differentiate or self-renew. Single-cell RNA sequencing revealed heterogeneity of satellite cells during both muscle homeostasis and regeneration, including a subpopulation enriched in Notch2 receptor expression. Furthermore, we reveal that differentiating cells express the Dll1 ligand. Using antagonistic antibodies we demonstrate that the DLL1 and NOTCH2 signaling pair is required for satellite cell self-renewal. Thus, differentiating cells provide the self-renewing signal during regeneration, enabling proportional regeneration in response to injury while maintaining the satellite cell pool. These findings have implications for therapeutic control of muscle regeneration. Overall design: Single-cell RNA-seq study of mouse satellite cells during homeostasis and regeneration at 4 days post injury, including after treatment with antagonistic antibodies against Notch2 (aN2), Dll1 (aDll1) or control antibody (aRW)"
Yartseva 2020,Yartseva_4dpi,NA,muscle,muscle stem cell,cell,male,PAX7.IRES.Cre. ki_Rosa26.LSL.tdTomato,NA,NA,TRUE,FALSE,Mus musculus,GSE142581,GSM4232372,3p_v2,fastq,SRR10764956;SRR10764957,NA,SRX7438906,SRP238712,SRS5883560,SAMN13677036,NA,NA,"Yartseva et al, Cell Reports, 2020",10.1016/j.celrep.2019.12.100,https://pubmed.ncbi.nlm.nih.gov/32023464/,Illumina HiSeq 4000,DELTA1/NOTCH2-mediated signaling regulates muscle stem cell self-renewal,"How satellite cells and their progenitors balance differentiation and self-renewal to achieve sustainable tissue regeneration is not well understood. A major roadblock to understanding satellite cell fate decisions has been the difficulty to study this process in vivo. By visualizing expression dynamics of myogenic transcription factors during early regeneration in vivo, we identified the time point at which cells undergo decisions to differentiate or self-renew. Single-cell RNA sequencing revealed heterogeneity of satellite cells during both muscle homeostasis and regeneration, including a subpopulation enriched in Notch2 receptor expression. Furthermore, we reveal that differentiating cells express the Dll1 ligand. Using antagonistic antibodies we demonstrate that the DLL1 and NOTCH2 signaling pair is required for satellite cell self-renewal. Thus, differentiating cells provide the self-renewing signal during regeneration, enabling proportional regeneration in response to injury while maintaining the satellite cell pool. These findings have implications for therapeutic control of muscle regeneration. Overall design: Single-cell RNA-seq study of mouse satellite cells during homeostasis and regeneration at 4 days post injury, including after treatment with antagonistic antibodies against Notch2 (aN2), Dll1 (aDll1) or control antibody (aRW)"
Yartseva 2020,actd - aRW - 0dpi,NA,muscle,muscle stem cell,cell,male,PAX7.IRES.Cre. ki_Rosa26.LSL.tdTomato,NA,NA,TRUE,FALSE,Mus musculus,GSE142581,GSM4232373,3p_v2,fastq,SRR10764958,NA,SRX7438907,SRP238712,SRS5883561,SAMN13677035,NA,NA,"Yartseva et al, Cell Reports, 2020",10.1016/j.celrep.2019.12.100,https://pubmed.ncbi.nlm.nih.gov/32023464/,Illumina HiSeq 4000,DELTA1/NOTCH2-mediated signaling regulates muscle stem cell self-renewal,"How satellite cells and their progenitors balance differentiation and self-renewal to achieve sustainable tissue regeneration is not well understood. A major roadblock to understanding satellite cell fate decisions has been the difficulty to study this process in vivo. By visualizing expression dynamics of myogenic transcription factors during early regeneration in vivo, we identified the time point at which cells undergo decisions to differentiate or self-renew. Single-cell RNA sequencing revealed heterogeneity of satellite cells during both muscle homeostasis and regeneration, including a subpopulation enriched in Notch2 receptor expression. Furthermore, we reveal that differentiating cells express the Dll1 ligand. Using antagonistic antibodies we demonstrate that the DLL1 and NOTCH2 signaling pair is required for satellite cell self-renewal. Thus, differentiating cells provide the self-renewing signal during regeneration, enabling proportional regeneration in response to injury while maintaining the satellite cell pool. These findings have implications for therapeutic control of muscle regeneration. Overall design: Single-cell RNA-seq study of mouse satellite cells during homeostasis and regeneration at 4 days post injury, including after treatment with antagonistic antibodies against Notch2 (aN2), Dll1 (aDll1) or control antibody (aRW)"
Yartseva 2020,actd - aN2 - 0dpi,NA,muscle,muscle stem cell,cell,male,PAX7.IRES.Cre. ki_Rosa26.LSL.tdTomato,NA,NA,TRUE,FALSE,Mus musculus,GSE142581,GSM4232374,3p_v2,fastq,SRR10764959,NA,SRX7438908,SRP238712,SRS5883562,SAMN13677034,NA,NA,"Yartseva et al, Cell Reports, 2020",10.1016/j.celrep.2019.12.100,https://pubmed.ncbi.nlm.nih.gov/32023464/,Illumina HiSeq 4000,DELTA1/NOTCH2-mediated signaling regulates muscle stem cell self-renewal,"How satellite cells and their progenitors balance differentiation and self-renewal to achieve sustainable tissue regeneration is not well understood. A major roadblock to understanding satellite cell fate decisions has been the difficulty to study this process in vivo. By visualizing expression dynamics of myogenic transcription factors during early regeneration in vivo, we identified the time point at which cells undergo decisions to differentiate or self-renew. Single-cell RNA sequencing revealed heterogeneity of satellite cells during both muscle homeostasis and regeneration, including a subpopulation enriched in Notch2 receptor expression. Furthermore, we reveal that differentiating cells express the Dll1 ligand. Using antagonistic antibodies we demonstrate that the DLL1 and NOTCH2 signaling pair is required for satellite cell self-renewal. Thus, differentiating cells provide the self-renewing signal during regeneration, enabling proportional regeneration in response to injury while maintaining the satellite cell pool. These findings have implications for therapeutic control of muscle regeneration. Overall design: Single-cell RNA-seq study of mouse satellite cells during homeostasis and regeneration at 4 days post injury, including after treatment with antagonistic antibodies against Notch2 (aN2), Dll1 (aDll1) or control antibody (aRW)"
Yartseva 2020,actd - aRW - 4dpi,NA,muscle,muscle stem cell,cell,male,PAX7.IRES.Cre. ki_Rosa26.LSL.tdTomato,NA,NA,TRUE,FALSE,Mus musculus,GSE142581,GSM4232375,3p_v2,fastq,SRR10764960,NA,SRX7438909,SRP238712,SRS5883563,SAMN13677033,NA,NA,"Yartseva et al, Cell Reports, 2020",10.1016/j.celrep.2019.12.100,https://pubmed.ncbi.nlm.nih.gov/32023464/,Illumina HiSeq 4000,DELTA1/NOTCH2-mediated signaling regulates muscle stem cell self-renewal,"How satellite cells and their progenitors balance differentiation and self-renewal to achieve sustainable tissue regeneration is not well understood. A major roadblock to understanding satellite cell fate decisions has been the difficulty to study this process in vivo. By visualizing expression dynamics of myogenic transcription factors during early regeneration in vivo, we identified the time point at which cells undergo decisions to differentiate or self-renew. Single-cell RNA sequencing revealed heterogeneity of satellite cells during both muscle homeostasis and regeneration, including a subpopulation enriched in Notch2 receptor expression. Furthermore, we reveal that differentiating cells express the Dll1 ligand. Using antagonistic antibodies we demonstrate that the DLL1 and NOTCH2 signaling pair is required for satellite cell self-renewal. Thus, differentiating cells provide the self-renewing signal during regeneration, enabling proportional regeneration in response to injury while maintaining the satellite cell pool. These findings have implications for therapeutic control of muscle regeneration. Overall design: Single-cell RNA-seq study of mouse satellite cells during homeostasis and regeneration at 4 days post injury, including after treatment with antagonistic antibodies against Notch2 (aN2), Dll1 (aDll1) or control antibody (aRW)"
Yartseva 2020,actd - aRW - 4dpi,NA,muscle,muscle stem cell,cell,male,PAX7.IRES.Cre. ki_Rosa26.LSL.tdTomato,NA,NA,TRUE,FALSE,Mus musculus,GSE142581,GSM4232376,3p_v2,fastq,SRR10764961,NA,SRX7438910,SRP238712,SRS5883564,SAMN13677032,NA,NA,"Yartseva et al, Cell Reports, 2020",10.1016/j.celrep.2019.12.100,https://pubmed.ncbi.nlm.nih.gov/32023464/,Illumina HiSeq 4000,DELTA1/NOTCH2-mediated signaling regulates muscle stem cell self-renewal,"How satellite cells and their progenitors balance differentiation and self-renewal to achieve sustainable tissue regeneration is not well understood. A major roadblock to understanding satellite cell fate decisions has been the difficulty to study this process in vivo. By visualizing expression dynamics of myogenic transcription factors during early regeneration in vivo, we identified the time point at which cells undergo decisions to differentiate or self-renew. Single-cell RNA sequencing revealed heterogeneity of satellite cells during both muscle homeostasis and regeneration, including a subpopulation enriched in Notch2 receptor expression. Furthermore, we reveal that differentiating cells express the Dll1 ligand. Using antagonistic antibodies we demonstrate that the DLL1 and NOTCH2 signaling pair is required for satellite cell self-renewal. Thus, differentiating cells provide the self-renewing signal during regeneration, enabling proportional regeneration in response to injury while maintaining the satellite cell pool. These findings have implications for therapeutic control of muscle regeneration. Overall design: Single-cell RNA-seq study of mouse satellite cells during homeostasis and regeneration at 4 days post injury, including after treatment with antagonistic antibodies against Notch2 (aN2), Dll1 (aDll1) or control antibody (aRW)"
Yartseva 2020,no - aRW - 4dpi,NA,muscle,muscle stem cell,cell,male,PAX7.IRES.Cre. ki_Rosa26.LSL.tdTomato,NA,NA,TRUE,FALSE,Mus musculus,GSE142581,GSM4232377,3p_v2,fastq,SRR10764962,NA,SRX7438911,SRP238712,SRS5883565,SAMN13677031,NA,NA,"Yartseva et al, Cell Reports, 2020",10.1016/j.celrep.2019.12.100,https://pubmed.ncbi.nlm.nih.gov/32023464/,Illumina HiSeq 4000,DELTA1/NOTCH2-mediated signaling regulates muscle stem cell self-renewal,"How satellite cells and their progenitors balance differentiation and self-renewal to achieve sustainable tissue regeneration is not well understood. A major roadblock to understanding satellite cell fate decisions has been the difficulty to study this process in vivo. By visualizing expression dynamics of myogenic transcription factors during early regeneration in vivo, we identified the time point at which cells undergo decisions to differentiate or self-renew. Single-cell RNA sequencing revealed heterogeneity of satellite cells during both muscle homeostasis and regeneration, including a subpopulation enriched in Notch2 receptor expression. Furthermore, we reveal that differentiating cells express the Dll1 ligand. Using antagonistic antibodies we demonstrate that the DLL1 and NOTCH2 signaling pair is required for satellite cell self-renewal. Thus, differentiating cells provide the self-renewing signal during regeneration, enabling proportional regeneration in response to injury while maintaining the satellite cell pool. These findings have implications for therapeutic control of muscle regeneration. Overall design: Single-cell RNA-seq study of mouse satellite cells during homeostasis and regeneration at 4 days post injury, including after treatment with antagonistic antibodies against Notch2 (aN2), Dll1 (aDll1) or control antibody (aRW)"
Yartseva 2020,actd - aN2 - 4dpi,NA,muscle,muscle stem cell,cell,male,PAX7.IRES.Cre. ki_Rosa26.LSL.tdTomato,NA,NA,TRUE,FALSE,Mus musculus,GSE142581,GSM4232378,3p_v2,fastq,SRR10764963,NA,SRX7438912,SRP238712,SRS5883566,SAMN13677030,NA,NA,"Yartseva et al, Cell Reports, 2020",10.1016/j.celrep.2019.12.100,https://pubmed.ncbi.nlm.nih.gov/32023464/,Illumina HiSeq 4000,DELTA1/NOTCH2-mediated signaling regulates muscle stem cell self-renewal,"How satellite cells and their progenitors balance differentiation and self-renewal to achieve sustainable tissue regeneration is not well understood. A major roadblock to understanding satellite cell fate decisions has been the difficulty to study this process in vivo. By visualizing expression dynamics of myogenic transcription factors during early regeneration in vivo, we identified the time point at which cells undergo decisions to differentiate or self-renew. Single-cell RNA sequencing revealed heterogeneity of satellite cells during both muscle homeostasis and regeneration, including a subpopulation enriched in Notch2 receptor expression. Furthermore, we reveal that differentiating cells express the Dll1 ligand. Using antagonistic antibodies we demonstrate that the DLL1 and NOTCH2 signaling pair is required for satellite cell self-renewal. Thus, differentiating cells provide the self-renewing signal during regeneration, enabling proportional regeneration in response to injury while maintaining the satellite cell pool. These findings have implications for therapeutic control of muscle regeneration. Overall design: Single-cell RNA-seq study of mouse satellite cells during homeostasis and regeneration at 4 days post injury, including after treatment with antagonistic antibodies against Notch2 (aN2), Dll1 (aDll1) or control antibody (aRW)"
Yartseva 2020,no - aN2 - 4dpi,NA,muscle,muscle stem cell,cell,male,PAX7.IRES.Cre. ki_Rosa26.LSL.tdTomato,NA,NA,TRUE,FALSE,Mus musculus,GSE142581,GSM4232379,3p_v2,fastq,SRR10764964,NA,SRX7438913,SRP238712,SRS5883567,SAMN13677029,NA,NA,"Yartseva et al, Cell Reports, 2020",10.1016/j.celrep.2019.12.100,https://pubmed.ncbi.nlm.nih.gov/32023464/,Illumina HiSeq 4000,DELTA1/NOTCH2-mediated signaling regulates muscle stem cell self-renewal,"How satellite cells and their progenitors balance differentiation and self-renewal to achieve sustainable tissue regeneration is not well understood. A major roadblock to understanding satellite cell fate decisions has been the difficulty to study this process in vivo. By visualizing expression dynamics of myogenic transcription factors during early regeneration in vivo, we identified the time point at which cells undergo decisions to differentiate or self-renew. Single-cell RNA sequencing revealed heterogeneity of satellite cells during both muscle homeostasis and regeneration, including a subpopulation enriched in Notch2 receptor expression. Furthermore, we reveal that differentiating cells express the Dll1 ligand. Using antagonistic antibodies we demonstrate that the DLL1 and NOTCH2 signaling pair is required for satellite cell self-renewal. Thus, differentiating cells provide the self-renewing signal during regeneration, enabling proportional regeneration in response to injury while maintaining the satellite cell pool. These findings have implications for therapeutic control of muscle regeneration. Overall design: Single-cell RNA-seq study of mouse satellite cells during homeostasis and regeneration at 4 days post injury, including after treatment with antagonistic antibodies against Notch2 (aN2), Dll1 (aDll1) or control antibody (aRW)"
Yartseva 2020,actd - aDll1 - 4dpi,NA,muscle,muscle stem cell,cell,male,PAX7.IRES.Cre. ki_Rosa26.LSL.tdTomato,NA,NA,TRUE,FALSE,Mus musculus,GSE142581,GSM4232380,3p_v2,fastq,SRR10764965,NA,SRX7438914,SRP238712,SRS5883568,SAMN13677028,NA,NA,"Yartseva et al, Cell Reports, 2020",10.1016/j.celrep.2019.12.100,https://pubmed.ncbi.nlm.nih.gov/32023464/,Illumina HiSeq 4000,DELTA1/NOTCH2-mediated signaling regulates muscle stem cell self-renewal,"How satellite cells and their progenitors balance differentiation and self-renewal to achieve sustainable tissue regeneration is not well understood. A major roadblock to understanding satellite cell fate decisions has been the difficulty to study this process in vivo. By visualizing expression dynamics of myogenic transcription factors during early regeneration in vivo, we identified the time point at which cells undergo decisions to differentiate or self-renew. Single-cell RNA sequencing revealed heterogeneity of satellite cells during both muscle homeostasis and regeneration, including a subpopulation enriched in Notch2 receptor expression. Furthermore, we reveal that differentiating cells express the Dll1 ligand. Using antagonistic antibodies we demonstrate that the DLL1 and NOTCH2 signaling pair is required for satellite cell self-renewal. Thus, differentiating cells provide the self-renewing signal during regeneration, enabling proportional regeneration in response to injury while maintaining the satellite cell pool. These findings have implications for therapeutic control of muscle regeneration. Overall design: Single-cell RNA-seq study of mouse satellite cells during homeostasis and regeneration at 4 days post injury, including after treatment with antagonistic antibodies against Notch2 (aN2), Dll1 (aDll1) or control antibody (aRW)"
Yartseva 2020,actd - aDll1 - 4dpi,NA,muscle,muscle stem cell,cell,male,PAX7.IRES.Cre. ki_Rosa26.LSL.tdTomato,NA,NA,TRUE,FALSE,Mus musculus,GSE142581,GSM4232381,3p_v2,fastq,SRR10764966,NA,SRX7438915,SRP238712,SRS5883569,SAMN13677027,NA,NA,"Yartseva et al, Cell Reports, 2020",10.1016/j.celrep.2019.12.100,https://pubmed.ncbi.nlm.nih.gov/32023464/,Illumina HiSeq 4000,DELTA1/NOTCH2-mediated signaling regulates muscle stem cell self-renewal,"How satellite cells and their progenitors balance differentiation and self-renewal to achieve sustainable tissue regeneration is not well understood. A major roadblock to understanding satellite cell fate decisions has been the difficulty to study this process in vivo. By visualizing expression dynamics of myogenic transcription factors during early regeneration in vivo, we identified the time point at which cells undergo decisions to differentiate or self-renew. Single-cell RNA sequencing revealed heterogeneity of satellite cells during both muscle homeostasis and regeneration, including a subpopulation enriched in Notch2 receptor expression. Furthermore, we reveal that differentiating cells express the Dll1 ligand. Using antagonistic antibodies we demonstrate that the DLL1 and NOTCH2 signaling pair is required for satellite cell self-renewal. Thus, differentiating cells provide the self-renewing signal during regeneration, enabling proportional regeneration in response to injury while maintaining the satellite cell pool. These findings have implications for therapeutic control of muscle regeneration. Overall design: Single-cell RNA-seq study of mouse satellite cells during homeostasis and regeneration at 4 days post injury, including after treatment with antagonistic antibodies against Notch2 (aN2), Dll1 (aDll1) or control antibody (aRW)"
De Micheli 2020a,D0_FACS_01,NA,muscle,tibialis anterior,cell,female,C57BL/6J,NA,NA,TRUE,TRUE,Mus musculus,GSE143435,GSM4259468,3p_v2,fastq,SRR10870267,NA,SRX7540258,SRP241203,SRS5978833,NA,NA,NA,"De Micheli et al, Cell Reports, 2020",10.1016/j.celrep.2020.02.067,https://pubmed.ncbi.nlm.nih.gov/32160558/,NextSeq 500,Single-cell transcriptomic atlas of FACS-sorted mouse muscle tissue cells,We report a series of single-cell transcriptomic datasets of FACS-sorted mouse muscle tissue cells from injured muscle produced using the Chromium 10X technology. Overall design: The overall objective of the study was to generate a transcriptomic atlas of FACS-sorted mouse muscle cell populations at different timepoints post notexin-injury using single-cell RNA-sequencing.
De Micheli 2020a,D0_FACS_02,NA,muscle,tibialis anterior,cell,female,C57BL/6J,NA,NA,TRUE,TRUE,Mus musculus,GSE143435,GSM4259469,3p_v2,fastq,SRR10870268,NA,SRX7540259,SRP241203,SRS5978834,NA,NA,NA,"De Micheli et al, Cell Reports, 2020",10.1016/j.celrep.2020.02.067,https://pubmed.ncbi.nlm.nih.gov/32160558/,NextSeq 500,Single-cell transcriptomic atlas of FACS-sorted mouse muscle tissue cells,We report a series of single-cell transcriptomic datasets of FACS-sorted mouse muscle tissue cells from injured muscle produced using the Chromium 10X technology. Overall design: The overall objective of the study was to generate a transcriptomic atlas of FACS-sorted mouse muscle cell populations at different timepoints post notexin-injury using single-cell RNA-sequencing.
De Micheli 2020a,D2_FACS,NA,muscle,tibialis anterior,cell,female,C57BL/6J,NA,NA,TRUE,TRUE,Mus musculus,GSE143435,GSM4259470,3p_v2,fastq,SRR10870269,NA,SRX7540260,SRP241203,SRS5978835,NA,NA,NA,"De Micheli et al, Cell Reports, 2020",10.1016/j.celrep.2020.02.067,https://pubmed.ncbi.nlm.nih.gov/32160558/,NextSeq 500,Single-cell transcriptomic atlas of FACS-sorted mouse muscle tissue cells,We report a series of single-cell transcriptomic datasets of FACS-sorted mouse muscle tissue cells from injured muscle produced using the Chromium 10X technology. Overall design: The overall objective of the study was to generate a transcriptomic atlas of FACS-sorted mouse muscle cell populations at different timepoints post notexin-injury using single-cell RNA-sequencing.
De Micheli 2020a,D5_FACS,NA,muscle,tibialis anterior,cell,female,C57BL/6J,NA,NA,TRUE,TRUE,Mus musculus,GSE143435,GSM4259471,3p_v2,fastq,SRR10870270,NA,SRX7540261,SRP241203,SRS5978836,NA,NA,NA,"De Micheli et al, Cell Reports, 2020",10.1016/j.celrep.2020.02.067,https://pubmed.ncbi.nlm.nih.gov/32160558/,NextSeq 500,Single-cell transcriptomic atlas of FACS-sorted mouse muscle tissue cells,We report a series of single-cell transcriptomic datasets of FACS-sorted mouse muscle tissue cells from injured muscle produced using the Chromium 10X technology. Overall design: The overall objective of the study was to generate a transcriptomic atlas of FACS-sorted mouse muscle cell populations at different timepoints post notexin-injury using single-cell RNA-sequencing.
De Micheli 2020a,D7_FACS,NA,muscle,tibialis anterior,cell,male,C57BL/6J,NA,NA,TRUE,TRUE,Mus musculus,GSE143435,GSM4259472,3p_v2,fastq,SRR10870271,NA,SRX7540262,SRP241203,SRS5978837,NA,NA,NA,"De Micheli et al, Cell Reports, 2020",10.1016/j.celrep.2020.02.067,https://pubmed.ncbi.nlm.nih.gov/32160558/,NextSeq 500,Single-cell transcriptomic atlas of FACS-sorted mouse muscle tissue cells,We report a series of single-cell transcriptomic datasets of FACS-sorted mouse muscle tissue cells from injured muscle produced using the Chromium 10X technology. Overall design: The overall objective of the study was to generate a transcriptomic atlas of FACS-sorted mouse muscle cell populations at different timepoints post notexin-injury using single-cell RNA-sequencing.
De Micheli 2020a,D0_A,NA,muscle,tibialis anterior,cell,female,C57BL/6J,NA,NA,TRUE,TRUE,Mus musculus,GSE143437,GSM4259473,3p_v2,fastq,SRR10870296,NA,SRX7540275,SRP241205,SRS5978850,NA,NA,NA,"De Micheli et al, Cell Reports, 2020",10.1016/j.celrep.2020.02.067,https://pubmed.ncbi.nlm.nih.gov/32160558/,NextSeq 500,Single-cell transcriptomic atlas of the mouse regenerating muscle tissue,We report a series of single-cell transcriptomic datasets of the mouse regenerating muscle tissue produced using the Chromium 10X technology. Overall design: The overall objective of the study was to generate a transcriptomic atlas of the distinct cell populations in the mouse muscle at different timepoints post notexin-injury using single-cell RNA-sequencing.
De Micheli 2020a,D0_B,NA,muscle,tibialis anterior,cell,female,C57BL/6J,NA,NA,TRUE,TRUE,Mus musculus,GSE143437,GSM4259474,3p_v2,fastq,SRR10870297,NA,SRX7540276,SRP241205,SRS5978851,NA,NA,NA,"De Micheli et al, Cell Reports, 2020",10.1016/j.celrep.2020.02.067,https://pubmed.ncbi.nlm.nih.gov/32160558/,NextSeq 500,Single-cell transcriptomic atlas of the mouse regenerating muscle tissue,We report a series of single-cell transcriptomic datasets of the mouse regenerating muscle tissue produced using the Chromium 10X technology. Overall design: The overall objective of the study was to generate a transcriptomic atlas of the distinct cell populations in the mouse muscle at different timepoints post notexin-injury using single-cell RNA-sequencing.
De Micheli 2020a,D2_C,NA,muscle,tibialis anterior,cell,female,C57BL/6J,NA,NA,TRUE,TRUE,Mus musculus,GSE143437,GSM4259476,3p_v2,fastq,SRR10870299,NA,SRX7540278,SRP241205,SRS5978853,NA,NA,NA,"De Micheli et al, Cell Reports, 2020",10.1016/j.celrep.2020.02.067,https://pubmed.ncbi.nlm.nih.gov/32160558/,NextSeq 500,Single-cell transcriptomic atlas of the mouse regenerating muscle tissue,We report a series of single-cell transcriptomic datasets of the mouse regenerating muscle tissue produced using the Chromium 10X technology. Overall design: The overall objective of the study was to generate a transcriptomic atlas of the distinct cell populations in the mouse muscle at different timepoints post notexin-injury using single-cell RNA-sequencing.
De Micheli 2020a,D2_D,NA,muscle,tibialis anterior,cell,female,C57BL/6J,NA,NA,TRUE,TRUE,Mus musculus,GSE143437,GSM4259477,3p_v2,fastq,SRR10870300,NA,SRX7540279,SRP241205,SRS5978854,NA,NA,NA,"De Micheli et al, Cell Reports, 2020",10.1016/j.celrep.2020.02.067,https://pubmed.ncbi.nlm.nih.gov/32160558/,NextSeq 500,Single-cell transcriptomic atlas of the mouse regenerating muscle tissue,We report a series of single-cell transcriptomic datasets of the mouse regenerating muscle tissue produced using the Chromium 10X technology. Overall design: The overall objective of the study was to generate a transcriptomic atlas of the distinct cell populations in the mouse muscle at different timepoints post notexin-injury using single-cell RNA-sequencing.
De Micheli 2020a,D5_A,NA,muscle,tibialis anterior,cell,male,C57BL/6J,NA,NA,TRUE,TRUE,Mus musculus,GSE143437,GSM4259478,3p_v2,fastq,SRR10870301,NA,SRX7540280,SRP241205,SRS5978855,NA,NA,NA,"De Micheli et al, Cell Reports, 2020",10.1016/j.celrep.2020.02.067,https://pubmed.ncbi.nlm.nih.gov/32160558/,NextSeq 500,Single-cell transcriptomic atlas of the mouse regenerating muscle tissue,We report a series of single-cell transcriptomic datasets of the mouse regenerating muscle tissue produced using the Chromium 10X technology. Overall design: The overall objective of the study was to generate a transcriptomic atlas of the distinct cell populations in the mouse muscle at different timepoints post notexin-injury using single-cell RNA-sequencing.
De Micheli 2020a,D5_B,NA,muscle,tibialis anterior,cell,female,C57BL/6J,NA,NA,TRUE,TRUE,Mus musculus,GSE143437,GSM4259479,3p_v2,fastq,SRR10870302,NA,SRX7540281,SRP241205,SRS5978856,NA,NA,NA,"De Micheli et al, Cell Reports, 2020",10.1016/j.celrep.2020.02.067,https://pubmed.ncbi.nlm.nih.gov/32160558/,NextSeq 500,Single-cell transcriptomic atlas of the mouse regenerating muscle tissue,We report a series of single-cell transcriptomic datasets of the mouse regenerating muscle tissue produced using the Chromium 10X technology. Overall design: The overall objective of the study was to generate a transcriptomic atlas of the distinct cell populations in the mouse muscle at different timepoints post notexin-injury using single-cell RNA-sequencing.
De Micheli 2020a,D5_C,NA,muscle,tibialis anterior,cell,male,C57BL/6J,NA,NA,TRUE,TRUE,Mus musculus,GSE143437,GSM4259480,3p_v2,fastq,SRR10870303,NA,SRX7540282,SRP241205,SRS5978857,NA,NA,NA,"De Micheli et al, Cell Reports, 2020",10.1016/j.celrep.2020.02.067,https://pubmed.ncbi.nlm.nih.gov/32160558/,NextSeq 500,Single-cell transcriptomic atlas of the mouse regenerating muscle tissue,We report a series of single-cell transcriptomic datasets of the mouse regenerating muscle tissue produced using the Chromium 10X technology. Overall design: The overall objective of the study was to generate a transcriptomic atlas of the distinct cell populations in the mouse muscle at different timepoints post notexin-injury using single-cell RNA-sequencing.
De Micheli 2020a,D7_C,NA,muscle,tibialis anterior,cell,female,C57BL/6J,NA,NA,TRUE,TRUE,Mus musculus,GSE143437,GSM4259481,3p_v2,fastq,SRR10870304,NA,SRX7540283,SRP241205,SRS5978858,NA,NA,NA,"De Micheli et al, Cell Reports, 2020",10.1016/j.celrep.2020.02.067,https://pubmed.ncbi.nlm.nih.gov/32160558/,NextSeq 500,Single-cell transcriptomic atlas of the mouse regenerating muscle tissue,We report a series of single-cell transcriptomic datasets of the mouse regenerating muscle tissue produced using the Chromium 10X technology. Overall design: The overall objective of the study was to generate a transcriptomic atlas of the distinct cell populations in the mouse muscle at different timepoints post notexin-injury using single-cell RNA-sequencing.
De Micheli 2020a,D7_D,NA,muscle,tibialis anterior,cell,female,C57BL/6J,NA,NA,TRUE,TRUE,Mus musculus,GSE143437,GSM4259482,3p_v2,fastq,SRR10870305,NA,SRX7540284,SRP241205,SRS5978859,NA,NA,NA,"De Micheli et al, Cell Reports, 2020",10.1016/j.celrep.2020.02.067,https://pubmed.ncbi.nlm.nih.gov/32160558/,NextSeq 500,Single-cell transcriptomic atlas of the mouse regenerating muscle tissue,We report a series of single-cell transcriptomic datasets of the mouse regenerating muscle tissue produced using the Chromium 10X technology. Overall design: The overall objective of the study was to generate a transcriptomic atlas of the distinct cell populations in the mouse muscle at different timepoints post notexin-injury using single-cell RNA-sequencing.
Kimmel 2020,Y1_LRC_Q,NA,muscle,muscle stem cell,cell,male,C57Bl/6; H2B-GFP +/-; rtTA +/-,NA,NA,TRUE,FALSE,Mus musculus,GSE143476,GSM4260192,3p_v2,fastq,SRR10874104;SRR10874105,NA,SRX7543861,SRP241629,SRS5981902,SAMN13830212,NA,NA,"Kimmel et al, Development, 2020",10.1242/dev.183855,https://pubmed.ncbi.nlm.nih.gov/32198156/,Illumina NovaSeq 6000,Aging induces aberrant state transition kinetics in murine muscle stem cells,"Label retaining and non-retaining muscle stem cells from young and aged H2B-GFP+/-;rtTA+/- were profiled by single cell RNA-seq at two timepoints Overall design: 2 young (3 mo) and 2 aged (20 mo) H2B-GFP+/-;rtTA were labeled to track proliferative history by pulsing DOX in development (E10.5-E16.5). Label retaining and non-retaining cells were isolated from these animals by FACS. A set of cells from each animal was profiled immediately, while another set of cells was activated for 18 hours in vitro (10% HS, DMEM, culture plastic + sarcoma derived ECM) prior to profiling. Single cell RNA-seq was performed following the 10X Chromium Single Cell v2 kit."
Kimmel 2020,Y1_LRC_A,NA,muscle,muscle stem cell,cell,male,C57Bl/6; H2B-GFP +/-; rtTA +/-,NA,NA,TRUE,FALSE,Mus musculus,GSE143476,GSM4260193,3p_v2,fastq,SRR10874106;SRR10874107,NA,SRX7543862,SRP241629,SRS5981903,SAMN13830211,NA,NA,"Kimmel et al, Development, 2020",10.1242/dev.183855,https://pubmed.ncbi.nlm.nih.gov/32198156/,Illumina NovaSeq 6000,Aging induces aberrant state transition kinetics in murine muscle stem cells,"Label retaining and non-retaining muscle stem cells from young and aged H2B-GFP+/-;rtTA+/- were profiled by single cell RNA-seq at two timepoints Overall design: 2 young (3 mo) and 2 aged (20 mo) H2B-GFP+/-;rtTA were labeled to track proliferative history by pulsing DOX in development (E10.5-E16.5). Label retaining and non-retaining cells were isolated from these animals by FACS. A set of cells from each animal was profiled immediately, while another set of cells was activated for 18 hours in vitro (10% HS, DMEM, culture plastic + sarcoma derived ECM) prior to profiling. Single cell RNA-seq was performed following the 10X Chromium Single Cell v2 kit."
Kimmel 2020,Y2_LRC_Q,NA,muscle,muscle stem cell,cell,male,C57Bl/6; H2B-GFP +/-; rtTA +/-,NA,NA,TRUE,FALSE,Mus musculus,GSE143476,GSM4260194,3p_v2,fastq,SRR10874108;SRR10874109,NA,SRX7543863,SRP241629,SRS5981904,SAMN13830210,NA,NA,"Kimmel et al, Development, 2020",10.1242/dev.183855,https://pubmed.ncbi.nlm.nih.gov/32198156/,Illumina NovaSeq 6000,Aging induces aberrant state transition kinetics in murine muscle stem cells,"Label retaining and non-retaining muscle stem cells from young and aged H2B-GFP+/-;rtTA+/- were profiled by single cell RNA-seq at two timepoints Overall design: 2 young (3 mo) and 2 aged (20 mo) H2B-GFP+/-;rtTA were labeled to track proliferative history by pulsing DOX in development (E10.5-E16.5). Label retaining and non-retaining cells were isolated from these animals by FACS. A set of cells from each animal was profiled immediately, while another set of cells was activated for 18 hours in vitro (10% HS, DMEM, culture plastic + sarcoma derived ECM) prior to profiling. Single cell RNA-seq was performed following the 10X Chromium Single Cell v2 kit."
Kimmel 2020,Y2_LRC_A,NA,muscle,muscle stem cell,cell,male,C57Bl/6; H2B-GFP +/-; rtTA +/-,NA,NA,TRUE,FALSE,Mus musculus,GSE143476,GSM4260195,3p_v2,fastq,SRR10874110;SRR10874111,NA,SRX7543864,SRP241629,SRS5981905,SAMN13830209,NA,NA,"Kimmel et al, Development, 2020",10.1242/dev.183855,https://pubmed.ncbi.nlm.nih.gov/32198156/,Illumina NovaSeq 6000,Aging induces aberrant state transition kinetics in murine muscle stem cells,"Label retaining and non-retaining muscle stem cells from young and aged H2B-GFP+/-;rtTA+/- were profiled by single cell RNA-seq at two timepoints Overall design: 2 young (3 mo) and 2 aged (20 mo) H2B-GFP+/-;rtTA were labeled to track proliferative history by pulsing DOX in development (E10.5-E16.5). Label retaining and non-retaining cells were isolated from these animals by FACS. A set of cells from each animal was profiled immediately, while another set of cells was activated for 18 hours in vitro (10% HS, DMEM, culture plastic + sarcoma derived ECM) prior to profiling. Single cell RNA-seq was performed following the 10X Chromium Single Cell v2 kit."
Kimmel 2020,Y1_nonLRC_Q,NA,muscle,muscle stem cell,cell,male,C57Bl/6; H2B-GFP +/-; rtTA +/-,NA,NA,TRUE,FALSE,Mus musculus,GSE143476,GSM4260196,3p_v2,fastq,SRR10874112;SRR10874113,NA,SRX7543865,SRP241629,SRS5981906,SAMN13830208,NA,NA,"Kimmel et al, Development, 2020",10.1242/dev.183855,https://pubmed.ncbi.nlm.nih.gov/32198156/,Illumina NovaSeq 6000,Aging induces aberrant state transition kinetics in murine muscle stem cells,"Label retaining and non-retaining muscle stem cells from young and aged H2B-GFP+/-;rtTA+/- were profiled by single cell RNA-seq at two timepoints Overall design: 2 young (3 mo) and 2 aged (20 mo) H2B-GFP+/-;rtTA were labeled to track proliferative history by pulsing DOX in development (E10.5-E16.5). Label retaining and non-retaining cells were isolated from these animals by FACS. A set of cells from each animal was profiled immediately, while another set of cells was activated for 18 hours in vitro (10% HS, DMEM, culture plastic + sarcoma derived ECM) prior to profiling. Single cell RNA-seq was performed following the 10X Chromium Single Cell v2 kit."
Kimmel 2020,Y1_nonLRC_A,NA,muscle,muscle stem cell,cell,male,C57Bl/6; H2B-GFP +/-; rtTA +/-,NA,NA,TRUE,FALSE,Mus musculus,GSE143476,GSM4260197,3p_v2,fastq,SRR10874114;SRR10874115,NA,SRX7543866,SRP241629,SRS5981907,SAMN13830207,NA,NA,"Kimmel et al, Development, 2020",10.1242/dev.183855,https://pubmed.ncbi.nlm.nih.gov/32198156/,Illumina NovaSeq 6000,Aging induces aberrant state transition kinetics in murine muscle stem cells,"Label retaining and non-retaining muscle stem cells from young and aged H2B-GFP+/-;rtTA+/- were profiled by single cell RNA-seq at two timepoints Overall design: 2 young (3 mo) and 2 aged (20 mo) H2B-GFP+/-;rtTA were labeled to track proliferative history by pulsing DOX in development (E10.5-E16.5). Label retaining and non-retaining cells were isolated from these animals by FACS. A set of cells from each animal was profiled immediately, while another set of cells was activated for 18 hours in vitro (10% HS, DMEM, culture plastic + sarcoma derived ECM) prior to profiling. Single cell RNA-seq was performed following the 10X Chromium Single Cell v2 kit."
Kimmel 2020,Y2_nonLRC_Q,NA,muscle,muscle stem cell,cell,male,C57Bl/6; H2B-GFP +/-; rtTA +/-,NA,NA,TRUE,FALSE,Mus musculus,GSE143476,GSM4260198,3p_v2,fastq,SRR10874116;SRR10874117,NA,SRX7543867,SRP241629,SRS5981909,SAMN13830206,NA,NA,"Kimmel et al, Development, 2020",10.1242/dev.183855,https://pubmed.ncbi.nlm.nih.gov/32198156/,Illumina NovaSeq 6000,Aging induces aberrant state transition kinetics in murine muscle stem cells,"Label retaining and non-retaining muscle stem cells from young and aged H2B-GFP+/-;rtTA+/- were profiled by single cell RNA-seq at two timepoints Overall design: 2 young (3 mo) and 2 aged (20 mo) H2B-GFP+/-;rtTA were labeled to track proliferative history by pulsing DOX in development (E10.5-E16.5). Label retaining and non-retaining cells were isolated from these animals by FACS. A set of cells from each animal was profiled immediately, while another set of cells was activated for 18 hours in vitro (10% HS, DMEM, culture plastic + sarcoma derived ECM) prior to profiling. Single cell RNA-seq was performed following the 10X Chromium Single Cell v2 kit."
Kimmel 2020,Y2_nonLRC_A,NA,muscle,muscle stem cell,cell,male,C57Bl/6; H2B-GFP +/-; rtTA +/-,NA,NA,TRUE,FALSE,Mus musculus,GSE143476,GSM4260199,3p_v2,fastq,SRR10874118;SRR10874119,NA,SRX7543868,SRP241629,SRS5981908,SAMN13830205,NA,NA,"Kimmel et al, Development, 2020",10.1242/dev.183855,https://pubmed.ncbi.nlm.nih.gov/32198156/,Illumina NovaSeq 6000,Aging induces aberrant state transition kinetics in murine muscle stem cells,"Label retaining and non-retaining muscle stem cells from young and aged H2B-GFP+/-;rtTA+/- were profiled by single cell RNA-seq at two timepoints Overall design: 2 young (3 mo) and 2 aged (20 mo) H2B-GFP+/-;rtTA were labeled to track proliferative history by pulsing DOX in development (E10.5-E16.5). Label retaining and non-retaining cells were isolated from these animals by FACS. A set of cells from each animal was profiled immediately, while another set of cells was activated for 18 hours in vitro (10% HS, DMEM, culture plastic + sarcoma derived ECM) prior to profiling. Single cell RNA-seq was performed following the 10X Chromium Single Cell v2 kit."
Kimmel 2020,A1_LRC_Q,NA,muscle,muscle stem cell,cell,male,C57Bl/6; H2B-GFP +/-; rtTA +/-,NA,NA,TRUE,FALSE,Mus musculus,GSE143476,GSM4260200,3p_v2,fastq,SRR10874120;SRR10874121,NA,SRX7543869,SRP241629,SRS5981910,SAMN13830204,NA,NA,"Kimmel et al, Development, 2020",10.1242/dev.183855,https://pubmed.ncbi.nlm.nih.gov/32198156/,Illumina NovaSeq 6000,Aging induces aberrant state transition kinetics in murine muscle stem cells,"Label retaining and non-retaining muscle stem cells from young and aged H2B-GFP+/-;rtTA+/- were profiled by single cell RNA-seq at two timepoints Overall design: 2 young (3 mo) and 2 aged (20 mo) H2B-GFP+/-;rtTA were labeled to track proliferative history by pulsing DOX in development (E10.5-E16.5). Label retaining and non-retaining cells were isolated from these animals by FACS. A set of cells from each animal was profiled immediately, while another set of cells was activated for 18 hours in vitro (10% HS, DMEM, culture plastic + sarcoma derived ECM) prior to profiling. Single cell RNA-seq was performed following the 10X Chromium Single Cell v2 kit."
Kimmel 2020,A1_LRC_A,NA,muscle,muscle stem cell,cell,male,C57Bl/6; H2B-GFP +/-; rtTA +/-,NA,NA,TRUE,FALSE,Mus musculus,GSE143476,GSM4260201,3p_v2,fastq,SRR10874122;SRR10874123,NA,SRX7543870,SRP241629,SRS5981911,SAMN13830203,NA,NA,"Kimmel et al, Development, 2020",10.1242/dev.183855,https://pubmed.ncbi.nlm.nih.gov/32198156/,Illumina NovaSeq 6000,Aging induces aberrant state transition kinetics in murine muscle stem cells,"Label retaining and non-retaining muscle stem cells from young and aged H2B-GFP+/-;rtTA+/- were profiled by single cell RNA-seq at two timepoints Overall design: 2 young (3 mo) and 2 aged (20 mo) H2B-GFP+/-;rtTA were labeled to track proliferative history by pulsing DOX in development (E10.5-E16.5). Label retaining and non-retaining cells were isolated from these animals by FACS. A set of cells from each animal was profiled immediately, while another set of cells was activated for 18 hours in vitro (10% HS, DMEM, culture plastic + sarcoma derived ECM) prior to profiling. Single cell RNA-seq was performed following the 10X Chromium Single Cell v2 kit."
Kimmel 2020,A2_LRC_Q,NA,muscle,muscle stem cell,cell,male,C57Bl/6; H2B-GFP +/-; rtTA +/-,NA,NA,TRUE,FALSE,Mus musculus,GSE143476,GSM4260202,3p_v2,fastq,SRR10874124;SRR10874125,NA,SRX7543871,SRP241629,SRS5981912,SAMN13830202,NA,NA,"Kimmel et al, Development, 2020",10.1242/dev.183855,https://pubmed.ncbi.nlm.nih.gov/32198156/,Illumina NovaSeq 6000,Aging induces aberrant state transition kinetics in murine muscle stem cells,"Label retaining and non-retaining muscle stem cells from young and aged H2B-GFP+/-;rtTA+/- were profiled by single cell RNA-seq at two timepoints Overall design: 2 young (3 mo) and 2 aged (20 mo) H2B-GFP+/-;rtTA were labeled to track proliferative history by pulsing DOX in development (E10.5-E16.5). Label retaining and non-retaining cells were isolated from these animals by FACS. A set of cells from each animal was profiled immediately, while another set of cells was activated for 18 hours in vitro (10% HS, DMEM, culture plastic + sarcoma derived ECM) prior to profiling. Single cell RNA-seq was performed following the 10X Chromium Single Cell v2 kit."
Kimmel 2020,A2_LRC_A,NA,muscle,muscle stem cell,cell,male,C57Bl/6; H2B-GFP +/-; rtTA +/-,NA,NA,TRUE,FALSE,Mus musculus,GSE143476,GSM4260203,3p_v2,fastq,SRR10874126;SRR10874127,NA,SRX7543872,SRP241629,SRS5981913,SAMN13830201,NA,NA,"Kimmel et al, Development, 2020",10.1242/dev.183855,https://pubmed.ncbi.nlm.nih.gov/32198156/,Illumina NovaSeq 6000,Aging induces aberrant state transition kinetics in murine muscle stem cells,"Label retaining and non-retaining muscle stem cells from young and aged H2B-GFP+/-;rtTA+/- were profiled by single cell RNA-seq at two timepoints Overall design: 2 young (3 mo) and 2 aged (20 mo) H2B-GFP+/-;rtTA were labeled to track proliferative history by pulsing DOX in development (E10.5-E16.5). Label retaining and non-retaining cells were isolated from these animals by FACS. A set of cells from each animal was profiled immediately, while another set of cells was activated for 18 hours in vitro (10% HS, DMEM, culture plastic + sarcoma derived ECM) prior to profiling. Single cell RNA-seq was performed following the 10X Chromium Single Cell v2 kit."
Kimmel 2020,A1_nonLRC_Q,NA,muscle,muscle stem cell,cell,male,C57Bl/6; H2B-GFP +/-; rtTA +/-,NA,NA,TRUE,FALSE,Mus musculus,GSE143476,GSM4260204,3p_v2,fastq,SRR10874128;SRR10874129,NA,SRX7543873,SRP241629,SRS5981914,SAMN13830200,NA,NA,"Kimmel et al, Development, 2020",10.1242/dev.183855,https://pubmed.ncbi.nlm.nih.gov/32198156/,Illumina NovaSeq 6000,Aging induces aberrant state transition kinetics in murine muscle stem cells,"Label retaining and non-retaining muscle stem cells from young and aged H2B-GFP+/-;rtTA+/- were profiled by single cell RNA-seq at two timepoints Overall design: 2 young (3 mo) and 2 aged (20 mo) H2B-GFP+/-;rtTA were labeled to track proliferative history by pulsing DOX in development (E10.5-E16.5). Label retaining and non-retaining cells were isolated from these animals by FACS. A set of cells from each animal was profiled immediately, while another set of cells was activated for 18 hours in vitro (10% HS, DMEM, culture plastic + sarcoma derived ECM) prior to profiling. Single cell RNA-seq was performed following the 10X Chromium Single Cell v2 kit."
Kimmel 2020,A1_nonLRC_A,NA,muscle,muscle stem cell,cell,male,C57Bl/6; H2B-GFP +/-; rtTA +/-,NA,NA,TRUE,FALSE,Mus musculus,GSE143476,GSM4260205,3p_v2,fastq,SRR10874130;SRR10874131,NA,SRX7543874,SRP241629,SRS5981915,SAMN13830199,NA,NA,"Kimmel et al, Development, 2020",10.1242/dev.183855,https://pubmed.ncbi.nlm.nih.gov/32198156/,Illumina NovaSeq 6000,Aging induces aberrant state transition kinetics in murine muscle stem cells,"Label retaining and non-retaining muscle stem cells from young and aged H2B-GFP+/-;rtTA+/- were profiled by single cell RNA-seq at two timepoints Overall design: 2 young (3 mo) and 2 aged (20 mo) H2B-GFP+/-;rtTA were labeled to track proliferative history by pulsing DOX in development (E10.5-E16.5). Label retaining and non-retaining cells were isolated from these animals by FACS. A set of cells from each animal was profiled immediately, while another set of cells was activated for 18 hours in vitro (10% HS, DMEM, culture plastic + sarcoma derived ECM) prior to profiling. Single cell RNA-seq was performed following the 10X Chromium Single Cell v2 kit."
Kimmel 2020,A2_nonLRC_Q,NA,muscle,muscle stem cell,cell,male,C57Bl/6; H2B-GFP +/-; rtTA +/-,NA,NA,TRUE,FALSE,Mus musculus,GSE143476,GSM4260206,3p_v2,fastq,SRR10874132;SRR10874133,NA,SRX7543875,SRP241629,SRS5981916,SAMN13830198,NA,NA,"Kimmel et al, Development, 2020",10.1242/dev.183855,https://pubmed.ncbi.nlm.nih.gov/32198156/,Illumina NovaSeq 6000,Aging induces aberrant state transition kinetics in murine muscle stem cells,"Label retaining and non-retaining muscle stem cells from young and aged H2B-GFP+/-;rtTA+/- were profiled by single cell RNA-seq at two timepoints Overall design: 2 young (3 mo) and 2 aged (20 mo) H2B-GFP+/-;rtTA were labeled to track proliferative history by pulsing DOX in development (E10.5-E16.5). Label retaining and non-retaining cells were isolated from these animals by FACS. A set of cells from each animal was profiled immediately, while another set of cells was activated for 18 hours in vitro (10% HS, DMEM, culture plastic + sarcoma derived ECM) prior to profiling. Single cell RNA-seq was performed following the 10X Chromium Single Cell v2 kit."
Kimmel 2020,A2_nonLRC_A,NA,muscle,muscle stem cell,cell,male,C57Bl/6; H2B-GFP +/-; rtTA +/-,NA,NA,TRUE,FALSE,Mus musculus,GSE143476,GSM4260207,3p_v2,fastq,SRR10874134;SRR10874135,NA,SRX7543876,SRP241629,SRS5981917,SAMN13830197,NA,NA,"Kimmel et al, Development, 2020",10.1242/dev.183855,https://pubmed.ncbi.nlm.nih.gov/32198156/,Illumina NovaSeq 6000,Aging induces aberrant state transition kinetics in murine muscle stem cells,"Label retaining and non-retaining muscle stem cells from young and aged H2B-GFP+/-;rtTA+/- were profiled by single cell RNA-seq at two timepoints Overall design: 2 young (3 mo) and 2 aged (20 mo) H2B-GFP+/-;rtTA were labeled to track proliferative history by pulsing DOX in development (E10.5-E16.5). Label retaining and non-retaining cells were isolated from these animals by FACS. A set of cells from each animal was profiled immediately, while another set of cells was activated for 18 hours in vitro (10% HS, DMEM, culture plastic + sarcoma derived ECM) prior to profiling. Single cell RNA-seq was performed following the 10X Chromium Single Cell v2 kit."
De Micheli 2020c,hu07_021219,NA,muscle,Flexor hallucis longus,cell,NA,NA,NA,NA,TRUE,TRUE,Homo sapiens,GSE143704,GSM4272893,3p_v3,fastq,SRR10897760,NA,SRX7566587,SRP242029,SRS6002992,NA,NA,NA,"De Micheli et al, Skeletal Muscle, 2020",10.1186/s13395-020-00236-3,https://pubmed.ncbi.nlm.nih.gov/32624006/,NextSeq 500,Single-cell transcriptomic atlas of human donor muscle tissue,The overall objective of the study was to survey the cellular and gene expression heterogeneity of human muscle tissue by single-cell RNA-sequencing. Overall design: We report a series of single-cell transcriptomic datasets of human donor muscle tissue produced using the Chromium 10X technology.
De Micheli 2020c,hu01_061419,NA,muscle,serratus,cell,NA,NA,NA,NA,TRUE,TRUE,Homo sapiens,GSE143704,GSM4272894,3p_v3,fastq,SRR10897761,NA,SRX7566588,SRP242029,SRS6002993,NA,NA,NA,"De Micheli et al, Skeletal Muscle, 2020",10.1186/s13395-020-00236-3,https://pubmed.ncbi.nlm.nih.gov/32624006/,NextSeq 500,Single-cell transcriptomic atlas of human donor muscle tissue,The overall objective of the study was to survey the cellular and gene expression heterogeneity of human muscle tissue by single-cell RNA-sequencing. Overall design: We report a series of single-cell transcriptomic datasets of human donor muscle tissue produced using the Chromium 10X technology.
De Micheli 2020c,hu02_062419,NA,muscle,Flexor hallucis longus,cell,NA,NA,NA,NA,TRUE,TRUE,Homo sapiens,GSE143704,GSM4272895,3p_v3,fastq,SRR10897762,NA,SRX7566589,SRP242029,SRS6002994,NA,NA,NA,"De Micheli et al, Skeletal Muscle, 2020",10.1186/s13395-020-00236-3,https://pubmed.ncbi.nlm.nih.gov/32624006/,NextSeq 500,Single-cell transcriptomic atlas of human donor muscle tissue,The overall objective of the study was to survey the cellular and gene expression heterogeneity of human muscle tissue by single-cell RNA-sequencing. Overall design: We report a series of single-cell transcriptomic datasets of human donor muscle tissue produced using the Chromium 10X technology.
De Micheli 2020c,hu03_062719,NA,muscle,orbicularis oris,cell,NA,NA,NA,NA,TRUE,TRUE,Homo sapiens,GSE143704,GSM4272896,3p_v3,fastq,SRR10897763,NA,SRX7566590,SRP242029,SRS6002995,NA,NA,NA,"De Micheli et al, Skeletal Muscle, 2020",10.1186/s13395-020-00236-3,https://pubmed.ncbi.nlm.nih.gov/32624006/,NextSeq 500,Single-cell transcriptomic atlas of human donor muscle tissue,The overall objective of the study was to survey the cellular and gene expression heterogeneity of human muscle tissue by single-cell RNA-sequencing. Overall design: We report a series of single-cell transcriptomic datasets of human donor muscle tissue produced using the Chromium 10X technology.
De Micheli 2020c,hu04_080619,NA,muscle,eye lid,cell,NA,NA,NA,NA,TRUE,TRUE,Homo sapiens,GSE143704,GSM4272897,3p_v3,fastq,SRR10897764,NA,SRX7566591,SRP242029,SRS6002996,NA,NA,NA,"De Micheli et al, Skeletal Muscle, 2020",10.1186/s13395-020-00236-3,https://pubmed.ncbi.nlm.nih.gov/32624006/,NextSeq 500,Single-cell transcriptomic atlas of human donor muscle tissue,The overall objective of the study was to survey the cellular and gene expression heterogeneity of human muscle tissue by single-cell RNA-sequencing. Overall design: We report a series of single-cell transcriptomic datasets of human donor muscle tissue produced using the Chromium 10X technology.
De Micheli 2020c,hu08_092618,NA,muscle,vastus lateralis,cell,NA,NA,NA,NA,TRUE,TRUE,Homo sapiens,GSE143704,GSM4272898,3p_v2,fastq,SRR10897765,NA,SRX7566592,SRP242029,SRS6002997,NA,NA,NA,"De Micheli et al, Skeletal Muscle, 2020",10.1186/s13395-020-00236-3,https://pubmed.ncbi.nlm.nih.gov/32624006/,NextSeq 500,Single-cell transcriptomic atlas of human donor muscle tissue,The overall objective of the study was to survey the cellular and gene expression heterogeneity of human muscle tissue by single-cell RNA-sequencing. Overall design: We report a series of single-cell transcriptomic datasets of human donor muscle tissue produced using the Chromium 10X technology.
De Micheli 2020c,hu09_092718,NA,muscle,external oblique,cell,NA,NA,NA,NA,TRUE,TRUE,Homo sapiens,GSE143704,GSM4272899,3p_v2,fastq,SRR10897766,NA,SRX7566593,SRP242029,SRS6002998,NA,NA,NA,"De Micheli et al, Skeletal Muscle, 2020",10.1186/s13395-020-00236-3,https://pubmed.ncbi.nlm.nih.gov/32624006/,NextSeq 500,Single-cell transcriptomic atlas of human donor muscle tissue,The overall objective of the study was to survey the cellular and gene expression heterogeneity of human muscle tissue by single-cell RNA-sequencing. Overall design: We report a series of single-cell transcriptomic datasets of human donor muscle tissue produced using the Chromium 10X technology.
De Micheli 2020c,hu10_101018,NA,muscle,rectus abdominus,cell,NA,NA,NA,NA,TRUE,TRUE,Homo sapiens,GSE143704,GSM4272900,3p_v2,fastq,SRR10897767,NA,SRX7566594,SRP242029,SRS6002999,NA,NA,NA,"De Micheli et al, Skeletal Muscle, 2020",10.1186/s13395-020-00236-3,https://pubmed.ncbi.nlm.nih.gov/32624006/,NextSeq 500,Single-cell transcriptomic atlas of human donor muscle tissue,The overall objective of the study was to survey the cellular and gene expression heterogeneity of human muscle tissue by single-cell RNA-sequencing. Overall design: We report a series of single-cell transcriptomic datasets of human donor muscle tissue produced using the Chromium 10X technology.
De Micheli 2020c,hu05_111418,NA,muscle,trapezius,cell,NA,NA,NA,NA,TRUE,TRUE,Homo sapiens,GSE143704,GSM4272901,3p_v3,fastq,SRR10897768,NA,SRX7566595,SRP242029,SRS6003000,NA,NA,NA,"De Micheli et al, Skeletal Muscle, 2020",10.1186/s13395-020-00236-3,https://pubmed.ncbi.nlm.nih.gov/32624006/,NextSeq 500,Single-cell transcriptomic atlas of human donor muscle tissue,The overall objective of the study was to survey the cellular and gene expression heterogeneity of human muscle tissue by single-cell RNA-sequencing. Overall design: We report a series of single-cell transcriptomic datasets of human donor muscle tissue produced using the Chromium 10X technology.
De Micheli 2020c,hu06_120518,NA,muscle,right external oblique,cell,NA,NA,NA,NA,TRUE,TRUE,Homo sapiens,GSE143704,GSM4272902,3p_v3,fastq,SRR10897769,NA,SRX7566596,SRP242029,SRS6003001,NA,NA,NA,"De Micheli et al, Skeletal Muscle, 2020",10.1186/s13395-020-00236-3,https://pubmed.ncbi.nlm.nih.gov/32624006/,NextSeq 500,Single-cell transcriptomic atlas of human donor muscle tissue,The overall objective of the study was to survey the cellular and gene expression heterogeneity of human muscle tissue by single-cell RNA-sequencing. Overall design: We report a series of single-cell transcriptomic datasets of human donor muscle tissue produced using the Chromium 10X technology.
Chestnut 2020,10X_Etv2_heterozygous_20ss,Jul11_2016_15-18ss_etv2gfp; ,muscle,NA,NA,NA,NA,NA,75bp R1,TRUE,TRUE,Danio rerio,GSE143750,GSM4230286,NA,fastq,SRR10753170;SRR10753171;SRR10753172;SRR10753173;SRR10753174;SRR10753175;SRR10753176;SRR10753177;SRR10753178;SRR10753179;SRR10753180;SRR10753181;SRR10753182;SRR10753183;SRR10753184;SRR10753185;SRR10753186;SRR10753187;SRR10753188;SRR10753189;SRR10753190;SRR10753191;SRR10753192;SRR10753193;SRR10753194;SRR10753195;SRR10753196;SRR10753197;SRR10753198;SRR10753199;SRR10753200;SRR10753201;SRR10753202;SRR10753203;SRR10753204;SRR10753205;SRR10753206;SRR10753207;SRR10753208;SRR10753209;SRR10753210;SRR10753211;SRR10753212;SRR10753213;SRR10753214;SRR10753215;SRR10753216;SRR10753217,NA,SRX7427898,SRP238479,SRS5873831,SAMN13663991,NA,NA,"Chestnut et al, Nat Comm, 2020",10.1038/s41467-020-16515-y,https://pubmed.ncbi.nlm.nih.gov/32493965/,Illumina HiSeq 2500,Single-cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2-deficient vascular progenitors into skeletal muscle,"During vertebrate embryogenesis, vascular endothelial cells originate in the lateral plate mesoderm (LPM) next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single-cell transcriptomic analysis of hematovascular development in wild-type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line, in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly, a cell population with the skeletal muscle signature was observed in etv2-deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites, elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2-deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors, thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally, we demonstrate that arterial progenitors co-express multiple arterial and venous markers during early stages of vasculogenesis, suggesting multi-potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular, muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each"
Chestnut 2020,10X_Etv2_homozygous_20ss,Aug1_2016_20ss_etv2gfp; 20 somite stage,muscle,NA,NA,NA,NA,NA,75bp R1,TRUE,TRUE,Danio rerio,GSE143750,GSM4230287,NA,fastq,SRR10753218;SRR10753219;SRR10753220;SRR10753221;SRR10753222;SRR10753223;SRR10753224;SRR10753225;SRR10753226;SRR10753227;SRR10753228;SRR10753229;SRR10753230;SRR10753231;SRR10753232;SRR10753233;SRR10753234;SRR10753235;SRR10753236;SRR10753237;SRR10753238;SRR10753239;SRR10753240;SRR10753241;SRR10753242;SRR10753243;SRR10753244;SRR10753245;SRR10753246;SRR10753247;SRR10753248;SRR10753249;SRR10753250;SRR10753251;SRR10753252;SRR10753253;SRR10753254;SRR10753255;SRR10753256;SRR10753257;SRR10753258;SRR10753259;SRR10753260;SRR10753261;SRR10753262;SRR10753263;SRR10753264;SRR10753265,NA,SRX7427899,SRP238479,SRS5873832,SAMN13663990,NA,NA,"Chestnut et al, Nat Comm, 2020",10.1038/s41467-020-16515-y,https://pubmed.ncbi.nlm.nih.gov/32493965/,Illumina HiSeq 2500,Single-cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2-deficient vascular progenitors into skeletal muscle,"During vertebrate embryogenesis, vascular endothelial cells originate in the lateral plate mesoderm (LPM) next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single-cell transcriptomic analysis of hematovascular development in wild-type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line, in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly, a cell population with the skeletal muscle signature was observed in etv2-deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites, elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2-deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors, thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally, we demonstrate that arterial progenitors co-express multiple arterial and venous markers during early stages of vasculogenesis, suggesting multi-potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular, muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each"
Stepien 2020,d0IR1,day 0 control,muscle,macrophage,cell,female,C57BL/6J,NA,NA,TRUE,TRUE,Mus musculus,GSE144270,GSM4284745,3p_v2,bam,SRR11007782,NA,SRX7634926,SRP245347,SRS6065656,SAMN13927200,NA,NA,"Stepien et al, J Immunol, 2020",10.4049/jimmunol.1900814,https://pubmed.ncbi.nlm.nih.gov/32161098/,Illumina HiSeq 4000,Myeloid cell analysis during a pro-fibrotic ischemia-reperfusion and cardiotoxin muscle injury.,"Myeloid cells are critical to the development of fibrosis following muscle injury, however, the mechanism of their role in fibrosis formation remains unclear. Here we demonstrate that myeloid cell-derived TGF-?1 signaling is increased in a pro-fibrotic ischemia-reperfusion and cardiotoxin (IR/CTX) muscle injury model. This study analyzes scRNAsequencing from the fibrotic region after a pro-fibrotic ischemia-reperfusion and cardiotoxin muscle injury. Overall design: We used 10X genomics to perform single cell sequencing of cells from the fibrotic area after a pro-fibrotic ischemia-reperfusion and cardiotoxin muscle injury."
Stepien 2020,d0IR2,day 0 control,muscle,macrophage,cell,female,C57BL/6J,NA,NA,TRUE,TRUE,Mus musculus,GSE144270,GSM4284746,3p_v2,bam,SRR11007783,NA,SRX7634927,SRP245347,SRS6065658,SAMN13927206,NA,NA,"Stepien et al, J Immunol, 2020",10.4049/jimmunol.1900814,https://pubmed.ncbi.nlm.nih.gov/32161098/,Illumina HiSeq 4000,Myeloid cell analysis during a pro-fibrotic ischemia-reperfusion and cardiotoxin muscle injury.,"Myeloid cells are critical to the development of fibrosis following muscle injury, however, the mechanism of their role in fibrosis formation remains unclear. Here we demonstrate that myeloid cell-derived TGF-?1 signaling is increased in a pro-fibrotic ischemia-reperfusion and cardiotoxin (IR/CTX) muscle injury model. This study analyzes scRNAsequencing from the fibrotic region after a pro-fibrotic ischemia-reperfusion and cardiotoxin muscle injury. Overall design: We used 10X genomics to perform single cell sequencing of cells from the fibrotic area after a pro-fibrotic ischemia-reperfusion and cardiotoxin muscle injury."
Stepien 2020,d3IR1,day 3 IR/CTX injury,muscle,macrophage,cell,male,C57BL/6J,NA,NA,TRUE,TRUE,Mus musculus,GSE144270,GSM4284747,3p_v2,bam,SRR10969329,NA,SRX7634928,SRP245347,SRS6065657,SAMN13927205,NA,NA,"Stepien et al, J Immunol, 2020",10.4049/jimmunol.1900814,https://pubmed.ncbi.nlm.nih.gov/32161098/,Illumina HiSeq 4000,Myeloid cell analysis during a pro-fibrotic ischemia-reperfusion and cardiotoxin muscle injury.,"Myeloid cells are critical to the development of fibrosis following muscle injury, however, the mechanism of their role in fibrosis formation remains unclear. Here we demonstrate that myeloid cell-derived TGF-?1 signaling is increased in a pro-fibrotic ischemia-reperfusion and cardiotoxin (IR/CTX) muscle injury model. This study analyzes scRNAsequencing from the fibrotic region after a pro-fibrotic ischemia-reperfusion and cardiotoxin muscle injury. Overall design: We used 10X genomics to perform single cell sequencing of cells from the fibrotic area after a pro-fibrotic ischemia-reperfusion and cardiotoxin muscle injury."
Stepien 2020,d3IR2,day 3 IR/CTX injury,muscle,macrophage,cell,male,C57BL/6J,NA,NA,TRUE,TRUE,Mus musculus,GSE144270,GSM4284748,3p_v2,bam,SRR10969330,NA,SRX7634929,SRP245347,SRS6065659,SAMN13927203,NA,NA,"Stepien et al, J Immunol, 2020",10.4049/jimmunol.1900814,https://pubmed.ncbi.nlm.nih.gov/32161098/,Illumina HiSeq 4000,Myeloid cell analysis during a pro-fibrotic ischemia-reperfusion and cardiotoxin muscle injury.,"Myeloid cells are critical to the development of fibrosis following muscle injury, however, the mechanism of their role in fibrosis formation remains unclear. Here we demonstrate that myeloid cell-derived TGF-?1 signaling is increased in a pro-fibrotic ischemia-reperfusion and cardiotoxin (IR/CTX) muscle injury model. This study analyzes scRNAsequencing from the fibrotic region after a pro-fibrotic ischemia-reperfusion and cardiotoxin muscle injury. Overall design: We used 10X genomics to perform single cell sequencing of cells from the fibrotic area after a pro-fibrotic ischemia-reperfusion and cardiotoxin muscle injury."
Stepien 2020,d3IR3,day 3 IR/CTX injury,muscle,macrophage,cell,male,C57BL/6J,NA,NA,TRUE,TRUE,Mus musculus,GSE144270,GSM4284749,3p_v2,bam,SRR10969331,NA,SRX7634930,SRP245347,SRS6065660,SAMN13927202,NA,NA,"Stepien et al, J Immunol, 2020",10.4049/jimmunol.1900814,https://pubmed.ncbi.nlm.nih.gov/32161098/,Illumina HiSeq 4000,Myeloid cell analysis during a pro-fibrotic ischemia-reperfusion and cardiotoxin muscle injury.,"Myeloid cells are critical to the development of fibrosis following muscle injury, however, the mechanism of their role in fibrosis formation remains unclear. Here we demonstrate that myeloid cell-derived TGF-?1 signaling is increased in a pro-fibrotic ischemia-reperfusion and cardiotoxin (IR/CTX) muscle injury model. This study analyzes scRNAsequencing from the fibrotic region after a pro-fibrotic ischemia-reperfusion and cardiotoxin muscle injury. Overall design: We used 10X genomics to perform single cell sequencing of cells from the fibrotic area after a pro-fibrotic ischemia-reperfusion and cardiotoxin muscle injury."
Baht 2020,Uninjured Control,NA,muscle,tibialis anterior,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE145236,GSM4319248,3p_v2,bam,SRR11107252,NA,SRX7744923,SRP249928,SRS6165328,SAMN14128630,NA,NA,"Baht et al, Nat Metab, 2020",10.1038/s42255-020-0184-y,https://pubmed.ncbi.nlm.nih.gov/32694780/,NextSeq 500,Single Cell RNAseq on whole muscle one day after injury and uninjured control,Cellular landscape changes drastically after injury Overall design: The Tibialis Anterior (TA) muscle was injected with barium chloride and collected 24 hours after.
Baht 2020,Injured (1d),Treatment protocol IM injection of 1.2% BaCl,muscle,tibialis anterior,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE145236,GSM4319249,3p_v2,bam,SRR11107253,NA,SRX7744924,SRP249928,SRS6165329,SAMN14128629,NA,NA,"Baht et al, Nat Metab, 2020",10.1038/s42255-020-0184-y,https://pubmed.ncbi.nlm.nih.gov/32694780/,NextSeq 500,Single Cell RNAseq on whole muscle one day after injury and uninjured control,Cellular landscape changes drastically after injury Overall design: The Tibialis Anterior (TA) muscle was injected with barium chloride and collected 24 hours after.
Kimmel 2021,Aged_1_Pre-differentiation,Freshly-isolated 0 hours,muscle,cultured primary cells,cell,NA,NA,NA,NA,TRUE,FALSE,Mus musculus,GSE145256,GSM4310251,3p_v3,fastq,SRR11080211,NA,SRX7719263,SRP249325,SRS6141574,SAMN14096384,NA,NA,"Kimmel et al, Cell Reports, 2021",10.1016/j.celrep.2021.109046,https://pubmed.ncbi.nlm.nih.gov/33910007/,Illumina HiSeq 2500,Differentiation reveals the plasticity of age-related change in murine muscle progenitors,"Skeletal muscle experiences a decline in lean mass and regenerative potential with age, in part due to intrinsic changes in progenitor cells. However, it remains unclear if age-related changes in progenitors persist across a differentiation trajectory or if new age-related changes manifest in differentiated cells. To investigate this possibility, we performed single cell RNA-seq on muscle mononuclear cells from young and aged mice and profiled muscle stem cells (MuSCs) and fibro/adipose progenitors (FAPs) after differentiation. Differentiation increased the magnitude of age-related change in MuSCs and FAPs, but also masked a subset of age-related changes present in progenitors. Using a dynamical systems approach and RNA velocity, we found that aged MuSCs follow the same differentiation trajectory as young cells, but stall in differentiation near a commitment decision. Our results suggest that age-related changes are plastic across differentiation trajectories and that fate commitment decisions are delayed in aged myogenic cells. Overall design: Muscle mononuclear cells were isolated from 2 young (3 m.o.) and 2 aged (20 m.o.) C57Bl/6 mice. All cells in the muscle mononuclear compartment were transcriptionally profiled immediately after isolation using the 10X Chromium Single Cell Transcriptome v3 technology. Muscle stem cells and fibro/adipose progenitors were additionally profiled both  after a differentiation challenge using the same library preparation method."
Kimmel 2021,Aged_2_Pre-differentiation,Freshly-isolated 0 hours,muscle,cultured primary cells,cell,NA,NA,NA,NA,TRUE,FALSE,Mus musculus,GSE145256,GSM4310252,3p_v3,fastq,SRR11080212,NA,SRX7719264,SRP249325,SRS6141575,SAMN14096391,NA,NA,"Kimmel et al, Cell Reports, 2021",10.1016/j.celrep.2021.109046,https://pubmed.ncbi.nlm.nih.gov/33910007/,Illumina HiSeq 2500,Differentiation reveals the plasticity of age-related change in murine muscle progenitors,"Skeletal muscle experiences a decline in lean mass and regenerative potential with age, in part due to intrinsic changes in progenitor cells. However, it remains unclear if age-related changes in progenitors persist across a differentiation trajectory or if new age-related changes manifest in differentiated cells. To investigate this possibility, we performed single cell RNA-seq on muscle mononuclear cells from young and aged mice and profiled muscle stem cells (MuSCs) and fibro/adipose progenitors (FAPs) after differentiation. Differentiation increased the magnitude of age-related change in MuSCs and FAPs, but also masked a subset of age-related changes present in progenitors. Using a dynamical systems approach and RNA velocity, we found that aged MuSCs follow the same differentiation trajectory as young cells, but stall in differentiation near a commitment decision. Our results suggest that age-related changes are plastic across differentiation trajectories and that fate commitment decisions are delayed in aged myogenic cells. Overall design: Muscle mononuclear cells were isolated from 2 young (3 m.o.) and 2 aged (20 m.o.) C57Bl/6 mice. All cells in the muscle mononuclear compartment were transcriptionally profiled immediately after isolation using the 10X Chromium Single Cell Transcriptome v3 technology. Muscle stem cells and fibro/adipose progenitors were additionally profiled both  after a differentiation challenge using the same library preparation method."
Kimmel 2021,Young_1_Pre-differentiation,Freshly-isolated 0 hours,muscle,cultured primary cells,cell,NA,NA,NA,NA,TRUE,FALSE,Mus musculus,GSE145256,GSM4310253,3p_v3,fastq,SRR11080213,NA,SRX7719265,SRP249325,SRS6141576,SAMN14096390,NA,NA,"Kimmel et al, Cell Reports, 2021",10.1016/j.celrep.2021.109046,https://pubmed.ncbi.nlm.nih.gov/33910007/,Illumina HiSeq 2500,Differentiation reveals the plasticity of age-related change in murine muscle progenitors,"Skeletal muscle experiences a decline in lean mass and regenerative potential with age, in part due to intrinsic changes in progenitor cells. However, it remains unclear if age-related changes in progenitors persist across a differentiation trajectory or if new age-related changes manifest in differentiated cells. To investigate this possibility, we performed single cell RNA-seq on muscle mononuclear cells from young and aged mice and profiled muscle stem cells (MuSCs) and fibro/adipose progenitors (FAPs) after differentiation. Differentiation increased the magnitude of age-related change in MuSCs and FAPs, but also masked a subset of age-related changes present in progenitors. Using a dynamical systems approach and RNA velocity, we found that aged MuSCs follow the same differentiation trajectory as young cells, but stall in differentiation near a commitment decision. Our results suggest that age-related changes are plastic across differentiation trajectories and that fate commitment decisions are delayed in aged myogenic cells. Overall design: Muscle mononuclear cells were isolated from 2 young (3 m.o.) and 2 aged (20 m.o.) C57Bl/6 mice. All cells in the muscle mononuclear compartment were transcriptionally profiled immediately after isolation using the 10X Chromium Single Cell Transcriptome v3 technology. Muscle stem cells and fibro/adipose progenitors were additionally profiled both  after a differentiation challenge using the same library preparation method."
Kimmel 2021,Young_2_Pre-differenitation,Freshly-isolated 0 hours,muscle,cultured primary cells,cell,NA,NA,NA,NA,TRUE,FALSE,Mus musculus,GSE145256,GSM4310254,3p_v3,fastq,SRR11080214,NA,SRX7719266,SRP249325,SRS6141577,SAMN14096389,NA,NA,"Kimmel et al, Cell Reports, 2021",10.1016/j.celrep.2021.109046,https://pubmed.ncbi.nlm.nih.gov/33910007/,Illumina HiSeq 2500,Differentiation reveals the plasticity of age-related change in murine muscle progenitors,"Skeletal muscle experiences a decline in lean mass and regenerative potential with age, in part due to intrinsic changes in progenitor cells. However, it remains unclear if age-related changes in progenitors persist across a differentiation trajectory or if new age-related changes manifest in differentiated cells. To investigate this possibility, we performed single cell RNA-seq on muscle mononuclear cells from young and aged mice and profiled muscle stem cells (MuSCs) and fibro/adipose progenitors (FAPs) after differentiation. Differentiation increased the magnitude of age-related change in MuSCs and FAPs, but also masked a subset of age-related changes present in progenitors. Using a dynamical systems approach and RNA velocity, we found that aged MuSCs follow the same differentiation trajectory as young cells, but stall in differentiation near a commitment decision. Our results suggest that age-related changes are plastic across differentiation trajectories and that fate commitment decisions are delayed in aged myogenic cells. Overall design: Muscle mononuclear cells were isolated from 2 young (3 m.o.) and 2 aged (20 m.o.) C57Bl/6 mice. All cells in the muscle mononuclear compartment were transcriptionally profiled immediately after isolation using the 10X Chromium Single Cell Transcriptome v3 technology. Muscle stem cells and fibro/adipose progenitors were additionally profiled both  after a differentiation challenge using the same library preparation method."
Kimmel 2021,Aged_1_Post-differentiation,Differentiated 60 hours,muscle,cultured primary cells,cell,NA,NA,NA,NA,TRUE,FALSE,Mus musculus,GSE145256,GSM4310255,3p_v3,fastq,SRR11080215,NA,SRX7719267,SRP249325,SRS6141578,SAMN14096388,NA,NA,"Kimmel et al, Cell Reports, 2021",10.1016/j.celrep.2021.109046,https://pubmed.ncbi.nlm.nih.gov/33910007/,Illumina HiSeq 2500,Differentiation reveals the plasticity of age-related change in murine muscle progenitors,"Skeletal muscle experiences a decline in lean mass and regenerative potential with age, in part due to intrinsic changes in progenitor cells. However, it remains unclear if age-related changes in progenitors persist across a differentiation trajectory or if new age-related changes manifest in differentiated cells. To investigate this possibility, we performed single cell RNA-seq on muscle mononuclear cells from young and aged mice and profiled muscle stem cells (MuSCs) and fibro/adipose progenitors (FAPs) after differentiation. Differentiation increased the magnitude of age-related change in MuSCs and FAPs, but also masked a subset of age-related changes present in progenitors. Using a dynamical systems approach and RNA velocity, we found that aged MuSCs follow the same differentiation trajectory as young cells, but stall in differentiation near a commitment decision. Our results suggest that age-related changes are plastic across differentiation trajectories and that fate commitment decisions are delayed in aged myogenic cells. Overall design: Muscle mononuclear cells were isolated from 2 young (3 m.o.) and 2 aged (20 m.o.) C57Bl/6 mice. All cells in the muscle mononuclear compartment were transcriptionally profiled immediately after isolation using the 10X Chromium Single Cell Transcriptome v3 technology. Muscle stem cells and fibro/adipose progenitors were additionally profiled both  after a differentiation challenge using the same library preparation method."
Kimmel 2021,Aged_2_Post-differentiation,Differentiated 60 hours,muscle,cultured primary cells,cell,NA,NA,NA,NA,TRUE,FALSE,Mus musculus,GSE145256,GSM4310256,3p_v3,fastq,SRR11080216,NA,SRX7719268,SRP249325,SRS6141579,SAMN14096387,NA,NA,"Kimmel et al, Cell Reports, 2021",10.1016/j.celrep.2021.109046,https://pubmed.ncbi.nlm.nih.gov/33910007/,Illumina HiSeq 2500,Differentiation reveals the plasticity of age-related change in murine muscle progenitors,"Skeletal muscle experiences a decline in lean mass and regenerative potential with age, in part due to intrinsic changes in progenitor cells. However, it remains unclear if age-related changes in progenitors persist across a differentiation trajectory or if new age-related changes manifest in differentiated cells. To investigate this possibility, we performed single cell RNA-seq on muscle mononuclear cells from young and aged mice and profiled muscle stem cells (MuSCs) and fibro/adipose progenitors (FAPs) after differentiation. Differentiation increased the magnitude of age-related change in MuSCs and FAPs, but also masked a subset of age-related changes present in progenitors. Using a dynamical systems approach and RNA velocity, we found that aged MuSCs follow the same differentiation trajectory as young cells, but stall in differentiation near a commitment decision. Our results suggest that age-related changes are plastic across differentiation trajectories and that fate commitment decisions are delayed in aged myogenic cells. Overall design: Muscle mononuclear cells were isolated from 2 young (3 m.o.) and 2 aged (20 m.o.) C57Bl/6 mice. All cells in the muscle mononuclear compartment were transcriptionally profiled immediately after isolation using the 10X Chromium Single Cell Transcriptome v3 technology. Muscle stem cells and fibro/adipose progenitors were additionally profiled both  after a differentiation challenge using the same library preparation method."
Kimmel 2021,Young_1_Post-differentiation,Differentiated 60 hours,muscle,cultured primary cells,cell,NA,NA,NA,NA,TRUE,FALSE,Mus musculus,GSE145256,GSM4310257,3p_v3,fastq,SRR11080217,NA,SRX7719269,SRP249325,SRS6141580,SAMN14096386,NA,NA,"Kimmel et al, Cell Reports, 2021",10.1016/j.celrep.2021.109046,https://pubmed.ncbi.nlm.nih.gov/33910007/,Illumina HiSeq 2500,Differentiation reveals the plasticity of age-related change in murine muscle progenitors,"Skeletal muscle experiences a decline in lean mass and regenerative potential with age, in part due to intrinsic changes in progenitor cells. However, it remains unclear if age-related changes in progenitors persist across a differentiation trajectory or if new age-related changes manifest in differentiated cells. To investigate this possibility, we performed single cell RNA-seq on muscle mononuclear cells from young and aged mice and profiled muscle stem cells (MuSCs) and fibro/adipose progenitors (FAPs) after differentiation. Differentiation increased the magnitude of age-related change in MuSCs and FAPs, but also masked a subset of age-related changes present in progenitors. Using a dynamical systems approach and RNA velocity, we found that aged MuSCs follow the same differentiation trajectory as young cells, but stall in differentiation near a commitment decision. Our results suggest that age-related changes are plastic across differentiation trajectories and that fate commitment decisions are delayed in aged myogenic cells. Overall design: Muscle mononuclear cells were isolated from 2 young (3 m.o.) and 2 aged (20 m.o.) C57Bl/6 mice. All cells in the muscle mononuclear compartment were transcriptionally profiled immediately after isolation using the 10X Chromium Single Cell Transcriptome v3 technology. Muscle stem cells and fibro/adipose progenitors were additionally profiled both  after a differentiation challenge using the same library preparation method."
Kimmel 2021,Young_2_Post-differentiation,Differentiated 60 hours,muscle,cultured primary cells,cell,NA,NA,NA,NA,TRUE,FALSE,Mus musculus,GSE145256,GSM4310258,3p_v3,fastq,SRR11080218,NA,SRX7719270,SRP249325,SRS6141581,SAMN14096385,NA,NA,"Kimmel et al, Cell Reports, 2021",10.1016/j.celrep.2021.109046,https://pubmed.ncbi.nlm.nih.gov/33910007/,Illumina HiSeq 2500,Differentiation reveals the plasticity of age-related change in murine muscle progenitors,"Skeletal muscle experiences a decline in lean mass and regenerative potential with age, in part due to intrinsic changes in progenitor cells. However, it remains unclear if age-related changes in progenitors persist across a differentiation trajectory or if new age-related changes manifest in differentiated cells. To investigate this possibility, we performed single cell RNA-seq on muscle mononuclear cells from young and aged mice and profiled muscle stem cells (MuSCs) and fibro/adipose progenitors (FAPs) after differentiation. Differentiation increased the magnitude of age-related change in MuSCs and FAPs, but also masked a subset of age-related changes present in progenitors. Using a dynamical systems approach and RNA velocity, we found that aged MuSCs follow the same differentiation trajectory as young cells, but stall in differentiation near a commitment decision. Our results suggest that age-related changes are plastic across differentiation trajectories and that fate commitment decisions are delayed in aged myogenic cells. Overall design: Muscle mononuclear cells were isolated from 2 young (3 m.o.) and 2 aged (20 m.o.) C57Bl/6 mice. All cells in the muscle mononuclear compartment were transcriptionally profiled immediately after isolation using the 10X Chromium Single Cell Transcriptome v3 technology. Muscle stem cells and fibro/adipose progenitors were additionally profiled both  after a differentiation challenge using the same library preparation method."
Petrany 2020,WT_TA_24mo,NA,muscle,tibialis anterior,nucleus,male,C57BL/6,NA,NA,TRUE,TRUE,Mus musculus,GSE147127,GSM4418991,3p_v3,fastq,SRR11336245;SRR11336246,NA,SRX7939762,SRP253104,SRS6330487,NA,NA,NA,"Petrany et al, Nat Comm, 2020",10.1038/s41467-020-20063-w,https://pubmed.ncbi.nlm.nih.gov/33311464/,Illumina NovaSeq 6000,Single-nucleus RNA-seq identifies transcriptional heterogeneity in multinucleated skeletal myofibers,"While the majority of cells contain a single nucleus, cell types such as trophoblasts, osteoclasts, and skeletal myofibers require multinucleation. One advantage of multinucleation can be the assignment of distinct functions to different nuclei, but comprehensive interrogation of transcriptional heterogeneity within multinucleated tissues has been challenging due to the presence of a shared cytoplasm. Here, we utilized single-nucleus RNA-sequencing (snRNA-seq) to determine the extent of transcriptional diversity within multinucleated skeletal myofibers. Nuclei from mouse skeletal muscle were profiled across the lifespan, which revealed the emergence of distinct myonuclear populations in postnatal development and their reactivation in aging muscle. Our datasets also provided a platform for discovery of novel genes associated with rare specialized regions of the muscle cell, including markers of the myotendinous junction and functionally validated factors expressed at the neuromuscular junction. These findings reveal that myonuclei within syncytial muscle fibers possess distinct transcriptional profiles that regulate muscle biology. Overall design: Single-nucleus RNA-seq of tibialis anteior muscle of BL6 wild-type mice across the lifespan: 10 days, 21 days, 5 months (TA and soleus), 24 months, 30 months"
Petrany 2020,WT_TA_5mo,NA,muscle,tibialis anterior,nucleus,male,C57BL/6,NA,NA,TRUE,TRUE,Mus musculus,GSE147127,GSM4418992,3p_v3,fastq,SRR11336247;SRR11336248,NA,SRX7939763,SRP253104,SRS6330488,NA,NA,NA,"Petrany et al, Nat Comm, 2020",10.1038/s41467-020-20063-w,https://pubmed.ncbi.nlm.nih.gov/33311464/,Illumina NovaSeq 6000,Single-nucleus RNA-seq identifies transcriptional heterogeneity in multinucleated skeletal myofibers,"While the majority of cells contain a single nucleus, cell types such as trophoblasts, osteoclasts, and skeletal myofibers require multinucleation. One advantage of multinucleation can be the assignment of distinct functions to different nuclei, but comprehensive interrogation of transcriptional heterogeneity within multinucleated tissues has been challenging due to the presence of a shared cytoplasm. Here, we utilized single-nucleus RNA-sequencing (snRNA-seq) to determine the extent of transcriptional diversity within multinucleated skeletal myofibers. Nuclei from mouse skeletal muscle were profiled across the lifespan, which revealed the emergence of distinct myonuclear populations in postnatal development and their reactivation in aging muscle. Our datasets also provided a platform for discovery of novel genes associated with rare specialized regions of the muscle cell, including markers of the myotendinous junction and functionally validated factors expressed at the neuromuscular junction. These findings reveal that myonuclei within syncytial muscle fibers possess distinct transcriptional profiles that regulate muscle biology. Overall design: Single-nucleus RNA-seq of tibialis anteior muscle of BL6 wild-type mice across the lifespan: 10 days, 21 days, 5 months (TA and soleus), 24 months, 30 months"
Petrany 2020,WT_TA_30mo,NA,muscle,tibialis anterior,nucleus,male,C57BL/6,NA,NA,TRUE,TRUE,Mus musculus,GSE147127,GSM4418993,3p_v3,fastq,SRR11336249;SRR11336250,NA,SRX7939764,SRP253104,SRS6330489,NA,NA,NA,"Petrany et al, Nat Comm, 2020",10.1038/s41467-020-20063-w,https://pubmed.ncbi.nlm.nih.gov/33311464/,Illumina NovaSeq 6000,Single-nucleus RNA-seq identifies transcriptional heterogeneity in multinucleated skeletal myofibers,"While the majority of cells contain a single nucleus, cell types such as trophoblasts, osteoclasts, and skeletal myofibers require multinucleation. One advantage of multinucleation can be the assignment of distinct functions to different nuclei, but comprehensive interrogation of transcriptional heterogeneity within multinucleated tissues has been challenging due to the presence of a shared cytoplasm. Here, we utilized single-nucleus RNA-sequencing (snRNA-seq) to determine the extent of transcriptional diversity within multinucleated skeletal myofibers. Nuclei from mouse skeletal muscle were profiled across the lifespan, which revealed the emergence of distinct myonuclear populations in postnatal development and their reactivation in aging muscle. Our datasets also provided a platform for discovery of novel genes associated with rare specialized regions of the muscle cell, including markers of the myotendinous junction and functionally validated factors expressed at the neuromuscular junction. These findings reveal that myonuclei within syncytial muscle fibers possess distinct transcriptional profiles that regulate muscle biology. Overall design: Single-nucleus RNA-seq of tibialis anteior muscle of BL6 wild-type mice across the lifespan: 10 days, 21 days, 5 months (TA and soleus), 24 months, 30 months"
Petrany 2020,WT_TA_P10,NA,muscle,tibialis anterior,nucleus,male,C57BL/6,NA,NA,TRUE,TRUE,Mus musculus,GSE147127,GSM4418994,3p_v3,fastq,SRR11336251;SRR11336252,NA,SRX7939765,SRP253104,SRS6330490,NA,NA,NA,"Petrany et al, Nat Comm, 2020",10.1038/s41467-020-20063-w,https://pubmed.ncbi.nlm.nih.gov/33311464/,Illumina NovaSeq 6000,Single-nucleus RNA-seq identifies transcriptional heterogeneity in multinucleated skeletal myofibers,"While the majority of cells contain a single nucleus, cell types such as trophoblasts, osteoclasts, and skeletal myofibers require multinucleation. One advantage of multinucleation can be the assignment of distinct functions to different nuclei, but comprehensive interrogation of transcriptional heterogeneity within multinucleated tissues has been challenging due to the presence of a shared cytoplasm. Here, we utilized single-nucleus RNA-sequencing (snRNA-seq) to determine the extent of transcriptional diversity within multinucleated skeletal myofibers. Nuclei from mouse skeletal muscle were profiled across the lifespan, which revealed the emergence of distinct myonuclear populations in postnatal development and their reactivation in aging muscle. Our datasets also provided a platform for discovery of novel genes associated with rare specialized regions of the muscle cell, including markers of the myotendinous junction and functionally validated factors expressed at the neuromuscular junction. These findings reveal that myonuclei within syncytial muscle fibers possess distinct transcriptional profiles that regulate muscle biology. Overall design: Single-nucleus RNA-seq of tibialis anteior muscle of BL6 wild-type mice across the lifespan: 10 days, 21 days, 5 months (TA and soleus), 24 months, 30 months"
Petrany 2020,WT_TA_P21,NA,muscle,tibialis anterior,nucleus,male,C57BL/6,NA,NA,TRUE,TRUE,Mus musculus,GSE147127,GSM4418995,3p_v3,fastq,SRR11336253;SRR11336254,NA,SRX7939766,SRP253104,SRS6330491,NA,NA,NA,"Petrany et al, Nat Comm, 2020",10.1038/s41467-020-20063-w,https://pubmed.ncbi.nlm.nih.gov/33311464/,Illumina NovaSeq 6000,Single-nucleus RNA-seq identifies transcriptional heterogeneity in multinucleated skeletal myofibers,"While the majority of cells contain a single nucleus, cell types such as trophoblasts, osteoclasts, and skeletal myofibers require multinucleation. One advantage of multinucleation can be the assignment of distinct functions to different nuclei, but comprehensive interrogation of transcriptional heterogeneity within multinucleated tissues has been challenging due to the presence of a shared cytoplasm. Here, we utilized single-nucleus RNA-sequencing (snRNA-seq) to determine the extent of transcriptional diversity within multinucleated skeletal myofibers. Nuclei from mouse skeletal muscle were profiled across the lifespan, which revealed the emergence of distinct myonuclear populations in postnatal development and their reactivation in aging muscle. Our datasets also provided a platform for discovery of novel genes associated with rare specialized regions of the muscle cell, including markers of the myotendinous junction and functionally validated factors expressed at the neuromuscular junction. These findings reveal that myonuclei within syncytial muscle fibers possess distinct transcriptional profiles that regulate muscle biology. Overall design: Single-nucleus RNA-seq of tibialis anteior muscle of BL6 wild-type mice across the lifespan: 10 days, 21 days, 5 months (TA and soleus), 24 months, 30 months"
Petrany 2020,WT_soleus_5mo,NA,muscle,soleus,nucleus,male,C57BL/6,NA,NA,TRUE,TRUE,Mus musculus,GSE147127,GSM4418996,3p_v3,fastq,SRR11336255;SRR11336256,NA,SRX7939767,SRP253104,SRS6330492,NA,NA,NA,"Petrany et al, Nat Comm, 2020",10.1038/s41467-020-20063-w,https://pubmed.ncbi.nlm.nih.gov/33311464/,Illumina NovaSeq 6000,Single-nucleus RNA-seq identifies transcriptional heterogeneity in multinucleated skeletal myofibers,"While the majority of cells contain a single nucleus, cell types such as trophoblasts, osteoclasts, and skeletal myofibers require multinucleation. One advantage of multinucleation can be the assignment of distinct functions to different nuclei, but comprehensive interrogation of transcriptional heterogeneity within multinucleated tissues has been challenging due to the presence of a shared cytoplasm. Here, we utilized single-nucleus RNA-sequencing (snRNA-seq) to determine the extent of transcriptional diversity within multinucleated skeletal myofibers. Nuclei from mouse skeletal muscle were profiled across the lifespan, which revealed the emergence of distinct myonuclear populations in postnatal development and their reactivation in aging muscle. Our datasets also provided a platform for discovery of novel genes associated with rare specialized regions of the muscle cell, including markers of the myotendinous junction and functionally validated factors expressed at the neuromuscular junction. These findings reveal that myonuclei within syncytial muscle fibers possess distinct transcriptional profiles that regulate muscle biology. Overall design: Single-nucleus RNA-seq of tibialis anteior muscle of BL6 wild-type mice across the lifespan: 10 days, 21 days, 5 months (TA and soleus), 24 months, 30 months"
Dos Santos 2020,snRNA-seq_Soleus,NA,muscle,soleus,nucleus,female,C5Bl6/N,NA,NA,TRUE,TRUE,Mus musculus,GSE150065,GSM4522962,3p_v3,fastq,SRR11729338,NA,SRX8288537,SRP260473,SRS6610269,NA,NA,NA,"Dos Santos et al, Nat Comm, 2020",10.1038/s41467-020-18789-8,https://pubmed.ncbi.nlm.nih.gov/33037211/,NextSeq 500,Single-nucleus RNA-seq and FISH reveal coordinated transcriptional activity in mammalian myofibers,"Skeletal muscle fibers are large syncytia but it is currently unknown whether gene expression is coordinately regulated in their numerous nuclei. By snRNA-seq and snATAC-seq, we showed that slow, fast, myotendinous and neuromuscular junction myonuclei each have different transcriptional programs, associated with distinct chromatin states and combinations of transcription factors. In adult mice, identified myofiber types predominantly express either a slow or one of the three fast isoforms of Myosin heavy chain (MYH) proteins, while a small number of hybrid fibers can express more than one MYH. By snRNA-seq and FISH, we showed that the majority of myonuclei within a myofiber are synchronized, coordinately expressing only one fast Myh isoform with a preferential pane of muscle-specific genes. Importantly, this coordination of expression occurs early during post-natal development and depends on innervation. These findings highlight a unique mechanism of coordination of gene expression in a syncytium. Overall design: Single nuclei RNA-seq and single nuclei ATAC-seq"
Dos Santos 2020,snRNA-seq_Quadriceps,NA,muscle,quadricep,nucleus,female,C5Bl6/N,NA,NA,TRUE,TRUE,Mus musculus,GSE150065,GSM4522963,3p_v3,fastq,SRR11729339,NA,SRX8288538,SRP260473,SRS6610270,NA,NA,NA,"Dos Santos et al, Nat Comm, 2020",10.1038/s41467-020-18789-8,https://pubmed.ncbi.nlm.nih.gov/33037211/,NextSeq 500,Single-nucleus RNA-seq and FISH reveal coordinated transcriptional activity in mammalian myofibers,"Skeletal muscle fibers are large syncytia but it is currently unknown whether gene expression is coordinately regulated in their numerous nuclei. By snRNA-seq and snATAC-seq, we showed that slow, fast, myotendinous and neuromuscular junction myonuclei each have different transcriptional programs, associated with distinct chromatin states and combinations of transcription factors. In adult mice, identified myofiber types predominantly express either a slow or one of the three fast isoforms of Myosin heavy chain (MYH) proteins, while a small number of hybrid fibers can express more than one MYH. By snRNA-seq and FISH, we showed that the majority of myonuclei within a myofiber are synchronized, coordinately expressing only one fast Myh isoform with a preferential pane of muscle-specific genes. Importantly, this coordination of expression occurs early during post-natal development and depends on innervation. These findings highlight a unique mechanism of coordination of gene expression in a syncytium. Overall design: Single nuclei RNA-seq and single nuclei ATAC-seq"
Dos Santos 2020,snRNA-seq_Tibialis,NA,muscle,tibialis anterior,nucleus,female,C5Bl6/N,NA,NA,TRUE,TRUE,Mus musculus,GSE150065,GSM4522964,3p_v3,fastq,SRR11729340,NA,SRX8288539,SRP260473,SRS6610271,NA,NA,NA,"Dos Santos et al, Nat Comm, 2020",10.1038/s41467-020-18789-8,https://pubmed.ncbi.nlm.nih.gov/33037211/,NextSeq 500,Single-nucleus RNA-seq and FISH reveal coordinated transcriptional activity in mammalian myofibers,"Skeletal muscle fibers are large syncytia but it is currently unknown whether gene expression is coordinately regulated in their numerous nuclei. By snRNA-seq and snATAC-seq, we showed that slow, fast, myotendinous and neuromuscular junction myonuclei each have different transcriptional programs, associated with distinct chromatin states and combinations of transcription factors. In adult mice, identified myofiber types predominantly express either a slow or one of the three fast isoforms of Myosin heavy chain (MYH) proteins, while a small number of hybrid fibers can express more than one MYH. By snRNA-seq and FISH, we showed that the majority of myonuclei within a myofiber are synchronized, coordinately expressing only one fast Myh isoform with a preferential pane of muscle-specific genes. Importantly, this coordination of expression occurs early during post-natal development and depends on innervation. These findings highlight a unique mechanism of coordination of gene expression in a syncytium. Overall design: Single nuclei RNA-seq and single nuclei ATAC-seq"
Dos Santos 2020,snRNA-seq_Mix,NA,muscle,hindlimb,nucleus,female,C5Bl6/N,NA,NA,TRUE,TRUE,Mus musculus,GSE150065,GSM4522965,3p_v3,fastq,SRR11729341,NA,SRX8288540,SRP260473,SRS6610272,NA,NA,NA,"Dos Santos et al, Nat Comm, 2020",10.1038/s41467-020-18789-8,https://pubmed.ncbi.nlm.nih.gov/33037211/,NextSeq 500,Single-nucleus RNA-seq and FISH reveal coordinated transcriptional activity in mammalian myofibers,"Skeletal muscle fibers are large syncytia but it is currently unknown whether gene expression is coordinately regulated in their numerous nuclei. By snRNA-seq and snATAC-seq, we showed that slow, fast, myotendinous and neuromuscular junction myonuclei each have different transcriptional programs, associated with distinct chromatin states and combinations of transcription factors. In adult mice, identified myofiber types predominantly express either a slow or one of the three fast isoforms of Myosin heavy chain (MYH) proteins, while a small number of hybrid fibers can express more than one MYH. By snRNA-seq and FISH, we showed that the majority of myonuclei within a myofiber are synchronized, coordinately expressing only one fast Myh isoform with a preferential pane of muscle-specific genes. Importantly, this coordination of expression occurs early during post-natal development and depends on innervation. These findings highlight a unique mechanism of coordination of gene expression in a syncytium. Overall design: Single nuclei RNA-seq and single nuclei ATAC-seq"
Oprescu 2022,Non-injured,NA,muscle,tibialis anterior,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE150366,GSM4547586,3p_v3,fastq,SRR11776873;SRR11776874,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Oprescu 2022,5_DPI,NA,muscle,tibialis anterior,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE150366,GSM4547587,3p_v3,fastq,SRR11776875;SRR11776876,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Oprescu 2022,10_DPI,NA,muscle,tibialis anterior,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE150366,GSM4547588,3p_v3,fastq,SRR11776877;SRR11776878,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Ritchie 2020,MuSC 90 percent library,illumina only,muscle,NA,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE154868,GSM4681739,3p_v2,fastq,SRR12282456,NA,SRX8785880,SRP273166,SRS7054507,SAMN15594465,NA,NA,unpublished,NA,unpublished,Illumina HiSeq 2500,Long and short-read single cell RNA-seq profiling of mouse muscle stem cells,Single cell RNA-seq was used to identify the gene expression signatures and transcript isoforms that distinguish quiescent and activated muscle stem cells in mouse. Overall design: Quiescent skeletal muscle stem cells isolated from uninjured muscles and activated muscle stem cells isolated post injury were profiled using the Chromium platform (10x Genomics) with sequencing from both short-read (Illumina) and long-read (Nanopore) technologies.
Han 2021,E14_singlecell_Osr2-KICreRunx2flfl,E14_singlecell_Osr2-KICre;Runx2fl/fl,muscle,palate,cell,NA,Osr2-KICre;Runx2fl/fl3,NA,Error R1 missing_fastq provided,TRUE,TRUE,Danio rerio,GSE155928,GSM4716009,3p_v3,fastq,SRR12416692;SRR12416691,NA,SRX8912693,SRP276908,SRS7169416,NA,NA,NA,"Han et al, eLife, 2021",10.7554/eLife.62387,https://pubmed.ncbi.nlm.nih.gov/33482080/,Illumina NovaSeq 6000,Transcriptome and chromatin accessiblity analysis of mice soft palate to unreveal the role of Runx2 in regulating palate muscle development.,"We report the application of single cell transcriptome, bulk transcriptome, and chromatin accessibility analysis for investigating the role of Runx2 in regulating soft palate muscle development. By isolating single cells from soft palate tissue of wild type embryos at E13.5, E14.5 and E15.5, we describe the heterogeneity of soft palate mesenchyme during development by analyzing single cell transcriptome. Combined analysis of bulk and single cell transcriptome of soft palate from wild type and Runx2 mutant suggests Runx2 activate expression of perimysial markers. Finally, we show that Runx2 activates expression of perimysial markers probably by repressing Twist1 through chromatin accessibility analysis. This study provides the first single cell level heterogeneity analysis of developing soft palate and shows the important role of Runx2 in regulating soft palate muscle development. Overall design: Transcriptome and chromatin accessiblity profiling of developing mouse soft palate"
Han 2021,E13_singlecell_control,E13_singlecell_control,muscle,palate,cell,NA,NA,NA,Error R1 missing_fastq provided,TRUE,TRUE,Danio rerio,GSE155928,GSM5222799,3p_v3,fastq,SRR14130123;SRR14130122,NA,SRX10500253,SRP276908,SRS8625207,NA,NA,NA,"Han et al, eLife, 2021",10.7554/eLife.62387,https://pubmed.ncbi.nlm.nih.gov/33482080/,Illumina NovaSeq 6000,Transcriptome and chromatin accessiblity analysis of mice soft palate to unreveal the role of Runx2 in regulating palate muscle development.,"We report the application of single cell transcriptome, bulk transcriptome, and chromatin accessibility analysis for investigating the role of Runx2 in regulating soft palate muscle development. By isolating single cells from soft palate tissue of wild type embryos at E13.5, E14.5 and E15.5, we describe the heterogeneity of soft palate mesenchyme during development by analyzing single cell transcriptome. Combined analysis of bulk and single cell transcriptome of soft palate from wild type and Runx2 mutant suggests Runx2 activate expression of perimysial markers. Finally, we show that Runx2 activates expression of perimysial markers probably by repressing Twist1 through chromatin accessibility analysis. This study provides the first single cell level heterogeneity analysis of developing soft palate and shows the important role of Runx2 in regulating soft palate muscle development. Overall design: Transcriptome and chromatin accessiblity profiling of developing mouse soft palate"
Han 2021,E14_singlecell_control1,E14_singlecell_control1,muscle,palate,cell,NA,NA,NA,Error R1 missing_fastq provided,TRUE,TRUE,Danio rerio,GSE155928,GSM5222800,3p_v3,fastq,SRR14130125;SRR14130124,NA,SRX10500254,SRP276908,SRS8625210,NA,NA,NA,"Han et al, eLife, 2021",10.7554/eLife.62387,https://pubmed.ncbi.nlm.nih.gov/33482080/,Illumina NovaSeq 6000,Transcriptome and chromatin accessiblity analysis of mice soft palate to unreveal the role of Runx2 in regulating palate muscle development.,"We report the application of single cell transcriptome, bulk transcriptome, and chromatin accessibility analysis for investigating the role of Runx2 in regulating soft palate muscle development. By isolating single cells from soft palate tissue of wild type embryos at E13.5, E14.5 and E15.5, we describe the heterogeneity of soft palate mesenchyme during development by analyzing single cell transcriptome. Combined analysis of bulk and single cell transcriptome of soft palate from wild type and Runx2 mutant suggests Runx2 activate expression of perimysial markers. Finally, we show that Runx2 activates expression of perimysial markers probably by repressing Twist1 through chromatin accessibility analysis. This study provides the first single cell level heterogeneity analysis of developing soft palate and shows the important role of Runx2 in regulating soft palate muscle development. Overall design: Transcriptome and chromatin accessiblity profiling of developing mouse soft palate"
Han 2021,E14_singlecell_control2,E14_singlecell_control2,muscle,palate,cell,NA,NA,NA,Error R1 missing_fastq provided,TRUE,TRUE,Danio rerio,GSE155928,GSM5222801,3p_v3,fastq,SRR14130126;SRR14130127,NA,SRX10500255,SRP276908,SRS8625211,NA,NA,NA,"Han et al, eLife, 2021",10.7554/eLife.62387,https://pubmed.ncbi.nlm.nih.gov/33482080/,Illumina NovaSeq 6000,Transcriptome and chromatin accessiblity analysis of mice soft palate to unreveal the role of Runx2 in regulating palate muscle development.,"We report the application of single cell transcriptome, bulk transcriptome, and chromatin accessibility analysis for investigating the role of Runx2 in regulating soft palate muscle development. By isolating single cells from soft palate tissue of wild type embryos at E13.5, E14.5 and E15.5, we describe the heterogeneity of soft palate mesenchyme during development by analyzing single cell transcriptome. Combined analysis of bulk and single cell transcriptome of soft palate from wild type and Runx2 mutant suggests Runx2 activate expression of perimysial markers. Finally, we show that Runx2 activates expression of perimysial markers probably by repressing Twist1 through chromatin accessibility analysis. This study provides the first single cell level heterogeneity analysis of developing soft palate and shows the important role of Runx2 in regulating soft palate muscle development. Overall design: Transcriptome and chromatin accessiblity profiling of developing mouse soft palate"
Han 2021,E15_singlecell_control,E15_singlecell_control,muscle,palate,cell,NA,NA,NA,Error R1 missing_fastq provided,TRUE,TRUE,Danio rerio,GSE155928,GSM5222802,3p_v3,fastq,SRR14130129;SRR14130128,NA,SRX10500256,SRP276908,SRS8625212,NA,NA,NA,"Han et al, eLife, 2021",10.7554/eLife.62387,https://pubmed.ncbi.nlm.nih.gov/33482080/,Illumina NovaSeq 6000,Transcriptome and chromatin accessiblity analysis of mice soft palate to unreveal the role of Runx2 in regulating palate muscle development.,"We report the application of single cell transcriptome, bulk transcriptome, and chromatin accessibility analysis for investigating the role of Runx2 in regulating soft palate muscle development. By isolating single cells from soft palate tissue of wild type embryos at E13.5, E14.5 and E15.5, we describe the heterogeneity of soft palate mesenchyme during development by analyzing single cell transcriptome. Combined analysis of bulk and single cell transcriptome of soft palate from wild type and Runx2 mutant suggests Runx2 activate expression of perimysial markers. Finally, we show that Runx2 activates expression of perimysial markers probably by repressing Twist1 through chromatin accessibility analysis. This study provides the first single cell level heterogeneity analysis of developing soft palate and shows the important role of Runx2 in regulating soft palate muscle development. Overall design: Transcriptome and chromatin accessiblity profiling of developing mouse soft palate"
Han 2021,E14control1,E14control1,muscle,palate,cell,NA,NA,NA,Error R1 missing_fastq provided,TRUE,TRUE,Danio rerio,GSE155928,GSM5222803,3p_v3,fastq,SRR14130130,NA,SRX10500257,SRP276908,SRS8625214,NA,NA,NA,"Han et al, eLife, 2021",10.7554/eLife.62387,https://pubmed.ncbi.nlm.nih.gov/33482080/,NextSeq 500,Transcriptome and chromatin accessiblity analysis of mice soft palate to unreveal the role of Runx2 in regulating palate muscle development.,"We report the application of single cell transcriptome, bulk transcriptome, and chromatin accessibility analysis for investigating the role of Runx2 in regulating soft palate muscle development. By isolating single cells from soft palate tissue of wild type embryos at E13.5, E14.5 and E15.5, we describe the heterogeneity of soft palate mesenchyme during development by analyzing single cell transcriptome. Combined analysis of bulk and single cell transcriptome of soft palate from wild type and Runx2 mutant suggests Runx2 activate expression of perimysial markers. Finally, we show that Runx2 activates expression of perimysial markers probably by repressing Twist1 through chromatin accessibility analysis. This study provides the first single cell level heterogeneity analysis of developing soft palate and shows the important role of Runx2 in regulating soft palate muscle development. Overall design: Transcriptome and chromatin accessiblity profiling of developing mouse soft palate"
Han 2021,E14control2,E14control2,muscle,palate,cell,NA,NA,NA,Error R1 missing_fastq provided,TRUE,TRUE,Danio rerio,GSE155928,GSM5222804,3p_v3,fastq,SRR14130131,NA,SRX10500258,SRP276908,SRS8625213,NA,NA,NA,"Han et al, eLife, 2021",10.7554/eLife.62387,https://pubmed.ncbi.nlm.nih.gov/33482080/,NextSeq 500,Transcriptome and chromatin accessiblity analysis of mice soft palate to unreveal the role of Runx2 in regulating palate muscle development.,"We report the application of single cell transcriptome, bulk transcriptome, and chromatin accessibility analysis for investigating the role of Runx2 in regulating soft palate muscle development. By isolating single cells from soft palate tissue of wild type embryos at E13.5, E14.5 and E15.5, we describe the heterogeneity of soft palate mesenchyme during development by analyzing single cell transcriptome. Combined analysis of bulk and single cell transcriptome of soft palate from wild type and Runx2 mutant suggests Runx2 activate expression of perimysial markers. Finally, we show that Runx2 activates expression of perimysial markers probably by repressing Twist1 through chromatin accessibility analysis. This study provides the first single cell level heterogeneity analysis of developing soft palate and shows the important role of Runx2 in regulating soft palate muscle development. Overall design: Transcriptome and chromatin accessiblity profiling of developing mouse soft palate"
Han 2021,E14control3,E14control3,muscle,palate,cell,NA,NA,NA,Error R1 missing_fastq provided,TRUE,TRUE,Danio rerio,GSE155928,GSM5222805,3p_v3,fastq,SRR14130132,NA,SRX10500259,SRP276908,SRS8625216,NA,NA,NA,"Han et al, eLife, 2021",10.7554/eLife.62387,https://pubmed.ncbi.nlm.nih.gov/33482080/,NextSeq 500,Transcriptome and chromatin accessiblity analysis of mice soft palate to unreveal the role of Runx2 in regulating palate muscle development.,"We report the application of single cell transcriptome, bulk transcriptome, and chromatin accessibility analysis for investigating the role of Runx2 in regulating soft palate muscle development. By isolating single cells from soft palate tissue of wild type embryos at E13.5, E14.5 and E15.5, we describe the heterogeneity of soft palate mesenchyme during development by analyzing single cell transcriptome. Combined analysis of bulk and single cell transcriptome of soft palate from wild type and Runx2 mutant suggests Runx2 activate expression of perimysial markers. Finally, we show that Runx2 activates expression of perimysial markers probably by repressing Twist1 through chromatin accessibility analysis. This study provides the first single cell level heterogeneity analysis of developing soft palate and shows the important role of Runx2 in regulating soft palate muscle development. Overall design: Transcriptome and chromatin accessiblity profiling of developing mouse soft palate"
Han 2021,E14.5_Osr2-KICreRunx2flfl1,E14.5 Osr2-KICre;Runx2fl/fl1,muscle,palate,cell,NA,Osr2-KICre;Runx2fl/fl3,NA,Error R1 missing_fastq provided,TRUE,TRUE,Danio rerio,GSE155928,GSM5222806,3p_v3,fastq,SRR14130133,NA,SRX10500260,SRP276908,SRS8625215,NA,NA,NA,"Han et al, eLife, 2021",10.7554/eLife.62387,https://pubmed.ncbi.nlm.nih.gov/33482080/,NextSeq 500,Transcriptome and chromatin accessiblity analysis of mice soft palate to unreveal the role of Runx2 in regulating palate muscle development.,"We report the application of single cell transcriptome, bulk transcriptome, and chromatin accessibility analysis for investigating the role of Runx2 in regulating soft palate muscle development. By isolating single cells from soft palate tissue of wild type embryos at E13.5, E14.5 and E15.5, we describe the heterogeneity of soft palate mesenchyme during development by analyzing single cell transcriptome. Combined analysis of bulk and single cell transcriptome of soft palate from wild type and Runx2 mutant suggests Runx2 activate expression of perimysial markers. Finally, we show that Runx2 activates expression of perimysial markers probably by repressing Twist1 through chromatin accessibility analysis. This study provides the first single cell level heterogeneity analysis of developing soft palate and shows the important role of Runx2 in regulating soft palate muscle development. Overall design: Transcriptome and chromatin accessiblity profiling of developing mouse soft palate"
Han 2021,E14.5_Osr2-KICreRunx2flfl2,E14.5 Osr2-KICre;Runx2fl/fl2,muscle,palate,cell,NA,Osr2-KICre;Runx2fl/fl3,NA,Error R1 missing_fastq provided,TRUE,TRUE,Danio rerio,GSE155928,GSM5222807,3p_v3,fastq,SRR14130134,NA,SRX10500261,SRP276908,SRS8625217,NA,NA,NA,"Han et al, eLife, 2021",10.7554/eLife.62387,https://pubmed.ncbi.nlm.nih.gov/33482080/,NextSeq 500,Transcriptome and chromatin accessiblity analysis of mice soft palate to unreveal the role of Runx2 in regulating palate muscle development.,"We report the application of single cell transcriptome, bulk transcriptome, and chromatin accessibility analysis for investigating the role of Runx2 in regulating soft palate muscle development. By isolating single cells from soft palate tissue of wild type embryos at E13.5, E14.5 and E15.5, we describe the heterogeneity of soft palate mesenchyme during development by analyzing single cell transcriptome. Combined analysis of bulk and single cell transcriptome of soft palate from wild type and Runx2 mutant suggests Runx2 activate expression of perimysial markers. Finally, we show that Runx2 activates expression of perimysial markers probably by repressing Twist1 through chromatin accessibility analysis. This study provides the first single cell level heterogeneity analysis of developing soft palate and shows the important role of Runx2 in regulating soft palate muscle development. Overall design: Transcriptome and chromatin accessiblity profiling of developing mouse soft palate"
Han 2021,E14.5_Osr2-KICreRunx2flfl3,E14.5 Osr2-KICre;Runx2fl/fl3,muscle,palate,cell,NA,Osr2-KICre;Runx2fl/fl3,NA,Error R1 missing_fastq provided,TRUE,TRUE,Danio rerio,GSE155928,GSM5222808,3p_v3,fastq,SRR14130135,NA,SRX10500262,SRP276908,SRS8625218,NA,NA,NA,"Han et al, eLife, 2021",10.7554/eLife.62387,https://pubmed.ncbi.nlm.nih.gov/33482080/,NextSeq 500,Transcriptome and chromatin accessiblity analysis of mice soft palate to unreveal the role of Runx2 in regulating palate muscle development.,"We report the application of single cell transcriptome, bulk transcriptome, and chromatin accessibility analysis for investigating the role of Runx2 in regulating soft palate muscle development. By isolating single cells from soft palate tissue of wild type embryos at E13.5, E14.5 and E15.5, we describe the heterogeneity of soft palate mesenchyme during development by analyzing single cell transcriptome. Combined analysis of bulk and single cell transcriptome of soft palate from wild type and Runx2 mutant suggests Runx2 activate expression of perimysial markers. Finally, we show that Runx2 activates expression of perimysial markers probably by repressing Twist1 through chromatin accessibility analysis. This study provides the first single cell level heterogeneity analysis of developing soft palate and shows the important role of Runx2 in regulating soft palate muscle development. Overall design: Transcriptome and chromatin accessiblity profiling of developing mouse soft palate"
Han 2021,Ad2_4_S1,Ad2_4_S1,muscle,palate,cell,NA,NA,NA,Error R1 missing_fastq provided,TRUE,TRUE,Danio rerio,GSE155928,GSM5222809,3p_v3,fastq,SRR14130136,NA,SRX10500263,SRP276908,SRS8625219,NA,NA,NA,"Han et al, eLife, 2021",10.7554/eLife.62387,https://pubmed.ncbi.nlm.nih.gov/33482080/,NextSeq 500,Transcriptome and chromatin accessiblity analysis of mice soft palate to unreveal the role of Runx2 in regulating palate muscle development.,"We report the application of single cell transcriptome, bulk transcriptome, and chromatin accessibility analysis for investigating the role of Runx2 in regulating soft palate muscle development. By isolating single cells from soft palate tissue of wild type embryos at E13.5, E14.5 and E15.5, we describe the heterogeneity of soft palate mesenchyme during development by analyzing single cell transcriptome. Combined analysis of bulk and single cell transcriptome of soft palate from wild type and Runx2 mutant suggests Runx2 activate expression of perimysial markers. Finally, we show that Runx2 activates expression of perimysial markers probably by repressing Twist1 through chromatin accessibility analysis. This study provides the first single cell level heterogeneity analysis of developing soft palate and shows the important role of Runx2 in regulating soft palate muscle development. Overall design: Transcriptome and chromatin accessiblity profiling of developing mouse soft palate"
Chemello 2020,Chemello_WT,NA,muscle,NA,cell,male,C57/BL6N,NA,NA,TRUE,TRUE,Mus musculus,GSE156497,GSM4732631,3p_v3.1,fastq,SRR12478037;SRR12478038;SRR12478039;SRR12478040,NA,SRX8971937,SRP278115,SRS7227600,SAMN15858612,NA,NA,"Chemello et al, PNAS, 2020",10.1073/pnas.2018391117,https://pubmed.ncbi.nlm.nih.gov/33148801/,NextSeq 500,Single nucleus RNA-seq analysis of the TA muscles from WT and Dmd Exon 51 Knockout mice,"Duchenne muscular dystrophy (DMD) is a fatal muscle disorder characterized by cycles of degeneration and regeneration of multinucleated myofibers and pathological activation of a variety of other associated cell types. Here, we describe the creation of a new mouse model of DMD caused by deletion of exon 51 of the dystrophin gene, which represents a prevalent mutation in humans. To understand the transcriptional abnormalities and heterogeneity associated with the nuclei of myofibers, as well as other mononucleated cell types that contribute to DMD disease pathogenesis, we performed single nucleus transcriptomics of skeletal muscle of mice with exon 51 deletion. Our results reveal distinctive and previously unrecognized myonuclear subtypes within dystrophic myofibers and uncover degenerative and regenerative transcriptional pathways underlying DMD pathogenesis. Our findings provide new insights into the molecular underpinnings of DMD, controlled by the transcriptional activity of different types of muscle and nonmuscle nuclei. Overall design: Nuclei were isolated from TA muscles of 1 month old WT or DMD ?Ex51 mice, and subjected to single nucleus RNA-seq using 10xGenomics Chromium platform."
Chemello 2020,Chemello_Delta51,NA,muscle,NA,cell,male,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE156497,GSM4732632,3p_v3.1,fastq,SRR12478041;SRR12478042;SRR12478043;SRR12478044,NA,SRX8971938,SRP278115,SRS7227598,SAMN15858611,NA,NA,"Chemello et al, PNAS, 2020",10.1073/pnas.2018391117,https://pubmed.ncbi.nlm.nih.gov/33148801/,NextSeq 500,Single nucleus RNA-seq analysis of the TA muscles from WT and Dmd Exon 51 Knockout mice,"Duchenne muscular dystrophy (DMD) is a fatal muscle disorder characterized by cycles of degeneration and regeneration of multinucleated myofibers and pathological activation of a variety of other associated cell types. Here, we describe the creation of a new mouse model of DMD caused by deletion of exon 51 of the dystrophin gene, which represents a prevalent mutation in humans. To understand the transcriptional abnormalities and heterogeneity associated with the nuclei of myofibers, as well as other mononucleated cell types that contribute to DMD disease pathogenesis, we performed single nucleus transcriptomics of skeletal muscle of mice with exon 51 deletion. Our results reveal distinctive and previously unrecognized myonuclear subtypes within dystrophic myofibers and uncover degenerative and regenerative transcriptional pathways underlying DMD pathogenesis. Our findings provide new insights into the molecular underpinnings of DMD, controlled by the transcriptional activity of different types of muscle and nonmuscle nuclei. Overall design: Nuclei were isolated from TA muscles of 1 month old WT or DMD ?Ex51 mice, and subjected to single nucleus RNA-seq using 10xGenomics Chromium platform."
Arostegui 2022,"Single cell RNA-seq - embryonic tdTomato MPs, Hic1CreERT2/CreERT2;Rosa26LSLtdTomato/tdTomato Embryonic Day 11.5",NA,muscle,embryonic forelimb,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE156952,GSM4748803,NA,bam,SRR12532143,NA,SRX9022062,NA,NA,SAMN15922181,NA,NA,NA,NA,NA,NA,NA,NA
Arostegui 2022,"Single cell RNA-seq - embryonic tdTomato MPs, Hic1CreERT2/CreERT2;Rosa26LSLtdTomato/tdTomato Embryonic Day 12.5",NA,muscle,embryonic forelimb,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE156952,GSM4748804,NA,bam,SRR12532144,NA,SRX9022063,NA,NA,SAMN15922180,NA,NA,NA,NA,NA,NA,NA,NA
Arostegui 2022,"Single cell RNA-seq - embryonic tdTomato MPs, Hic1CreERT2/CreERT2;Rosa26LSLtdTomato/tdTomato Embryonic Day 13.5",NA,muscle,embryonic forelimb,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE156952,GSM4748805,NA,bam,SRR12532145,NA,SRX9022064,NA,NA,SAMN15922179,NA,NA,NA,NA,NA,NA,NA,NA
Arostegui 2022,"Single cell RNA-seq - embryonic tdTomato MPs, Hic1CreERT2/CreERT2;Rosa26LSLtdTomato/tdTomato Embryonic Day 14.5",NA,muscle,embryonic forelimb,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE156952,GSM4748806,NA,bam,SRR12532146,NA,SRX9022065,NA,NA,SAMN15922178,NA,NA,NA,NA,NA,NA,NA,NA
Arostegui 2022,"Single cell RNA-seq - embryonic tdTomato MPs, Hic1CreERT2/CreERT2;Rosa26LSLtdTomato/tdTomato Embryonic Day 16.5",NA,muscle,embryonic forelimb,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE156952,GSM4748807,NA,bam,SRR12532147,NA,SRX9022066,NA,NA,SAMN15922177,NA,NA,NA,NA,NA,NA,NA,NA
Arostegui 2022,"Single cell RNA-seq - embryonic MPs, both Hic1;tdTomato+ and Hic1;tdTomato- Day 11.5 replicate 1",NA,muscle,embryonic forelimb,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE156952,GSM5059814,NA,bam,SRR13610821,NA,SRX10004769,NA,NA,SAMN17762314,NA,NA,NA,NA,NA,NA,NA,NA
Arostegui 2022,"Single cell RNA-seq - embryonic MPs, both Hic1;tdTomato+ and Hic1;tdTomato- Day 11.5 replicate 2",NA,muscle,embryonic forelimb,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE156952,GSM5059815,NA,bam,SRR13610822,NA,SRX10004770,NA,NA,SAMN17762313,NA,NA,NA,NA,NA,NA,NA,NA
Arostegui 2022,"Single cell RNA-seq - embryonic tdTomato MPs, Hic1CreERT2/CreERT2;Rosa26LSLtdTomato/tdTomato Embryonic Day 16.5 distal",NA,muscle,embryonic forelimb,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE156952,GSM6081418,NA,bam,SRR19018959,NA,SRX15090843,NA,NA,SAMN28013899,NA,NA,NA,NA,NA,NA,NA,NA
Fang 2021,Hindlimb skeletal muscle stromal cells,Adult hindlimb muscle,muscle,NA,cell,female,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE158691,GSM4805565,3p_v3,fastq,SRR12734271,NA,SRX9207535,SRP285675,SRS7442445,SAMN16283196,NA,NA,"Fang et al, Nat Biomed Eng, 2021",10.1038/s41551-021-00696-y,https://pubmed.ncbi.nlm.nih.gov/33737730/,Illumina NovaSeq 6000,Single cell RNA-sequencing of murine dermal cells and hindlimb skeletal muscle stromal cells.,"Traumatic injury often results in muscle loss and impairment, which is worsened under aged and diseased conditions. Activation of resident stem cells or transplantation of myogenic stem cells can promote muscle regeneration. However, major challenges remain in harvesting sufficient autologous myogenic stem cells and expanding such cells efficiently for muscle regeneration therapies. Here, we identified a chemical cocktail that selectively induced a robust expansion of myogenic stem cells from readily-obtainable dermal cells and from muscle stromal cells. By differential plating and lineage tracing, we showed that Pax7+ cells were the major source for chemical-induced myogenic stem cells (CiMCs). We further performed single-cell RNA sequencing (scRNA-seq) analysis to characterize the transcriptomic profile of CiMCs and demonstrate a specific expansion of myogenic cells from heterogeneous dermal cell population. Upon transplantation into the injured muscle, CiMCs were efficiently engrafted and improved functional muscle regeneration in both adult and aged mice. In addition, CiMC transplantation rescued muscle function in mice with Duchenne muscular dystrophy (DMD). Furthermore, an in situ therapeutic modality using this cocktail was developed by loading the chemical cocktail into injectable nanoparticles, which enabled a sustained release of the cocktail in injured muscle and a local expansion of resident satellite cells for muscle regeneration in adult and aged mice. These findings will lead to the development of novel in vitro and in situ stem cell therapies for effective skeletal muscle repair. Overall design: Freshly isolated neonatal dermal cells, neonatal dermal cells treated with FR medium for 3 days, adult dermal cells treated with FR medium for 3 days and freshly isolated adult hindlimb skeletal muscle stromal cells were subjected to single cell RNA sequencing. FR medium is 20 M F, 20 M R, 50 g/ml AA, and 50 ng/ml bFGF in high-glucose DMEM containing 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin."
Fan 2021,Muscle_Cells,no treatment,muscle,NA,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE158984,GSM4816918,3p_v2,fastq,SRR12769478;SRR12769479;SRR12769480;SRR12769481,NA,SRX9240090,SRP286306,SRS7473145,SAMN16362733,NA,NA,"Fan et al, Cell Metabolism, 2021",10.1016/j.cmet.2021.07.015,https://pubmed.ncbi.nlm.nih.gov/34358431/,NextSeq 500,Single cell RNA sequencing of skeletal muscle endothelial cells in sedentary and exercised mice,"Skeleteal muscle is composed of different fiber types, which classically have been defined by their myosin heavy chain content, but they also substantially differ in their metabolic properties and the nutrients they use for energy generation. Within skeletal muscle, blood vessels (endothelium) lie in parallel with muscle fibers. What is less well described is whether the functional properties of muscle ECs (mECs) are dependent on the specific fiber (and thus microenvironment) they interact with. Furthermore, the mechanisms of exercise-induced vascular expansion however are poorly understood. Here, we use single cell RNA sequencing to map angiodiversity in skeletal muscle and investigate the mechanism of excercise induced muscle angiogensis. Overall design: 1. Single cell RNA sequencing of endothelial cell that FACS sorted from gastrocnemius muscle of wild type C57BL6N mice. 2. Compare scRNAseq data of ECs isolated from the gastrocnemius of sedentary mice versus 14 days exercised (voluntary running) mice."
Fan 2021,Sedentary,single house sedentary,muscle,NA,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE158984,GSM4816919,3p_v2,fastq,SRR12769482;SRR12769483,NA,SRX9240091,SRP286306,SRS7473146,SAMN16362732,NA,NA,"Fan et al, Cell Metabolism, 2021",10.1016/j.cmet.2021.07.015,https://pubmed.ncbi.nlm.nih.gov/34358431/,Illumina NovaSeq 6000,Single cell RNA sequencing of skeletal muscle endothelial cells in sedentary and exercised mice,"Skeleteal muscle is composed of different fiber types, which classically have been defined by their myosin heavy chain content, but they also substantially differ in their metabolic properties and the nutrients they use for energy generation. Within skeletal muscle, blood vessels (endothelium) lie in parallel with muscle fibers. What is less well described is whether the functional properties of muscle ECs (mECs) are dependent on the specific fiber (and thus microenvironment) they interact with. Furthermore, the mechanisms of exercise-induced vascular expansion however are poorly understood. Here, we use single cell RNA sequencing to map angiodiversity in skeletal muscle and investigate the mechanism of excercise induced muscle angiogensis. Overall design: 1. Single cell RNA sequencing of endothelial cell that FACS sorted from gastrocnemius muscle of wild type C57BL6N mice. 2. Compare scRNAseq data of ECs isolated from the gastrocnemius of sedentary mice versus 14 days exercised (voluntary running) mice."
Fan 2021,2weeks_run,single house voluntary running 14 days,muscle,NA,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE158984,GSM4816920,3p_v2,fastq,SRR12769484;SRR12769485,NA,SRX9240092,SRP286306,SRS7473147,SAMN16362731,NA,NA,"Fan et al, Cell Metabolism, 2021",10.1016/j.cmet.2021.07.015,https://pubmed.ncbi.nlm.nih.gov/34358431/,Illumina NovaSeq 6000,Single cell RNA sequencing of skeletal muscle endothelial cells in sedentary and exercised mice,"Skeleteal muscle is composed of different fiber types, which classically have been defined by their myosin heavy chain content, but they also substantially differ in their metabolic properties and the nutrients they use for energy generation. Within skeletal muscle, blood vessels (endothelium) lie in parallel with muscle fibers. What is less well described is whether the functional properties of muscle ECs (mECs) are dependent on the specific fiber (and thus microenvironment) they interact with. Furthermore, the mechanisms of exercise-induced vascular expansion however are poorly understood. Here, we use single cell RNA sequencing to map angiodiversity in skeletal muscle and investigate the mechanism of excercise induced muscle angiogensis. Overall design: 1. Single cell RNA sequencing of endothelial cell that FACS sorted from gastrocnemius muscle of wild type C57BL6N mice. 2. Compare scRNAseq data of ECs isolated from the gastrocnemius of sedentary mice versus 14 days exercised (voluntary running) mice."
Fix 2021,16234X2 Young Ambulatory Control,NA,muscle,NA,cell,NA,NA,NA,fastq; error on R1 fastq missing; 63 works!,TRUE,TRUE,Mus musculus,GSE158987,GSM4816942,3p_v3,fastq,SRR12769462;SRR12769463,NA,SRX9240080,SRP286303,SRS7473135,SAMN16362797,NA,NA,"Fix et al, Aging Cell, 2021",10.1111/acel.13448,https://pubmed.ncbi.nlm.nih.gov/34365717/,Illumina NovaSeq 6000,Disrupted Macrophage Metabolic Reprogramming in Aged Soleus Muscle During Early Recovery following Disuse Atrophy,"Aged skeletal muscle is characterized by impaired muscle recovery following disuse and coincides with an impaired muscle pro-inflammatory macrophage response.  Macrophage inflammatory status (polarization) is regulated by its metabolic state, but to date, little is understood of macrophage metabolism and its relation to macrophage polarization in the context of muscle recovery and aging. Therefore, the purpose of this study was to thoroughly characterize macrophage metabolism and polarization in aged muscle during early recovery from disuse atrophy using single cell RNA sequencing and functional assays. Young (4-5 mo) and old (20-22 mo) male C57BL/6 mice underwent 14 days of hindlimb unloading followed by 4 days of ambulatory recovery.  CD45+ cells were isolated from solei muscles and analyzed using 10x Genomics single cell RNA sequencing.  We found that aged M1 macrophage clusters were characterized with an impaired inflammatory and glycolytic transcriptome and this impairment was accompanied by a suppression of HIF-1a and its immediate downstream target GLUT1. Overall design: Examination of CD45+ cells from young and old mouse muscle across varying conditions of ambulation, disuse, and recovery."
Fix 2021,17390X1 Young Hindlimb Unloading,NA,muscle,hindlimb,cell,NA,NA,NA,fastq; error on R1 fastq missing,TRUE,TRUE,Mus musculus,GSE158987,GSM4816943,3p_v3,fastq,SRR12769464;SRR12769465,NA,SRX9240081,SRP286303,SRS7473136,SAMN16362796,NA,NA,"Fix et al, Aging Cell, 2021",10.1111/acel.13448,https://pubmed.ncbi.nlm.nih.gov/34365717/,Illumina NovaSeq 6000,Disrupted Macrophage Metabolic Reprogramming in Aged Soleus Muscle During Early Recovery following Disuse Atrophy,"Aged skeletal muscle is characterized by impaired muscle recovery following disuse and coincides with an impaired muscle pro-inflammatory macrophage response.  Macrophage inflammatory status (polarization) is regulated by its metabolic state, but to date, little is understood of macrophage metabolism and its relation to macrophage polarization in the context of muscle recovery and aging. Therefore, the purpose of this study was to thoroughly characterize macrophage metabolism and polarization in aged muscle during early recovery from disuse atrophy using single cell RNA sequencing and functional assays. Young (4-5 mo) and old (20-22 mo) male C57BL/6 mice underwent 14 days of hindlimb unloading followed by 4 days of ambulatory recovery.  CD45+ cells were isolated from solei muscles and analyzed using 10x Genomics single cell RNA sequencing.  We found that aged M1 macrophage clusters were characterized with an impaired inflammatory and glycolytic transcriptome and this impairment was accompanied by a suppression of HIF-1a and its immediate downstream target GLUT1. Overall design: Examination of CD45+ cells from young and old mouse muscle across varying conditions of ambulation, disuse, and recovery."
Fix 2021,17320X1 Young Reloading Day 4,NA,muscle,NA,cell,NA,NA,NA,fastq; error on R1 fastq missing,TRUE,TRUE,Mus musculus,GSE158987,GSM4816944,3p_v3,fastq,SRR12769466;SRR12769467,NA,SRX9240082,SRP286303,SRS7473137,SAMN16362795,NA,NA,"Fix et al, Aging Cell, 2021",10.1111/acel.13448,https://pubmed.ncbi.nlm.nih.gov/34365717/,Illumina NovaSeq 6000,Disrupted Macrophage Metabolic Reprogramming in Aged Soleus Muscle During Early Recovery following Disuse Atrophy,"Aged skeletal muscle is characterized by impaired muscle recovery following disuse and coincides with an impaired muscle pro-inflammatory macrophage response.  Macrophage inflammatory status (polarization) is regulated by its metabolic state, but to date, little is understood of macrophage metabolism and its relation to macrophage polarization in the context of muscle recovery and aging. Therefore, the purpose of this study was to thoroughly characterize macrophage metabolism and polarization in aged muscle during early recovery from disuse atrophy using single cell RNA sequencing and functional assays. Young (4-5 mo) and old (20-22 mo) male C57BL/6 mice underwent 14 days of hindlimb unloading followed by 4 days of ambulatory recovery.  CD45+ cells were isolated from solei muscles and analyzed using 10x Genomics single cell RNA sequencing.  We found that aged M1 macrophage clusters were characterized with an impaired inflammatory and glycolytic transcriptome and this impairment was accompanied by a suppression of HIF-1a and its immediate downstream target GLUT1. Overall design: Examination of CD45+ cells from young and old mouse muscle across varying conditions of ambulation, disuse, and recovery."
Fix 2021,16234X1 Old Ambulatory Control,NA,muscle,NA,cell,NA,NA,NA,fastq; error on R1 fastq missing,TRUE,TRUE,Mus musculus,GSE158987,GSM4816945,3p_v3,fastq,SRR12769468;SRR12769469,NA,SRX9240083,SRP286303,SRS7473138,SAMN16362794,NA,NA,"Fix et al, Aging Cell, 2021",10.1111/acel.13448,https://pubmed.ncbi.nlm.nih.gov/34365717/,Illumina NovaSeq 6000,Disrupted Macrophage Metabolic Reprogramming in Aged Soleus Muscle During Early Recovery following Disuse Atrophy,"Aged skeletal muscle is characterized by impaired muscle recovery following disuse and coincides with an impaired muscle pro-inflammatory macrophage response.  Macrophage inflammatory status (polarization) is regulated by its metabolic state, but to date, little is understood of macrophage metabolism and its relation to macrophage polarization in the context of muscle recovery and aging. Therefore, the purpose of this study was to thoroughly characterize macrophage metabolism and polarization in aged muscle during early recovery from disuse atrophy using single cell RNA sequencing and functional assays. Young (4-5 mo) and old (20-22 mo) male C57BL/6 mice underwent 14 days of hindlimb unloading followed by 4 days of ambulatory recovery.  CD45+ cells were isolated from solei muscles and analyzed using 10x Genomics single cell RNA sequencing.  We found that aged M1 macrophage clusters were characterized with an impaired inflammatory and glycolytic transcriptome and this impairment was accompanied by a suppression of HIF-1a and its immediate downstream target GLUT1. Overall design: Examination of CD45+ cells from young and old mouse muscle across varying conditions of ambulation, disuse, and recovery."
Fix 2021,17390X2 Old Hindlimb Unloading,NA,muscle,hindlimb,cell,NA,NA,NA,fastq; error on R1 fastq missing,TRUE,TRUE,Mus musculus,GSE158987,GSM4816946,3p_v3,fastq,SRR12769470;SRR12769471,NA,SRX9240084,SRP286303,SRS7473139,SAMN16362793,NA,NA,"Fix et al, Aging Cell, 2021",10.1111/acel.13448,https://pubmed.ncbi.nlm.nih.gov/34365717/,Illumina NovaSeq 6000,Disrupted Macrophage Metabolic Reprogramming in Aged Soleus Muscle During Early Recovery following Disuse Atrophy,"Aged skeletal muscle is characterized by impaired muscle recovery following disuse and coincides with an impaired muscle pro-inflammatory macrophage response.  Macrophage inflammatory status (polarization) is regulated by its metabolic state, but to date, little is understood of macrophage metabolism and its relation to macrophage polarization in the context of muscle recovery and aging. Therefore, the purpose of this study was to thoroughly characterize macrophage metabolism and polarization in aged muscle during early recovery from disuse atrophy using single cell RNA sequencing and functional assays. Young (4-5 mo) and old (20-22 mo) male C57BL/6 mice underwent 14 days of hindlimb unloading followed by 4 days of ambulatory recovery.  CD45+ cells were isolated from solei muscles and analyzed using 10x Genomics single cell RNA sequencing.  We found that aged M1 macrophage clusters were characterized with an impaired inflammatory and glycolytic transcriptome and this impairment was accompanied by a suppression of HIF-1a and its immediate downstream target GLUT1. Overall design: Examination of CD45+ cells from young and old mouse muscle across varying conditions of ambulation, disuse, and recovery."
Fix 2021,17320X2 Old Reloading Day 4,NA,muscle,NA,cell,NA,NA,NA,fastq; error on R1 fastq missing,TRUE,TRUE,Mus musculus,GSE158987,GSM4816947,3p_v3,fastq,SRR12769472;SRR12769473,NA,SRX9240085,SRP286303,SRS7473140,SAMN16362792,NA,NA,"Fix et al, Aging Cell, 2021",10.1111/acel.13448,https://pubmed.ncbi.nlm.nih.gov/34365717/,Illumina NovaSeq 6000,Disrupted Macrophage Metabolic Reprogramming in Aged Soleus Muscle During Early Recovery following Disuse Atrophy,"Aged skeletal muscle is characterized by impaired muscle recovery following disuse and coincides with an impaired muscle pro-inflammatory macrophage response.  Macrophage inflammatory status (polarization) is regulated by its metabolic state, but to date, little is understood of macrophage metabolism and its relation to macrophage polarization in the context of muscle recovery and aging. Therefore, the purpose of this study was to thoroughly characterize macrophage metabolism and polarization in aged muscle during early recovery from disuse atrophy using single cell RNA sequencing and functional assays. Young (4-5 mo) and old (20-22 mo) male C57BL/6 mice underwent 14 days of hindlimb unloading followed by 4 days of ambulatory recovery.  CD45+ cells were isolated from solei muscles and analyzed using 10x Genomics single cell RNA sequencing.  We found that aged M1 macrophage clusters were characterized with an impaired inflammatory and glycolytic transcriptome and this impairment was accompanied by a suppression of HIF-1a and its immediate downstream target GLUT1. Overall design: Examination of CD45+ cells from young and old mouse muscle across varying conditions of ambulation, disuse, and recovery."
De Micheli 2020b,D2_Ev3,NA,muscle,tibialis anterior,cell,male,C57BL/6J,NA,NA,TRUE,TRUE,Mus musculus,GSE159500,GSM4831162,3p_v3,fastq,SRR12820638,NA,SRX9288317,SRP287306,SRS7515740,NA,NA,NA,"McKellar et al, Communications Biology, 2021",10.1038/s42003-021-02810-x,https://pubmed.ncbi.nlm.nih.gov/34773081/,NextSeq 500,Single-cell transcriptomic sampling of regenerating mouse muscle tissue,We report a series of single-cell transcriptomic datasets of regenerating mouse muscle tissue generated with the 10x Genomics Chromium v3 platform. Overall design: The overall objective of the study was to generate a high-resolution transcriptomic reference of the distinct cell populations in the mouse muscle at different timepoints after notexin-injury.
De Micheli 2020b,D7_Ev3,NA,muscle,tibialis anterior,cell,male,C57BL/6J,NA,NA,TRUE,TRUE,Mus musculus,GSE159500,GSM4831163,3p_v3,fastq,SRR12820639,NA,SRX9288318,SRP287306,SRS7515741,NA,NA,NA,"McKellar et al, Communications Biology, 2021",10.1038/s42003-021-02810-x,https://pubmed.ncbi.nlm.nih.gov/34773081/,NextSeq 500,Single-cell transcriptomic sampling of regenerating mouse muscle tissue,We report a series of single-cell transcriptomic datasets of regenerating mouse muscle tissue generated with the 10x Genomics Chromium v3 platform. Overall design: The overall objective of the study was to generate a high-resolution transcriptomic reference of the distinct cell populations in the mouse muscle at different timepoints after notexin-injury.
S He 2021,Muscle_cDNA,NA,muscle,NA,cell,NA,NA,NA,NA,TRUE,TRUE,Homo sapiens,GSE159929,GSM4850585,5p_v1,fastq,SRR13075726,NA,NA,NA,NA,SAMN16523253,NA,NA,"He et al, Genome Biology, 2020",10.1186/s13059-020-02210-0,https://pubmed.ncbi.nlm.nih.gov/33287869/,NA,NA,NA
Sunadome 2020,C2C12 on 100Kpa-hard,"C2C12 cells, cultured in different stiffness settings",muscle,cell line,cell,female,NA,NA,#NAME?,TRUE,FALSE,Mus musculus,GSE160098,GSM4859875,3p_v3.1,bam,SRR12898550,NA,SRX9363607,SRP288573,SRS7586103,SAMN16552266,NA,NA,NO_LINKED_PUBLICATION,NA,NO_LINKED_PUBLICATION,Illumina HiSeq 2500,Directionality of developing skeletal muscles is set by mechanical forces,"Formation of oriented myofibrils is a key event in the development of a functional musculoskeletal system. However, the mechanisms that control orientation of myocytes, their fusion and the resulting directionality of adult muscles remain enigmatic. Here, we utilized in vivo and in vitro live imaging, CAS9/CRISPR-mediated mutagenesis in fish, genetic experiments in mice and single cell transcriptomics to demonstrate that individual myocyte polarization and subsequent orientation depend on cell stretch imposed by skeletal expansion. Our data revealed that upon migration, individual facial myocytes form unpolarized clusters corresponding to future muscle groups. These clusters undergo oriented stretch and alignment during embryonic growth. Experimental in vivo perturbations of cartilage shape, size and distribution caused disruptions in directionality and number of myofibrils. Controlled in vitro 2D and 3D experiments applying continuous tension via artificial attachment points demonstrated a sufficiency for mechanical forces to instruct coherent polarization of myocyte populations. Consistently, perturbations of cartilage extension revealed a role of the developing skeleton in the directional outgrowth of non-muscle soft tissues during limb and facial morphogenesis. Overall design: We performed single cell transcriptomic analysis of cells collected daily from soft and hard culture conditions (Fig. 7b). cDNA libraries were prepared and sequenced from 2000 cells from each condition via 10X Genomics Chromium platform"
Sunadome 2020,C2C12 on 0.5Kpa-soft,"C2C12 cells, cultured in different stiffness settings",muscle,cell line,cell,female,NA,NA,#NAME?,TRUE,FALSE,Mus musculus,GSE160098,GSM4859876,3p_v3.1,bam,SRR12898551,NA,SRX9363608,SRP288573,SRS7586104,SAMN16552265,NA,NA,NO_LINKED_PUBLICATION,NA,NO_LINKED_PUBLICATION,Illumina HiSeq 2500,Directionality of developing skeletal muscles is set by mechanical forces,"Formation of oriented myofibrils is a key event in the development of a functional musculoskeletal system. However, the mechanisms that control orientation of myocytes, their fusion and the resulting directionality of adult muscles remain enigmatic. Here, we utilized in vivo and in vitro live imaging, CAS9/CRISPR-mediated mutagenesis in fish, genetic experiments in mice and single cell transcriptomics to demonstrate that individual myocyte polarization and subsequent orientation depend on cell stretch imposed by skeletal expansion. Our data revealed that upon migration, individual facial myocytes form unpolarized clusters corresponding to future muscle groups. These clusters undergo oriented stretch and alignment during embryonic growth. Experimental in vivo perturbations of cartilage shape, size and distribution caused disruptions in directionality and number of myofibrils. Controlled in vitro 2D and 3D experiments applying continuous tension via artificial attachment points demonstrated a sufficiency for mechanical forces to instruct coherent polarization of myocyte populations. Consistently, perturbations of cartilage extension revealed a role of the developing skeleton in the directional outgrowth of non-muscle soft tissues during limb and facial morphogenesis. Overall design: We performed single cell transcriptomic analysis of cells collected daily from soft and hard culture conditions (Fig. 7b). cDNA libraries were prepared and sequenced from 2000 cells from each condition via 10X Genomics Chromium platform"
McKellar 2021,Old_D0_A,NA,muscle,tibialis anterior,cell,female,C57BL/6J,NA,NA,TRUE,TRUE,Mus musculus,GSE162172,GSM4944170,3p_v3,fastq,SRR13143337,NA,SRX9583818,SRP294168,SRS7787307,NA,NA,NA,"McKellar et al, Communications Biology, 2021",10.1038/s42003-021-02810-x,https://pubmed.ncbi.nlm.nih.gov/34773081/,NextSeq 500,Single-cell transcriptomic sampling of regenerating aged mouse hindlimb muscle,We report a series of single-cell transcriptomic datasets of regenerating mouse muscle tissue generated with the 10x Genomics Chromium platform. Overall design: The overall objective of the study was to generate a high-resolution transcriptomic reference of the distinct cell populations in the mouse muscle at different timepoints after notexin-injury.
McKellar 2021,Old_D0_B,NA,muscle,tibialis anterior,cell,female,C57BL/6J,NA,NA,TRUE,TRUE,Mus musculus,GSE162172,GSM4944171,3p_v3,fastq,SRR13143338,NA,SRX9583819,SRP294168,SRS7787306,NA,NA,NA,"McKellar et al, Communications Biology, 2021",10.1038/s42003-021-02810-x,https://pubmed.ncbi.nlm.nih.gov/34773081/,NextSeq 500,Single-cell transcriptomic sampling of regenerating aged mouse hindlimb muscle,We report a series of single-cell transcriptomic datasets of regenerating mouse muscle tissue generated with the 10x Genomics Chromium platform. Overall design: The overall objective of the study was to generate a high-resolution transcriptomic reference of the distinct cell populations in the mouse muscle at different timepoints after notexin-injury.
McKellar 2021,Old_D0_C,NA,muscle,tibialis anterior,cell,female,C57BL/6J,NA,NA,TRUE,TRUE,Mus musculus,GSE162172,GSM4944172,3p_v3,fastq,SRR13143339,NA,SRX9583820,SRP294168,SRS7787308,NA,NA,NA,"McKellar et al, Communications Biology, 2021",10.1038/s42003-021-02810-x,https://pubmed.ncbi.nlm.nih.gov/34773081/,NextSeq 500,Single-cell transcriptomic sampling of regenerating aged mouse hindlimb muscle,We report a series of single-cell transcriptomic datasets of regenerating mouse muscle tissue generated with the 10x Genomics Chromium platform. Overall design: The overall objective of the study was to generate a high-resolution transcriptomic reference of the distinct cell populations in the mouse muscle at different timepoints after notexin-injury.
McKellar 2021,Old_D0_D,NA,muscle,tibialis anterior,cell,female,C57BL/6J,NA,NA,TRUE,TRUE,Mus musculus,GSE162172,GSM4944173,3p_v3,fastq,SRR13143340,NA,SRX9583821,SRP294168,SRS7787309,NA,NA,NA,"McKellar et al, Communications Biology, 2021",10.1038/s42003-021-02810-x,https://pubmed.ncbi.nlm.nih.gov/34773081/,NextSeq 500,Single-cell transcriptomic sampling of regenerating aged mouse hindlimb muscle,We report a series of single-cell transcriptomic datasets of regenerating mouse muscle tissue generated with the 10x Genomics Chromium platform. Overall design: The overall objective of the study was to generate a high-resolution transcriptomic reference of the distinct cell populations in the mouse muscle at different timepoints after notexin-injury.
McKellar 2021,Old_D1_A,NA,muscle,tibialis anterior,cell,female,C57BL/6J,NA,NA,TRUE,TRUE,Mus musculus,GSE162172,GSM4944174,3p_v3,fastq,SRR13143341,NA,SRX9583822,SRP294168,SRS7787312,NA,NA,NA,"McKellar et al, Communications Biology, 2021",10.1038/s42003-021-02810-x,https://pubmed.ncbi.nlm.nih.gov/34773081/,NextSeq 500,Single-cell transcriptomic sampling of regenerating aged mouse hindlimb muscle,We report a series of single-cell transcriptomic datasets of regenerating mouse muscle tissue generated with the 10x Genomics Chromium platform. Overall design: The overall objective of the study was to generate a high-resolution transcriptomic reference of the distinct cell populations in the mouse muscle at different timepoints after notexin-injury.
McKellar 2021,Old_D1_B,NA,muscle,tibialis anterior,cell,female,C57BL/6J,NA,NA,TRUE,TRUE,Mus musculus,GSE162172,GSM4944175,3p_v3,fastq,SRR13143342,NA,SRX9583823,SRP294168,SRS7787311,NA,NA,NA,"McKellar et al, Communications Biology, 2021",10.1038/s42003-021-02810-x,https://pubmed.ncbi.nlm.nih.gov/34773081/,NextSeq 500,Single-cell transcriptomic sampling of regenerating aged mouse hindlimb muscle,We report a series of single-cell transcriptomic datasets of regenerating mouse muscle tissue generated with the 10x Genomics Chromium platform. Overall design: The overall objective of the study was to generate a high-resolution transcriptomic reference of the distinct cell populations in the mouse muscle at different timepoints after notexin-injury.
McKellar 2021,Old_D2_A,NA,muscle,tibialis anterior,cell,female,C57BL/6J,NA,NA,TRUE,TRUE,Mus musculus,GSE162172,GSM4944176,3p_v3,fastq,SRR13143343,NA,SRX9583824,SRP294168,SRS7787310,NA,NA,NA,"McKellar et al, Communications Biology, 2021",10.1038/s42003-021-02810-x,https://pubmed.ncbi.nlm.nih.gov/34773081/,NextSeq 500,Single-cell transcriptomic sampling of regenerating aged mouse hindlimb muscle,We report a series of single-cell transcriptomic datasets of regenerating mouse muscle tissue generated with the 10x Genomics Chromium platform. Overall design: The overall objective of the study was to generate a high-resolution transcriptomic reference of the distinct cell populations in the mouse muscle at different timepoints after notexin-injury.
McKellar 2021,Old_D2_B,NA,muscle,tibialis anterior,cell,female,C57BL/6J,NA,NA,TRUE,TRUE,Mus musculus,GSE162172,GSM4944177,3p_v3,fastq,SRR13143344,NA,SRX9583825,SRP294168,SRS7787316,NA,NA,NA,"McKellar et al, Communications Biology, 2021",10.1038/s42003-021-02810-x,https://pubmed.ncbi.nlm.nih.gov/34773081/,NextSeq 500,Single-cell transcriptomic sampling of regenerating aged mouse hindlimb muscle,We report a series of single-cell transcriptomic datasets of regenerating mouse muscle tissue generated with the 10x Genomics Chromium platform. Overall design: The overall objective of the study was to generate a high-resolution transcriptomic reference of the distinct cell populations in the mouse muscle at different timepoints after notexin-injury.
McKellar 2021,Old_D2_C,NA,muscle,tibialis anterior,cell,female,C57BL/6J,NA,NA,TRUE,TRUE,Mus musculus,GSE162172,GSM4944178,3p_v3,fastq,SRR13143345,NA,SRX9583826,SRP294168,SRS7787313,NA,NA,NA,"McKellar et al, Communications Biology, 2021",10.1038/s42003-021-02810-x,https://pubmed.ncbi.nlm.nih.gov/34773081/,NextSeq 500,Single-cell transcriptomic sampling of regenerating aged mouse hindlimb muscle,We report a series of single-cell transcriptomic datasets of regenerating mouse muscle tissue generated with the 10x Genomics Chromium platform. Overall design: The overall objective of the study was to generate a high-resolution transcriptomic reference of the distinct cell populations in the mouse muscle at different timepoints after notexin-injury.
McKellar 2021,Old_D3_5_A,NA,muscle,tibialis anterior,cell,female,C57BL/6J,NA,NA,TRUE,TRUE,Mus musculus,GSE162172,GSM4944179,3p_v3,fastq,SRR13143346,NA,SRX9583827,SRP294168,SRS7787314,NA,NA,NA,"McKellar et al, Communications Biology, 2021",10.1038/s42003-021-02810-x,https://pubmed.ncbi.nlm.nih.gov/34773081/,NextSeq 500,Single-cell transcriptomic sampling of regenerating aged mouse hindlimb muscle,We report a series of single-cell transcriptomic datasets of regenerating mouse muscle tissue generated with the 10x Genomics Chromium platform. Overall design: The overall objective of the study was to generate a high-resolution transcriptomic reference of the distinct cell populations in the mouse muscle at different timepoints after notexin-injury.
McKellar 2021,Old_D3_5_B,NA,muscle,tibialis anterior,cell,female,C57BL/6J,NA,NA,TRUE,TRUE,Mus musculus,GSE162172,GSM4944180,3p_v3,fastq,SRR13143347,NA,SRX9583828,SRP294168,SRS7787315,NA,NA,NA,"McKellar et al, Communications Biology, 2021",10.1038/s42003-021-02810-x,https://pubmed.ncbi.nlm.nih.gov/34773081/,NextSeq 500,Single-cell transcriptomic sampling of regenerating aged mouse hindlimb muscle,We report a series of single-cell transcriptomic datasets of regenerating mouse muscle tissue generated with the 10x Genomics Chromium platform. Overall design: The overall objective of the study was to generate a high-resolution transcriptomic reference of the distinct cell populations in the mouse muscle at different timepoints after notexin-injury.
McKellar 2021,Old_D5_A,NA,muscle,tibialis anterior,cell,female,C57BL/6J,NA,NA,TRUE,TRUE,Mus musculus,GSE162172,GSM4944181,3p_v3,fastq,SRR13143348,NA,SRX9583829,SRP294168,SRS7787317,NA,NA,NA,"McKellar et al, Communications Biology, 2021",10.1038/s42003-021-02810-x,https://pubmed.ncbi.nlm.nih.gov/34773081/,NextSeq 500,Single-cell transcriptomic sampling of regenerating aged mouse hindlimb muscle,We report a series of single-cell transcriptomic datasets of regenerating mouse muscle tissue generated with the 10x Genomics Chromium platform. Overall design: The overall objective of the study was to generate a high-resolution transcriptomic reference of the distinct cell populations in the mouse muscle at different timepoints after notexin-injury.
McKellar 2021,Old_D5_B,NA,muscle,tibialis anterior,cell,female,C57BL/6J,NA,NA,TRUE,TRUE,Mus musculus,GSE162172,GSM4944182,3p_v3,fastq,SRR13143349,NA,SRX9583830,SRP294168,SRS7787319,NA,NA,NA,"McKellar et al, Communications Biology, 2021",10.1038/s42003-021-02810-x,https://pubmed.ncbi.nlm.nih.gov/34773081/,NextSeq 500,Single-cell transcriptomic sampling of regenerating aged mouse hindlimb muscle,We report a series of single-cell transcriptomic datasets of regenerating mouse muscle tissue generated with the 10x Genomics Chromium platform. Overall design: The overall objective of the study was to generate a high-resolution transcriptomic reference of the distinct cell populations in the mouse muscle at different timepoints after notexin-injury.
McKellar 2021,Old_D5_C,NA,muscle,tibialis anterior,cell,female,C57BL/6J,NA,NA,TRUE,TRUE,Mus musculus,GSE162172,GSM4944183,3p_v3,fastq,SRR13143350,NA,SRX9583831,SRP294168,SRS7787318,NA,NA,NA,"McKellar et al, Communications Biology, 2021",10.1038/s42003-021-02810-x,https://pubmed.ncbi.nlm.nih.gov/34773081/,NextSeq 500,Single-cell transcriptomic sampling of regenerating aged mouse hindlimb muscle,We report a series of single-cell transcriptomic datasets of regenerating mouse muscle tissue generated with the 10x Genomics Chromium platform. Overall design: The overall objective of the study was to generate a high-resolution transcriptomic reference of the distinct cell populations in the mouse muscle at different timepoints after notexin-injury.
McKellar 2021,Old_D7_A,NA,muscle,tibialis anterior,cell,female,C57BL/6J,NA,NA,TRUE,TRUE,Mus musculus,GSE162172,GSM4944184,3p_v3,fastq,SRR13143351,NA,SRX9583832,SRP294168,SRS7787320,NA,NA,NA,"McKellar et al, Communications Biology, 2021",10.1038/s42003-021-02810-x,https://pubmed.ncbi.nlm.nih.gov/34773081/,NextSeq 500,Single-cell transcriptomic sampling of regenerating aged mouse hindlimb muscle,We report a series of single-cell transcriptomic datasets of regenerating mouse muscle tissue generated with the 10x Genomics Chromium platform. Overall design: The overall objective of the study was to generate a high-resolution transcriptomic reference of the distinct cell populations in the mouse muscle at different timepoints after notexin-injury.
McKellar 2021,Old_D7_B,NA,muscle,tibialis anterior,cell,female,C57BL/6J,NA,NA,TRUE,TRUE,Mus musculus,GSE162172,GSM4944185,3p_v3,fastq,SRR13143352,NA,SRX9583833,SRP294168,SRS7787321,NA,NA,NA,"McKellar et al, Communications Biology, 2021",10.1038/s42003-021-02810-x,https://pubmed.ncbi.nlm.nih.gov/34773081/,NextSeq 500,Single-cell transcriptomic sampling of regenerating aged mouse hindlimb muscle,We report a series of single-cell transcriptomic datasets of regenerating mouse muscle tissue generated with the 10x Genomics Chromium platform. Overall design: The overall objective of the study was to generate a high-resolution transcriptomic reference of the distinct cell populations in the mouse muscle at different timepoints after notexin-injury.
McKellar 2021,Old_D7_C,NA,muscle,tibialis anterior,cell,female,C57BL/6J,NA,NA,TRUE,TRUE,Mus musculus,GSE162172,GSM4944186,3p_v3,fastq,SRR13143353,NA,SRX9583834,SRP294168,SRS7787322,NA,NA,NA,"McKellar et al, Communications Biology, 2021",10.1038/s42003-021-02810-x,https://pubmed.ncbi.nlm.nih.gov/34773081/,NextSeq 500,Single-cell transcriptomic sampling of regenerating aged mouse hindlimb muscle,We report a series of single-cell transcriptomic datasets of regenerating mouse muscle tissue generated with the 10x Genomics Chromium platform. Overall design: The overall objective of the study was to generate a high-resolution transcriptomic reference of the distinct cell populations in the mouse muscle at different timepoints after notexin-injury.
McKellar 2021,Old_D1_C,NA,muscle,tibialis anterior,cell,female,C57BL/6J,NA,NA,TRUE,TRUE,Mus musculus,GSE162172,GSM4944187,3p_v3,fastq,SRR13143354,NA,SRX9583835,SRP294168,SRS7787323,NA,NA,NA,"McKellar et al, Communications Biology, 2021",10.1038/s42003-021-02810-x,https://pubmed.ncbi.nlm.nih.gov/34773081/,NextSeq 500,Single-cell transcriptomic sampling of regenerating aged mouse hindlimb muscle,We report a series of single-cell transcriptomic datasets of regenerating mouse muscle tissue generated with the 10x Genomics Chromium platform. Overall design: The overall objective of the study was to generate a high-resolution transcriptomic reference of the distinct cell populations in the mouse muscle at different timepoints after notexin-injury.
McKellar 2021,Old_D1_D,NA,muscle,tibialis anterior,cell,female,C57BL/6J,NA,NA,TRUE,TRUE,Mus musculus,GSE162172,GSM4944188,3p_v3,fastq,SRR13143355,NA,SRX9583836,SRP294168,SRS7787324,NA,NA,NA,"McKellar et al, Communications Biology, 2021",10.1038/s42003-021-02810-x,https://pubmed.ncbi.nlm.nih.gov/34773081/,NextSeq 500,Single-cell transcriptomic sampling of regenerating aged mouse hindlimb muscle,We report a series of single-cell transcriptomic datasets of regenerating mouse muscle tissue generated with the 10x Genomics Chromium platform. Overall design: The overall objective of the study was to generate a high-resolution transcriptomic reference of the distinct cell populations in the mouse muscle at different timepoints after notexin-injury.
McKellar 2021,Old_D3_5_C,NA,muscle,tibialis anterior,cell,female,C57BL/6J,NA,NA,TRUE,TRUE,Mus musculus,GSE162172,GSM4944189,3p_v3,fastq,SRR13143356,NA,SRX9583837,SRP294168,SRS7787325,NA,NA,NA,"McKellar et al, Communications Biology, 2021",10.1038/s42003-021-02810-x,https://pubmed.ncbi.nlm.nih.gov/34773081/,NextSeq 500,Single-cell transcriptomic sampling of regenerating aged mouse hindlimb muscle,We report a series of single-cell transcriptomic datasets of regenerating mouse muscle tissue generated with the 10x Genomics Chromium platform. Overall design: The overall objective of the study was to generate a high-resolution transcriptomic reference of the distinct cell populations in the mouse muscle at different timepoints after notexin-injury.
McKellar 2021,Old_D3_5_D,NA,muscle,tibialis anterior,cell,female,C57BL/6J,NA,NA,TRUE,TRUE,Mus musculus,GSE162172,GSM4944190,3p_v3,fastq,SRR13143357,NA,SRX9583838,SRP294168,SRS7787326,NA,NA,NA,"McKellar et al, Communications Biology, 2021",10.1038/s42003-021-02810-x,https://pubmed.ncbi.nlm.nih.gov/34773081/,NextSeq 500,Single-cell transcriptomic sampling of regenerating aged mouse hindlimb muscle,We report a series of single-cell transcriptomic datasets of regenerating mouse muscle tissue generated with the 10x Genomics Chromium platform. Overall design: The overall objective of the study was to generate a high-resolution transcriptomic reference of the distinct cell populations in the mouse muscle at different timepoints after notexin-injury.
Larouche 2022,Uninjured,NA,muscle,rectus femoris,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE163376,GSM4977800,3p_v3,bam,SRR13263443,NA,NA,NA,NA,NA,NA,NA,NA,10.1073/pnas.2111445119,https://www.pnas.org/doi/10.1073/pnas.2111445119,Illumina NovaSeq 6000,Neutrophil and natural killer cell imbalances prevent muscle stem cellmediated regeneration following murine volumetric muscle loss,NA
Larouche 2022,VML_D7_2mm,NA,muscle,rectus femoris,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE163376,GSM4977801,3p_v3,bam,SRR13263444,NA,NA,NA,NA,NA,NA,NA,NA,10.1073/pnas.2111445119,https://www.pnas.org/doi/10.1073/pnas.2111445119,Illumina NovaSeq 6000,Neutrophil and natural killer cell imbalances prevent muscle stem cellmediated regeneration following murine volumetric muscle loss,NA
Larouche 2022,VML_D7_3mm_F,NA,muscle,rectus femoris,cell,female,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE163376,GSM4977802,3p_v3,bam,SRR13263445,NA,NA,NA,NA,NA,NA,NA,NA,10.1073/pnas.2111445119,https://www.pnas.org/doi/10.1073/pnas.2111445119,Illumina NovaSeq 6000,Neutrophil and natural killer cell imbalances prevent muscle stem cellmediated regeneration following murine volumetric muscle loss,NA
Larouche 2022,VML_D7_3mm_M,NA,muscle,rectus femoris,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE163376,GSM4977803,3p_v3,bam,SRR13263446,NA,NA,NA,NA,NA,NA,NA,NA,10.1073/pnas.2111445119,https://www.pnas.org/doi/10.1073/pnas.2111445119,Illumina NovaSeq 6000,Neutrophil and natural killer cell imbalances prevent muscle stem cellmediated regeneration following murine volumetric muscle loss,NA
Larouche 2022,VML_D14_2mm,NA,muscle,rectus femoris,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE163376,GSM4977804,3p_v3,bam,SRR13263447,NA,NA,NA,NA,NA,NA,NA,NA,10.1073/pnas.2111445119,https://www.pnas.org/doi/10.1073/pnas.2111445119,Illumina NovaSeq 6000,Neutrophil and natural killer cell imbalances prevent muscle stem cellmediated regeneration following murine volumetric muscle loss,NA
Larouche 2022,VML_D14_3mm,NA,muscle,rectus femoris,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE163376,GSM4977805,3p_v3,bam,SRR13263448,NA,NA,NA,NA,NA,NA,NA,NA,10.1073/pnas.2111445119,https://www.pnas.org/doi/10.1073/pnas.2111445119,Illumina NovaSeq 6000,Neutrophil and natural killer cell imbalances prevent muscle stem cellmediated regeneration following murine volumetric muscle loss,NA
Larouche 2022,VML_D28_2mm,NA,muscle,rectus femoris,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE163376,GSM4977806,3p_v3,bam,SRR13263449,NA,NA,NA,NA,NA,NA,NA,NA,10.1073/pnas.2111445119,https://www.pnas.org/doi/10.1073/pnas.2111445119,Illumina NovaSeq 6000,Neutrophil and natural killer cell imbalances prevent muscle stem cellmediated regeneration following murine volumetric muscle loss,NA
Larouche 2022,VML_D28_3mm,NA,muscle,rectus femoris,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE163376,GSM4977807,3p_v3,bam,SRR13263450,NA,NA,NA,NA,NA,NA,NA,NA,10.1073/pnas.2111445119,https://www.pnas.org/doi/10.1073/pnas.2111445119,Illumina NovaSeq 6000,Neutrophil and natural killer cell imbalances prevent muscle stem cellmediated regeneration following murine volumetric muscle loss,NA
Machado 2021,Dissociated Muscle,NA,muscle,hindlimb,nucleus,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE163856,GSM4988787,3p_v3,fastq,SRR13306146;SRR13306147;SRR13306148;SRR13306149;SRR13306150;SRR13306151;SRR13306152;SRR13306153;SRR13306154;SRR13306155;SRR13306156;SRR13306157;SRR13306158;SRR13306159;SRR13306160;SRR13306161,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Machado 2021,Injured Muscle,NA,muscle,hindlimb,nucleus,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE163856,GSM4988788,3p_v3,fastq,SRR13306162;SRR13306163;SRR13306164;SRR13306165;SRR13306166;SRR13306167;SRR13306168;SRR13306169;SRR13306170;SRR13306171;SRR13306172;SRR13306173;SRR13306174;SRR13306175;SRR13306176;SRR13306177;SRR13306178;SRR13306179;SRR13306180;SRR13306181;SRR13306182;SRR13306183;SRR13306184;SRR13306185;SRR13306186;SRR13306187;SRR13306188;SRR13306189;SRR13306190;SRR13306191;SRR13306192;SRR13306193,NA,NA,NA,NA,#TODO,NA,NA,"Machado et al, Cell Stem Cell, 2021",10.1016/j.stem.2021.01.017,https://pubmed.ncbi.nlm.nih.gov/33609440/,NA,NA,NA
Machado 2021,Intact Muscle,NA,muscle,hindlimb,nucleus,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE163856,GSM4988789,3p_v3,fastq,SRR13306194;SRR13306195;SRR13306196;SRR13306197;SRR13306198;SRR13306199;SRR13306200;SRR13306201;SRR13306202;SRR13306203;SRR13306204;SRR13306205;SRR13306206;SRR13306207;SRR13306208;SRR13306209;SRR13306210;SRR13306211;SRR13306212;SRR13306213;SRR13306214;SRR13306215;SRR13306216;SRR13306217;SRR13306218;SRR13306219;SRR13306220;SRR13306221;SRR13306222;SRR13306223;SRR13306224;SRR13306225,NA,NA,NA,NA,#TODO,NA,NA,"Machado et al, Cell Stem Cell, 2021",10.1016/j.stem.2021.01.017,https://pubmed.ncbi.nlm.nih.gov/33609440/,NA,NA,NA
Larouche 2021,Aged Uninjured MuSCs [d0_Aged],22-24 months; C57BL6J,muscle,muscle stem cell,cell,female,NA,NA,NA,TRUE,FALSE,Mus musculus,GSE165978,GSM5059685,3p_v3,bam,SRR13610659,NA,SRX10004691,SRP304270,SRS8173889,SAMN17761229,NA,NA,"Larouche et al, eLife, 2021",10.7554/eLife.66749,https://pubmed.ncbi.nlm.nih.gov/34323217/,Illumina NovaSeq 6000,Muscle Stem Cell Response to Perturbations of the Neuromuscular Junction Are Attenuated With Aging,"During aging and neuromuscular diseases, there is a progressive loss of skeletal muscle volume and function, which is often associated with denervation and a loss of muscle stem cells (MuSCs). A relationship between MuSCs and innervation has not been established however. Herein, we administered neuromuscular trauma to a MuSC lineage tracing model and observed a subset of MuSCs specifically engraft in a position proximal to the neuromuscular junction (NMJ). In aging and in a model of neuromuscular degeneration (Sod1-/-), this localized engraftment behavior was reduced. Genetic rescue of motor neurons in Sod1-/- mice reestablished integrity of the NMJ and partially restored MuSC ability to engraft into NMJ proximal positions. Using single cell RNA-sequencing of MuSCs, we demonstrate that a subset of MuSCs are molecularly distinguishable from MuSCs responding to myofiber injury. These data reveal unique features of MuSCs that respond to synaptic perturbations caused by aging and other stressors. Overall design: C57BL/6J wild-type female mice were obtained from Charles River Breeding Laboratories, the National Institute on Aging, or from a breeding colony at the University of Michigan (UM). All mice were fed normal chow ad libitum and housed on a 12:12 hour light-dark cycle under UM veterinary staff supervision. All procedures were approved by the University Committee on the Use and Care of Animals at UM and were in accordance with the U.S. National Institute of Health (NIH). Young female mice (4-6 months) and aged female mice (20-24 months) were randomly assigned to one of five groups: uninjured, day 3, and day 7 injured (n=4 per group). To induce skeletal muscle injury, mice were first anesthetized with 2% isoflurane and administered a 1.2% barium chloride (BaCl2) solution injected intramuscularly into several points of the tibialis anterior and gastrocnemius muscles for a total of 80 L per hindlimb."
Larouche 2021,Aged MuSCs 3dpi,22-24 months; C57BL6J,muscle,muscle stem cell,cell,female,NA,NA,NA,TRUE,FALSE,Mus musculus,GSE165978,GSM5059686,3p_v3,bam,SRR13610660,NA,SRX10004692,SRP304270,SRS8173890,SAMN17761228,NA,NA,"Larouche et al, eLife, 2021",10.7554/eLife.66749,https://pubmed.ncbi.nlm.nih.gov/34323217/,Illumina NovaSeq 6000,Muscle Stem Cell Response to Perturbations of the Neuromuscular Junction Are Attenuated With Aging,"During aging and neuromuscular diseases, there is a progressive loss of skeletal muscle volume and function, which is often associated with denervation and a loss of muscle stem cells (MuSCs). A relationship between MuSCs and innervation has not been established however. Herein, we administered neuromuscular trauma to a MuSC lineage tracing model and observed a subset of MuSCs specifically engraft in a position proximal to the neuromuscular junction (NMJ). In aging and in a model of neuromuscular degeneration (Sod1-/-), this localized engraftment behavior was reduced. Genetic rescue of motor neurons in Sod1-/- mice reestablished integrity of the NMJ and partially restored MuSC ability to engraft into NMJ proximal positions. Using single cell RNA-sequencing of MuSCs, we demonstrate that a subset of MuSCs are molecularly distinguishable from MuSCs responding to myofiber injury. These data reveal unique features of MuSCs that respond to synaptic perturbations caused by aging and other stressors. Overall design: C57BL/6J wild-type female mice were obtained from Charles River Breeding Laboratories, the National Institute on Aging, or from a breeding colony at the University of Michigan (UM). All mice were fed normal chow ad libitum and housed on a 12:12 hour light-dark cycle under UM veterinary staff supervision. All procedures were approved by the University Committee on the Use and Care of Animals at UM and were in accordance with the U.S. National Institute of Health (NIH). Young female mice (4-6 months) and aged female mice (20-24 months) were randomly assigned to one of five groups: uninjured, day 3, and day 7 injured (n=4 per group). To induce skeletal muscle injury, mice were first anesthetized with 2% isoflurane and administered a 1.2% barium chloride (BaCl2) solution injected intramuscularly into several points of the tibialis anterior and gastrocnemius muscles for a total of 80 L per hindlimb."
Larouche 2021,Aged MuSCs 7dpi,22-24 months; C57BL6J,muscle,muscle stem cell,cell,female,NA,NA,NA,TRUE,FALSE,Mus musculus,GSE165978,GSM5059687,3p_v3,bam,SRR13610661,NA,SRX10004693,SRP304270,SRS8173891,SAMN17761227,NA,NA,"Larouche et al, eLife, 2021",10.7554/eLife.66749,https://pubmed.ncbi.nlm.nih.gov/34323217/,Illumina NovaSeq 6000,Muscle Stem Cell Response to Perturbations of the Neuromuscular Junction Are Attenuated With Aging,"During aging and neuromuscular diseases, there is a progressive loss of skeletal muscle volume and function, which is often associated with denervation and a loss of muscle stem cells (MuSCs). A relationship between MuSCs and innervation has not been established however. Herein, we administered neuromuscular trauma to a MuSC lineage tracing model and observed a subset of MuSCs specifically engraft in a position proximal to the neuromuscular junction (NMJ). In aging and in a model of neuromuscular degeneration (Sod1-/-), this localized engraftment behavior was reduced. Genetic rescue of motor neurons in Sod1-/- mice reestablished integrity of the NMJ and partially restored MuSC ability to engraft into NMJ proximal positions. Using single cell RNA-sequencing of MuSCs, we demonstrate that a subset of MuSCs are molecularly distinguishable from MuSCs responding to myofiber injury. These data reveal unique features of MuSCs that respond to synaptic perturbations caused by aging and other stressors. Overall design: C57BL/6J wild-type female mice were obtained from Charles River Breeding Laboratories, the National Institute on Aging, or from a breeding colony at the University of Michigan (UM). All mice were fed normal chow ad libitum and housed on a 12:12 hour light-dark cycle under UM veterinary staff supervision. All procedures were approved by the University Committee on the Use and Care of Animals at UM and were in accordance with the U.S. National Institute of Health (NIH). Young female mice (4-6 months) and aged female mice (20-24 months) were randomly assigned to one of five groups: uninjured, day 3, and day 7 injured (n=4 per group). To induce skeletal muscle injury, mice were first anesthetized with 2% isoflurane and administered a 1.2% barium chloride (BaCl2) solution injected intramuscularly into several points of the tibialis anterior and gastrocnemius muscles for a total of 80 L per hindlimb."
Larouche 2021,Aged Uninjured MuSCs [d0_Geriatric],26 months; C57BL6J,muscle,muscle stem cell,cell,female,NA,NA,NA,TRUE,FALSE,Mus musculus,GSE165978,GSM5059688,3p_v3,bam,SRR13610662,NA,SRX10004694,SRP304270,SRS8173892,SAMN17761226,NA,NA,"Larouche et al, eLife, 2021",10.7554/eLife.66749,https://pubmed.ncbi.nlm.nih.gov/34323217/,Illumina NovaSeq 6000,Muscle Stem Cell Response to Perturbations of the Neuromuscular Junction Are Attenuated With Aging,"During aging and neuromuscular diseases, there is a progressive loss of skeletal muscle volume and function, which is often associated with denervation and a loss of muscle stem cells (MuSCs). A relationship between MuSCs and innervation has not been established however. Herein, we administered neuromuscular trauma to a MuSC lineage tracing model and observed a subset of MuSCs specifically engraft in a position proximal to the neuromuscular junction (NMJ). In aging and in a model of neuromuscular degeneration (Sod1-/-), this localized engraftment behavior was reduced. Genetic rescue of motor neurons in Sod1-/- mice reestablished integrity of the NMJ and partially restored MuSC ability to engraft into NMJ proximal positions. Using single cell RNA-sequencing of MuSCs, we demonstrate that a subset of MuSCs are molecularly distinguishable from MuSCs responding to myofiber injury. These data reveal unique features of MuSCs that respond to synaptic perturbations caused by aging and other stressors. Overall design: C57BL/6J wild-type female mice were obtained from Charles River Breeding Laboratories, the National Institute on Aging, or from a breeding colony at the University of Michigan (UM). All mice were fed normal chow ad libitum and housed on a 12:12 hour light-dark cycle under UM veterinary staff supervision. All procedures were approved by the University Committee on the Use and Care of Animals at UM and were in accordance with the U.S. National Institute of Health (NIH). Young female mice (4-6 months) and aged female mice (20-24 months) were randomly assigned to one of five groups: uninjured, day 3, and day 7 injured (n=4 per group). To induce skeletal muscle injury, mice were first anesthetized with 2% isoflurane and administered a 1.2% barium chloride (BaCl2) solution injected intramuscularly into several points of the tibialis anterior and gastrocnemius muscles for a total of 80 L per hindlimb."
Larouche 2021,Young Uninjured MuSCs [d0_Young],3-4 months; C57BL6J,muscle,muscle stem cell,cell,female,NA,NA,NA,TRUE,FALSE,Mus musculus,GSE165978,GSM5059689,3p_v3,bam,SRR13610663,NA,SRX10004695,SRP304270,SRS8173893,SAMN17761225,NA,NA,"Larouche et al, eLife, 2021",10.7554/eLife.66749,https://pubmed.ncbi.nlm.nih.gov/34323217/,Illumina NovaSeq 6000,Muscle Stem Cell Response to Perturbations of the Neuromuscular Junction Are Attenuated With Aging,"During aging and neuromuscular diseases, there is a progressive loss of skeletal muscle volume and function, which is often associated with denervation and a loss of muscle stem cells (MuSCs). A relationship between MuSCs and innervation has not been established however. Herein, we administered neuromuscular trauma to a MuSC lineage tracing model and observed a subset of MuSCs specifically engraft in a position proximal to the neuromuscular junction (NMJ). In aging and in a model of neuromuscular degeneration (Sod1-/-), this localized engraftment behavior was reduced. Genetic rescue of motor neurons in Sod1-/- mice reestablished integrity of the NMJ and partially restored MuSC ability to engraft into NMJ proximal positions. Using single cell RNA-sequencing of MuSCs, we demonstrate that a subset of MuSCs are molecularly distinguishable from MuSCs responding to myofiber injury. These data reveal unique features of MuSCs that respond to synaptic perturbations caused by aging and other stressors. Overall design: C57BL/6J wild-type female mice were obtained from Charles River Breeding Laboratories, the National Institute on Aging, or from a breeding colony at the University of Michigan (UM). All mice were fed normal chow ad libitum and housed on a 12:12 hour light-dark cycle under UM veterinary staff supervision. All procedures were approved by the University Committee on the Use and Care of Animals at UM and were in accordance with the U.S. National Institute of Health (NIH). Young female mice (4-6 months) and aged female mice (20-24 months) were randomly assigned to one of five groups: uninjured, day 3, and day 7 injured (n=4 per group). To induce skeletal muscle injury, mice were first anesthetized with 2% isoflurane and administered a 1.2% barium chloride (BaCl2) solution injected intramuscularly into several points of the tibialis anterior and gastrocnemius muscles for a total of 80 L per hindlimb."
Larouche 2021,SOD1 Rescue MuSCs,10-12 months; SynTgSod1-/-,muscle,muscle stem cell,cell,female,NA,NA,NA,TRUE,FALSE,Mus musculus,GSE165978,GSM5059690,3p_v3,bam,SRR13610664,NA,SRX10004696,SRP304270,SRS8173894,SAMN17761224,NA,NA,"Larouche et al, eLife, 2021",10.7554/eLife.66749,https://pubmed.ncbi.nlm.nih.gov/34323217/,Illumina NovaSeq 6000,Muscle Stem Cell Response to Perturbations of the Neuromuscular Junction Are Attenuated With Aging,"During aging and neuromuscular diseases, there is a progressive loss of skeletal muscle volume and function, which is often associated with denervation and a loss of muscle stem cells (MuSCs). A relationship between MuSCs and innervation has not been established however. Herein, we administered neuromuscular trauma to a MuSC lineage tracing model and observed a subset of MuSCs specifically engraft in a position proximal to the neuromuscular junction (NMJ). In aging and in a model of neuromuscular degeneration (Sod1-/-), this localized engraftment behavior was reduced. Genetic rescue of motor neurons in Sod1-/- mice reestablished integrity of the NMJ and partially restored MuSC ability to engraft into NMJ proximal positions. Using single cell RNA-sequencing of MuSCs, we demonstrate that a subset of MuSCs are molecularly distinguishable from MuSCs responding to myofiber injury. These data reveal unique features of MuSCs that respond to synaptic perturbations caused by aging and other stressors. Overall design: C57BL/6J wild-type female mice were obtained from Charles River Breeding Laboratories, the National Institute on Aging, or from a breeding colony at the University of Michigan (UM). All mice were fed normal chow ad libitum and housed on a 12:12 hour light-dark cycle under UM veterinary staff supervision. All procedures were approved by the University Committee on the Use and Care of Animals at UM and were in accordance with the U.S. National Institute of Health (NIH). Young female mice (4-6 months) and aged female mice (20-24 months) were randomly assigned to one of five groups: uninjured, day 3, and day 7 injured (n=4 per group). To induce skeletal muscle injury, mice were first anesthetized with 2% isoflurane and administered a 1.2% barium chloride (BaCl2) solution injected intramuscularly into several points of the tibialis anterior and gastrocnemius muscles for a total of 80 L per hindlimb."
Larouche 2021,SOD1 Knockout MuSCs,10-12 months; Sod1-/-,muscle,muscle stem cell,cell,female,NA,NA,NA,TRUE,FALSE,Mus musculus,GSE165978,GSM5059691,3p_v3,bam,SRR13610665,NA,SRX10004697,SRP304270,SRS8173895,SAMN17761223,NA,NA,"Larouche et al, eLife, 2021",10.7554/eLife.66749,https://pubmed.ncbi.nlm.nih.gov/34323217/,Illumina NovaSeq 6000,Muscle Stem Cell Response to Perturbations of the Neuromuscular Junction Are Attenuated With Aging,"During aging and neuromuscular diseases, there is a progressive loss of skeletal muscle volume and function, which is often associated with denervation and a loss of muscle stem cells (MuSCs). A relationship between MuSCs and innervation has not been established however. Herein, we administered neuromuscular trauma to a MuSC lineage tracing model and observed a subset of MuSCs specifically engraft in a position proximal to the neuromuscular junction (NMJ). In aging and in a model of neuromuscular degeneration (Sod1-/-), this localized engraftment behavior was reduced. Genetic rescue of motor neurons in Sod1-/- mice reestablished integrity of the NMJ and partially restored MuSC ability to engraft into NMJ proximal positions. Using single cell RNA-sequencing of MuSCs, we demonstrate that a subset of MuSCs are molecularly distinguishable from MuSCs responding to myofiber injury. These data reveal unique features of MuSCs that respond to synaptic perturbations caused by aging and other stressors. Overall design: C57BL/6J wild-type female mice were obtained from Charles River Breeding Laboratories, the National Institute on Aging, or from a breeding colony at the University of Michigan (UM). All mice were fed normal chow ad libitum and housed on a 12:12 hour light-dark cycle under UM veterinary staff supervision. All procedures were approved by the University Committee on the Use and Care of Animals at UM and were in accordance with the U.S. National Institute of Health (NIH). Young female mice (4-6 months) and aged female mice (20-24 months) were randomly assigned to one of five groups: uninjured, day 3, and day 7 injured (n=4 per group). To induce skeletal muscle injury, mice were first anesthetized with 2% isoflurane and administered a 1.2% barium chloride (BaCl2) solution injected intramuscularly into several points of the tibialis anterior and gastrocnemius muscles for a total of 80 L per hindlimb."
Larouche 2021,Aged Uninjured MuSCs [d0_Aged_v2],22-24 months; C57BL6J,muscle,muscle stem cell,cell,female,NA,NA,NA,TRUE,FALSE,Mus musculus,GSE165978,GSM5059692,3p_v2,bam,SRR13610666,NA,SRX10004698,SRP304270,SRS8173896,SAMN17761222,NA,NA,"Larouche et al, eLife, 2021",10.7554/eLife.66749,https://pubmed.ncbi.nlm.nih.gov/34323217/,Illumina NovaSeq 6000,Muscle Stem Cell Response to Perturbations of the Neuromuscular Junction Are Attenuated With Aging,"During aging and neuromuscular diseases, there is a progressive loss of skeletal muscle volume and function, which is often associated with denervation and a loss of muscle stem cells (MuSCs). A relationship between MuSCs and innervation has not been established however. Herein, we administered neuromuscular trauma to a MuSC lineage tracing model and observed a subset of MuSCs specifically engraft in a position proximal to the neuromuscular junction (NMJ). In aging and in a model of neuromuscular degeneration (Sod1-/-), this localized engraftment behavior was reduced. Genetic rescue of motor neurons in Sod1-/- mice reestablished integrity of the NMJ and partially restored MuSC ability to engraft into NMJ proximal positions. Using single cell RNA-sequencing of MuSCs, we demonstrate that a subset of MuSCs are molecularly distinguishable from MuSCs responding to myofiber injury. These data reveal unique features of MuSCs that respond to synaptic perturbations caused by aging and other stressors. Overall design: C57BL/6J wild-type female mice were obtained from Charles River Breeding Laboratories, the National Institute on Aging, or from a breeding colony at the University of Michigan (UM). All mice were fed normal chow ad libitum and housed on a 12:12 hour light-dark cycle under UM veterinary staff supervision. All procedures were approved by the University Committee on the Use and Care of Animals at UM and were in accordance with the U.S. National Institute of Health (NIH). Young female mice (4-6 months) and aged female mice (20-24 months) were randomly assigned to one of five groups: uninjured, day 3, and day 7 injured (n=4 per group). To induce skeletal muscle injury, mice were first anesthetized with 2% isoflurane and administered a 1.2% barium chloride (BaCl2) solution injected intramuscularly into several points of the tibialis anterior and gastrocnemius muscles for a total of 80 L per hindlimb."
Perez 2022,OldHM1,NA,muscle,vastus lateralis,nucleus,NA,NA,NA,NA,TRUE,TRUE,Homo sapiens,GSE167186,GSM5098737,5p_v1,fastq,SRR13759043,NA,NA,NA,NA,NA,NA,NA,"Melov et al, Aging, 2022",10.18632/aging.204435,https://pubmed.ncbi.nlm.nih.gov/36516485/,NA,NA,NA
Perez 2022,OldHM2,NA,muscle,vastus lateralis,nucleus,NA,NA,NA,NA,TRUE,TRUE,Homo sapiens,GSE167186,GSM5098738,5p_v1,fastq,SRR13759044,NA,NA,NA,NA,NA,NA,NA,"Melov et al, Aging, 2022",10.18632/aging.204435,https://pubmed.ncbi.nlm.nih.gov/36516485/,NA,NA,NA
Perez 2022,OldHM3,NA,muscle,vastus lateralis,nucleus,NA,NA,NA,NA,TRUE,TRUE,Homo sapiens,GSE167186,GSM5098739,5p_v1,fastq,SRR13759045,NA,NA,NA,NA,NA,NA,NA,"Melov et al, Aging, 2022",10.18632/aging.204435,https://pubmed.ncbi.nlm.nih.gov/36516485/,NA,NA,NA
Perez 2022,OldHM4,NA,muscle,vastus lateralis,nucleus,NA,NA,NA,NA,TRUE,TRUE,Homo sapiens,GSE167186,GSM5098740,5p_v1,fastq,SRR13759046,NA,NA,NA,NA,NA,NA,NA,"Melov et al, Aging, 2022",10.18632/aging.204435,https://pubmed.ncbi.nlm.nih.gov/36516485/,NA,NA,NA
Perez 2022,YouHM5,NA,muscle,vastus lateralis,nucleus,NA,NA,NA,NA,TRUE,TRUE,Homo sapiens,GSE167186,GSM5098741,5p_v1,fastq,SRR13759047,NA,NA,NA,NA,NA,NA,NA,"Melov et al, Aging, 2022",10.18632/aging.204435,https://pubmed.ncbi.nlm.nih.gov/36516485/,NA,NA,NA
Perez 2022,OldHM6,NA,muscle,vastus lateralis,nucleus,NA,NA,NA,NA,TRUE,TRUE,Homo sapiens,GSE167186,GSM5098742,5p_v1,fastq,SRR13759048,NA,NA,NA,NA,NA,NA,NA,"Melov et al, Aging, 2022",10.18632/aging.204435,https://pubmed.ncbi.nlm.nih.gov/36516485/,NA,NA,NA
Perez 2022,OldHM7,NA,muscle,vastus lateralis,nucleus,NA,NA,NA,NA,TRUE,TRUE,Homo sapiens,GSE167186,GSM5098743,5p_v1,fastq,SRR13759049,NA,NA,NA,NA,NA,NA,NA,"Melov et al, Aging, 2022",10.18632/aging.204435,https://pubmed.ncbi.nlm.nih.gov/36516485/,NA,NA,NA
Perez 2022,YouHM8,NA,muscle,vastus lateralis,nucleus,NA,NA,NA,NA,TRUE,TRUE,Homo sapiens,GSE167186,GSM5098744,5p_v1,fastq,SRR13759050,NA,NA,NA,NA,NA,NA,NA,"Melov et al, Aging, 2022",10.18632/aging.204435,https://pubmed.ncbi.nlm.nih.gov/36516485/,NA,NA,NA
Perez 2022,OldHM9,NA,muscle,vastus lateralis,nucleus,NA,NA,NA,NA,TRUE,TRUE,Homo sapiens,GSE167186,GSM5098745,5p_v1,fastq,SRR13759051,NA,NA,NA,NA,NA,NA,NA,"Melov et al, Aging, 2022",10.18632/aging.204435,https://pubmed.ncbi.nlm.nih.gov/36516485/,NA,NA,NA
Perez 2022,YouHM10,NA,muscle,vastus lateralis,nucleus,NA,NA,NA,NA,TRUE,TRUE,Homo sapiens,GSE167186,GSM5098746,5p_v1,fastq,SRR13759052,NA,NA,NA,NA,NA,NA,NA,"Melov et al, Aging, 2022",10.18632/aging.204435,https://pubmed.ncbi.nlm.nih.gov/36516485/,NA,NA,NA
Perez 2022,OldHM11,NA,muscle,vastus lateralis,nucleus,NA,NA,NA,NA,TRUE,TRUE,Homo sapiens,GSE167186,GSM5098747,5p_v1,fastq,SRR13759053,NA,NA,NA,NA,NA,NA,NA,"Melov et al, Aging, 2022",10.18632/aging.204435,https://pubmed.ncbi.nlm.nih.gov/36516485/,NA,NA,NA
Perez 2022,OldHM12,NA,muscle,vastus lateralis,nucleus,NA,NA,NA,NA,TRUE,TRUE,Homo sapiens,GSE167186,GSM5098748,5p_v1,fastq,SRR13759054,NA,NA,NA,NA,NA,NA,NA,"Melov et al, Aging, 2022",10.18632/aging.204435,https://pubmed.ncbi.nlm.nih.gov/36516485/,NA,NA,NA
Perez 2022,YouHM13,NA,muscle,vastus lateralis,nucleus,NA,NA,NA,NA,TRUE,TRUE,Homo sapiens,GSE167186,GSM5098749,5p_v1,fastq,SRR13759055,NA,NA,NA,NA,NA,NA,NA,"Melov et al, Aging, 2022",10.18632/aging.204435,https://pubmed.ncbi.nlm.nih.gov/36516485/,NA,NA,NA
Perez 2022,OldHM15,NA,muscle,vastus lateralis,nucleus,NA,NA,NA,NA,TRUE,TRUE,Homo sapiens,GSE167186,GSM5098750,5p_v1,fastq,SRR13759056,NA,NA,NA,NA,NA,NA,NA,"Melov et al, Aging, 2022",10.18632/aging.204435,https://pubmed.ncbi.nlm.nih.gov/36516485/,NA,NA,NA
Perez 2022,YouHM21,NA,muscle,vastus lateralis,nucleus,NA,NA,NA,NA,TRUE,TRUE,Homo sapiens,GSE167186,GSM5098751,5p_v1,fastq,SRR13759057,NA,NA,NA,NA,NA,NA,NA,"Melov et al, Aging, 2022",10.18632/aging.204435,https://pubmed.ncbi.nlm.nih.gov/36516485/,NA,NA,NA
Perez 2022,YouHM22,NA,muscle,vastus lateralis,nucleus,NA,NA,NA,NA,TRUE,TRUE,Homo sapiens,GSE167186,GSM5098752,5p_v1,fastq,SRR13759058,NA,NA,NA,NA,NA,NA,NA,"Melov et al, Aging, 2022",10.18632/aging.204435,https://pubmed.ncbi.nlm.nih.gov/36516485/,NA,NA,NA
Perez 2022,OldHM23,NA,muscle,vastus lateralis,nucleus,NA,NA,NA,NA,TRUE,TRUE,Homo sapiens,GSE167186,GSM5098753,5p_v1,fastq,SRR13759059,NA,NA,NA,NA,NA,NA,NA,"Melov et al, Aging, 2022",10.18632/aging.204435,https://pubmed.ncbi.nlm.nih.gov/36516485/,NA,NA,NA
Hasson 2021,WT MTJ scRNAseq,NA,muscle,forelimb MTJ,NA,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE168153,GSM5129995,3p_v2,fastq,SRR13844629;SRR13844630;SRR13844631;SRR13844632,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Kim 2022,Induced myogenic progenitors cells (iMPCs),NA,muscle,cell line,cell,NA,NA,NA,NA,TRUE,FALSE,Mus musculus,GSE169054,GSM5175907,3p_v3,fastq,SRR13983265;SRR13983266,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Limbad 2022,SAT_PBS scRNA-seq,NA,muscle,muscle stem cell,cell,NA,NA,NA,101bp R1,TRUE,FALSE,Mus musculus,GSE169531,GSM5208913,3p_v2,fastq,SRR14061694,NA,NA,NA,NA,NA,NA,NA,NA,10.1016/j.isci.2022.103848,https://pubmed.ncbi.nlm.nih.gov/35198901/,NA,NA,NA
Limbad 2022,SAT_DOXO scRNA-seq,NA,muscle,muscle stem cell,cell,NA,NA,NA,101bp R1,TRUE,FALSE,Mus musculus,GSE169531,GSM5208914,3p_v2,fastq,SRR14061695,NA,NA,NA,NA,NA,NA,NA,NA,10.1016/j.isci.2022.103848,https://pubmed.ncbi.nlm.nih.gov/35198901/,NA,NA,NA
Limbad 2022,SAT_DABT scRNA-seq,NA,muscle,muscle stem cell,cell,NA,NA,NA,101bp R1,TRUE,FALSE,Mus musculus,GSE169531,GSM5208915,3p_v2,fastq,SRR14061696,NA,NA,NA,NA,NA,NA,NA,NA,10.1016/j.isci.2022.103848,https://pubmed.ncbi.nlm.nih.gov/35198901/,NA,NA,NA
Limbad 2022,FAP_PBS scRNA-seq,NA,muscle,fibro/adipogenic progenitors,cell,NA,NA,NA,101bp R1,TRUE,FALSE,Mus musculus,GSE169531,GSM5208916,3p_v2,fastq,SRR14061697,NA,NA,NA,NA,NA,NA,NA,NA,10.1016/j.isci.2022.103848,https://pubmed.ncbi.nlm.nih.gov/35198901/,NA,NA,NA
Limbad 2022,FAP_DOXO scRNA-seq,NA,muscle,fibro/adipogenic progenitors,cell,NA,NA,NA,101bp R1,TRUE,FALSE,Mus musculus,GSE169531,GSM5208917,3p_v2,fastq,SRR14061698,NA,NA,NA,NA,NA,NA,NA,NA,10.1016/j.isci.2022.103848,https://pubmed.ncbi.nlm.nih.gov/35198901/,NA,NA,NA
Limbad 2022,FAP_DABT scRNA-seq,NA,muscle,fibro/adipogenic progenitors,cell,NA,NA,NA,101bp R1,TRUE,FALSE,Mus musculus,GSE169531,GSM5208918,3p_v2,fastq,SRR14061699,NA,NA,NA,NA,NA,NA,NA,NA,10.1016/j.isci.2022.103848,https://pubmed.ncbi.nlm.nih.gov/35198901/,NA,NA,NA
Yagi 2021,primary_fSCs,muscle stem cells freshly isolated from skeletal muscles; Skeletal muscles (8-10 weeks age of mice) not cultured in vitro (freshly isolated from in vivo),muscle,cultured primary cells,cell,NA,NA,NA,NA,TRUE,FALSE,Mus musculus,GSE171039,GSM5217005,3p_v3,bam,SRR14092514,NA,SRX10466192,SRP312561,SRS8596486,SAMN18524925,NA,NA,"Yagi et al, Genes Dev, 2021",10.1101/gad.348678.121,https://pubmed.ncbi.nlm.nih.gov/34413137/,NextSeq 500,Dissecting mechanisms by which MyoD and small molecules convert fibroblasts to muscle progenitor cells,"The generation of myotubes from fibroblasts upon forced MyoD expression is a classic example of factor-induced reprogramming in mammals. We recently discovered that additional modulation of signaling pathways with small molecules facilitates reprogramming to more primitive induced muscle progenitor cells (iMPCs). However, the mechanisms by which a single transcription factor drives differentiated cells into distinct developmental states remain unknown. We therefore dissected the transcriptional and epigenetic dynamics of fibroblasts undergoing MyoD-dependent reprogramming to either myotubes or iMPCs using a novel MyoD transgenic model. To this end, we performed single cell RNA sequencing for Pax7-nGFP positive iMPCs/satellite cells and cells undergoing dedifferentiation (i.e. Dox+FRG) or transdifferentiation (i.e. Dox) Our analyses elucidate the role of MyoD in myogenic reprogramming and derive general principles by which transcription factors and signaling pathways cooperate to rewire cell identity. Our results may also inform on potential therapeutic applications of direct reprogramming. Overall design: single cell RNA-seq was performed for 10 samples"
Yagi 2021,expanded_cSCs,muscle stem cells cultured in vitro for 6 days; Skeletal muscles (8-10 weeks age of mice) cultured in satellite cell medium for 6 days,muscle,cultured primary cells,cell,NA,NA,NA,NA,TRUE,FALSE,Mus musculus,GSE171039,GSM5217006,3p_v3,bam,SRR14092515,NA,SRX10466193,SRP312561,SRS8596487,SAMN18524924,NA,NA,"Yagi et al, Genes Dev, 2021",10.1101/gad.348678.121,https://pubmed.ncbi.nlm.nih.gov/34413137/,Illumina NovaSeq 6000,Dissecting mechanisms by which MyoD and small molecules convert fibroblasts to muscle progenitor cells,"The generation of myotubes from fibroblasts upon forced MyoD expression is a classic example of factor-induced reprogramming in mammals. We recently discovered that additional modulation of signaling pathways with small molecules facilitates reprogramming to more primitive induced muscle progenitor cells (iMPCs). However, the mechanisms by which a single transcription factor drives differentiated cells into distinct developmental states remain unknown. We therefore dissected the transcriptional and epigenetic dynamics of fibroblasts undergoing MyoD-dependent reprogramming to either myotubes or iMPCs using a novel MyoD transgenic model. To this end, we performed single cell RNA sequencing for Pax7-nGFP positive iMPCs/satellite cells and cells undergoing dedifferentiation (i.e. Dox+FRG) or transdifferentiation (i.e. Dox) Our analyses elucidate the role of MyoD in myogenic reprogramming and derive general principles by which transcription factors and signaling pathways cooperate to rewire cell identity. Our results may also inform on potential therapeutic applications of direct reprogramming. Overall design: single cell RNA-seq was performed for 10 samples"
Yagi 2021,diff_cSCs,muscle stem cells cultured in vitro for 2 days with horse serum; Skeletal muscles (8-10 weeks age of mice) cultured in satellite cell medium for 4 days then cultured in differentiating medium for 2 days,muscle,cultured primary cells,cell,NA,NA,NA,NA,TRUE,FALSE,Mus musculus,GSE171039,GSM5217007,3p_v3,bam,SRR14092516,NA,SRX10466194,SRP312561,SRS8596488,SAMN18524923,NA,NA,"Yagi et al, Genes Dev, 2021",10.1101/gad.348678.121,https://pubmed.ncbi.nlm.nih.gov/34413137/,Illumina NovaSeq 6000,Dissecting mechanisms by which MyoD and small molecules convert fibroblasts to muscle progenitor cells,"The generation of myotubes from fibroblasts upon forced MyoD expression is a classic example of factor-induced reprogramming in mammals. We recently discovered that additional modulation of signaling pathways with small molecules facilitates reprogramming to more primitive induced muscle progenitor cells (iMPCs). However, the mechanisms by which a single transcription factor drives differentiated cells into distinct developmental states remain unknown. We therefore dissected the transcriptional and epigenetic dynamics of fibroblasts undergoing MyoD-dependent reprogramming to either myotubes or iMPCs using a novel MyoD transgenic model. To this end, we performed single cell RNA sequencing for Pax7-nGFP positive iMPCs/satellite cells and cells undergoing dedifferentiation (i.e. Dox+FRG) or transdifferentiation (i.e. Dox) Our analyses elucidate the role of MyoD in myogenic reprogramming and derive general principles by which transcription factors and signaling pathways cooperate to rewire cell identity. Our results may also inform on potential therapeutic applications of direct reprogramming. Overall design: single cell RNA-seq was performed for 10 samples"
Yagi 2021,MEF_Day0,Mouse embryonic fibroblasts (MEFs); E13.5 embryo cultured in MEF medium for 2 days,muscle,cultured primary cells,cell,NA,NA,NA,NA,TRUE,FALSE,Mus musculus,GSE171039,GSM5217008,3p_v3,bam,SRR14092517,NA,SRX10466195,SRP312561,SRS8596489,SAMN18524922,NA,NA,"Yagi et al, Genes Dev, 2021",10.1101/gad.348678.121,https://pubmed.ncbi.nlm.nih.gov/34413137/,Illumina NovaSeq 6000,Dissecting mechanisms by which MyoD and small molecules convert fibroblasts to muscle progenitor cells,"The generation of myotubes from fibroblasts upon forced MyoD expression is a classic example of factor-induced reprogramming in mammals. We recently discovered that additional modulation of signaling pathways with small molecules facilitates reprogramming to more primitive induced muscle progenitor cells (iMPCs). However, the mechanisms by which a single transcription factor drives differentiated cells into distinct developmental states remain unknown. We therefore dissected the transcriptional and epigenetic dynamics of fibroblasts undergoing MyoD-dependent reprogramming to either myotubes or iMPCs using a novel MyoD transgenic model. To this end, we performed single cell RNA sequencing for Pax7-nGFP positive iMPCs/satellite cells and cells undergoing dedifferentiation (i.e. Dox+FRG) or transdifferentiation (i.e. Dox) Our analyses elucidate the role of MyoD in myogenic reprogramming and derive general principles by which transcription factors and signaling pathways cooperate to rewire cell identity. Our results may also inform on potential therapeutic applications of direct reprogramming. Overall design: single cell RNA-seq was performed for 10 samples"
Yagi 2021,MEF_Dox_Day2,Myocytes/Myotubes derived from MEFs; E13.5 embryo overexpressing MyoD for 2 days,muscle,cultured primary cells,cell,NA,NA,NA,NA,TRUE,FALSE,Mus musculus,GSE171039,GSM5217009,3p_v3,bam,SRR14092518,NA,SRX10466196,SRP312561,SRS8596490,SAMN18524921,NA,NA,"Yagi et al, Genes Dev, 2021",10.1101/gad.348678.121,https://pubmed.ncbi.nlm.nih.gov/34413137/,Illumina NovaSeq 6000,Dissecting mechanisms by which MyoD and small molecules convert fibroblasts to muscle progenitor cells,"The generation of myotubes from fibroblasts upon forced MyoD expression is a classic example of factor-induced reprogramming in mammals. We recently discovered that additional modulation of signaling pathways with small molecules facilitates reprogramming to more primitive induced muscle progenitor cells (iMPCs). However, the mechanisms by which a single transcription factor drives differentiated cells into distinct developmental states remain unknown. We therefore dissected the transcriptional and epigenetic dynamics of fibroblasts undergoing MyoD-dependent reprogramming to either myotubes or iMPCs using a novel MyoD transgenic model. To this end, we performed single cell RNA sequencing for Pax7-nGFP positive iMPCs/satellite cells and cells undergoing dedifferentiation (i.e. Dox+FRG) or transdifferentiation (i.e. Dox) Our analyses elucidate the role of MyoD in myogenic reprogramming and derive general principles by which transcription factors and signaling pathways cooperate to rewire cell identity. Our results may also inform on potential therapeutic applications of direct reprogramming. Overall design: single cell RNA-seq was performed for 10 samples"
Yagi 2021,MEF_DoxFRG_Day2,"Muscle progenitor cells/Myocytes/Myotubes derived from MEFs; E13.5 embryo overexpressing MyoD in the presense of Forskolin, Repsox and GSK3 inhibitor (FRG) for 2 days",muscle,cultured primary cells,cell,NA,NA,NA,NA,TRUE,FALSE,Mus musculus,GSE171039,GSM5217010,3p_v3,bam,SRR14092519,NA,SRX10466197,SRP312561,SRS8596491,SAMN18524920,NA,NA,"Yagi et al, Genes Dev, 2021",10.1101/gad.348678.121,https://pubmed.ncbi.nlm.nih.gov/34413137/,Illumina NovaSeq 6000,Dissecting mechanisms by which MyoD and small molecules convert fibroblasts to muscle progenitor cells,"The generation of myotubes from fibroblasts upon forced MyoD expression is a classic example of factor-induced reprogramming in mammals. We recently discovered that additional modulation of signaling pathways with small molecules facilitates reprogramming to more primitive induced muscle progenitor cells (iMPCs). However, the mechanisms by which a single transcription factor drives differentiated cells into distinct developmental states remain unknown. We therefore dissected the transcriptional and epigenetic dynamics of fibroblasts undergoing MyoD-dependent reprogramming to either myotubes or iMPCs using a novel MyoD transgenic model. To this end, we performed single cell RNA sequencing for Pax7-nGFP positive iMPCs/satellite cells and cells undergoing dedifferentiation (i.e. Dox+FRG) or transdifferentiation (i.e. Dox) Our analyses elucidate the role of MyoD in myogenic reprogramming and derive general principles by which transcription factors and signaling pathways cooperate to rewire cell identity. Our results may also inform on potential therapeutic applications of direct reprogramming. Overall design: single cell RNA-seq was performed for 10 samples"
Yagi 2021,MEF_DoxFRG_Day8,"Muscle progenitor cells/Myocytes/Myotubes derived from MEFs; E13.5 embryo overexpressing MyoD in the presense of Forskolin, Repsox and GSK3 inhibitor (FRG) for 8 days",muscle,cultured primary cells,cell,NA,NA,NA,NA,TRUE,FALSE,Mus musculus,GSE171039,GSM5217011,3p_v3,bam,SRR14092520,NA,SRX10466198,SRP312561,SRS8596492,SAMN18524919,NA,NA,"Yagi et al, Genes Dev, 2021",10.1101/gad.348678.121,https://pubmed.ncbi.nlm.nih.gov/34413137/,Illumina NovaSeq 6000,Dissecting mechanisms by which MyoD and small molecules convert fibroblasts to muscle progenitor cells,"The generation of myotubes from fibroblasts upon forced MyoD expression is a classic example of factor-induced reprogramming in mammals. We recently discovered that additional modulation of signaling pathways with small molecules facilitates reprogramming to more primitive induced muscle progenitor cells (iMPCs). However, the mechanisms by which a single transcription factor drives differentiated cells into distinct developmental states remain unknown. We therefore dissected the transcriptional and epigenetic dynamics of fibroblasts undergoing MyoD-dependent reprogramming to either myotubes or iMPCs using a novel MyoD transgenic model. To this end, we performed single cell RNA sequencing for Pax7-nGFP positive iMPCs/satellite cells and cells undergoing dedifferentiation (i.e. Dox+FRG) or transdifferentiation (i.e. Dox) Our analyses elucidate the role of MyoD in myogenic reprogramming and derive general principles by which transcription factors and signaling pathways cooperate to rewire cell identity. Our results may also inform on potential therapeutic applications of direct reprogramming. Overall design: single cell RNA-seq was performed for 10 samples"
Yagi 2021,MEF_Dox_Day4,Myocytes/Myotubes derived from MEFs; E13.5 embryo overexpressing MyoD for 4 days,muscle,cultured primary cells,cell,NA,NA,NA,NA,TRUE,FALSE,Mus musculus,GSE171039,GSM5217012,3p_v3,bam,SRR14092521,NA,SRX10466199,SRP312561,SRS8596493,SAMN18524918,NA,NA,"Yagi et al, Genes Dev, 2021",10.1101/gad.348678.121,https://pubmed.ncbi.nlm.nih.gov/34413137/,Illumina NovaSeq 6000,Dissecting mechanisms by which MyoD and small molecules convert fibroblasts to muscle progenitor cells,"The generation of myotubes from fibroblasts upon forced MyoD expression is a classic example of factor-induced reprogramming in mammals. We recently discovered that additional modulation of signaling pathways with small molecules facilitates reprogramming to more primitive induced muscle progenitor cells (iMPCs). However, the mechanisms by which a single transcription factor drives differentiated cells into distinct developmental states remain unknown. We therefore dissected the transcriptional and epigenetic dynamics of fibroblasts undergoing MyoD-dependent reprogramming to either myotubes or iMPCs using a novel MyoD transgenic model. To this end, we performed single cell RNA sequencing for Pax7-nGFP positive iMPCs/satellite cells and cells undergoing dedifferentiation (i.e. Dox+FRG) or transdifferentiation (i.e. Dox) Our analyses elucidate the role of MyoD in myogenic reprogramming and derive general principles by which transcription factors and signaling pathways cooperate to rewire cell identity. Our results may also inform on potential therapeutic applications of direct reprogramming. Overall design: single cell RNA-seq was performed for 10 samples"
Yagi 2021,MEF_DoxFRG_Day4,"Muscle progenitor cells/Myocytes/Myotubes derived from MEFs; E13.5 embryo overexpressing MyoD in the presense of Forskolin, Repsox and GSK3 inhibitor (FRG) for 4 days",muscle,cultured primary cells,cell,NA,NA,NA,NA,TRUE,FALSE,Mus musculus,GSE171039,GSM5217013,3p_v3,bam,SRR14092522,NA,SRX10466200,SRP312561,SRS8596494,SAMN18524917,NA,NA,"Yagi et al, Genes Dev, 2021",10.1101/gad.348678.121,https://pubmed.ncbi.nlm.nih.gov/34413137/,Illumina NovaSeq 6000,Dissecting mechanisms by which MyoD and small molecules convert fibroblasts to muscle progenitor cells,"The generation of myotubes from fibroblasts upon forced MyoD expression is a classic example of factor-induced reprogramming in mammals. We recently discovered that additional modulation of signaling pathways with small molecules facilitates reprogramming to more primitive induced muscle progenitor cells (iMPCs). However, the mechanisms by which a single transcription factor drives differentiated cells into distinct developmental states remain unknown. We therefore dissected the transcriptional and epigenetic dynamics of fibroblasts undergoing MyoD-dependent reprogramming to either myotubes or iMPCs using a novel MyoD transgenic model. To this end, we performed single cell RNA sequencing for Pax7-nGFP positive iMPCs/satellite cells and cells undergoing dedifferentiation (i.e. Dox+FRG) or transdifferentiation (i.e. Dox) Our analyses elucidate the role of MyoD in myogenic reprogramming and derive general principles by which transcription factors and signaling pathways cooperate to rewire cell identity. Our results may also inform on potential therapeutic applications of direct reprogramming. Overall design: single cell RNA-seq was performed for 10 samples"
Yagi 2021,iMPCs,"Muscle progenitor cells derived from MEFs; E13.5 embryo overexpressing MyoD in the presense of Forskolin, Repsox and GSK3 inhibitor (FRG) for 10 days, Pax7-nGFP sorted by FACS",muscle,cultured primary cells,cell,NA,NA,NA,NA,TRUE,FALSE,Mus musculus,GSE171039,GSM5217014,3p_v3,bam,SRR14092523,NA,SRX10466201,SRP312561,SRS8596495,SAMN18524916,NA,NA,"Yagi et al, Genes Dev, 2021",10.1101/gad.348678.121,https://pubmed.ncbi.nlm.nih.gov/34413137/,Illumina NovaSeq 6000,Dissecting mechanisms by which MyoD and small molecules convert fibroblasts to muscle progenitor cells,"The generation of myotubes from fibroblasts upon forced MyoD expression is a classic example of factor-induced reprogramming in mammals. We recently discovered that additional modulation of signaling pathways with small molecules facilitates reprogramming to more primitive induced muscle progenitor cells (iMPCs). However, the mechanisms by which a single transcription factor drives differentiated cells into distinct developmental states remain unknown. We therefore dissected the transcriptional and epigenetic dynamics of fibroblasts undergoing MyoD-dependent reprogramming to either myotubes or iMPCs using a novel MyoD transgenic model. To this end, we performed single cell RNA sequencing for Pax7-nGFP positive iMPCs/satellite cells and cells undergoing dedifferentiation (i.e. Dox+FRG) or transdifferentiation (i.e. Dox) Our analyses elucidate the role of MyoD in myogenic reprogramming and derive general principles by which transcription factors and signaling pathways cooperate to rewire cell identity. Our results may also inform on potential therapeutic applications of direct reprogramming. Overall design: single cell RNA-seq was performed for 10 samples"
Zhang 2022,Young Muscle-scRNAseq-rep1,NA,muscle,hindlimb,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE172410,GSM5255166,3p_v3,fastq,SRR14283941,NA,SRX10642650,NA,NA,SAMN18809789,NA,NA,"Zhang et al, Nat Aging, 2022",10.1038/s43587-022-00250-8,https://pubmed.ncbi.nlm.nih.gov/36147777/,NA,NA,NA
Zhang 2022,Young Muscle-scRNAseq-rep2,NA,muscle,hindlimb,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE172410,GSM5255167,3p_v3,fastq,SRR14283942,NA,SRX10642651,NA,NA,SAMN18809788,NA,NA,"Zhang et al, Nat Aging, 2022",10.1038/s43587-022-00250-8,https://pubmed.ncbi.nlm.nih.gov/36147777/,NA,NA,NA
Zhang 2022,Young Muscle-scRNAseq-rep3,NA,muscle,hindlimb,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE172410,GSM5255168,3p_v3,fastq,SRR14283943,NA,SRX10642652,NA,NA,SAMN18809787,NA,NA,"Zhang et al, Nat Aging, 2022",10.1038/s43587-022-00250-8,https://pubmed.ncbi.nlm.nih.gov/36147777/,NA,NA,NA
Zhang 2022,Old Muscle-scRNAseq-rep1,NA,muscle,hindlimb,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE172410,GSM5255169,3p_v3,fastq,SRR14283944,NA,SRX10642653,NA,NA,SAMN18809786,NA,NA,"Zhang et al, Nat Aging, 2022",10.1038/s43587-022-00250-8,https://pubmed.ncbi.nlm.nih.gov/36147777/,NA,NA,NA
Zhang 2022,Old Muscle-scRNAseq-rep2,NA,muscle,hindlimb,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE172410,GSM5255170,3p_v3,fastq,SRR14283945,NA,SRX10642654,NA,NA,SAMN18809785,NA,NA,"Zhang et al, Nat Aging, 2022",10.1038/s43587-022-00250-8,https://pubmed.ncbi.nlm.nih.gov/36147777/,NA,NA,NA
Zhang 2022,Old Muscle-scRNAseq-rep3,NA,muscle,hindlimb,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE172410,GSM5255171,3p_v3,fastq,SRR14283946,NA,SRX10642655,NA,NA,SAMN18809784,NA,NA,"Zhang et al, Nat Aging, 2022",10.1038/s43587-022-00250-8,https://pubmed.ncbi.nlm.nih.gov/36147777/,NA,NA,NA
Dyer 2022,SJRHB031320_D1,A single-cell/nucleus atlas of pediatric rhabdomyosarcoma,muscle,tumor,cell,NA,NA,NA,some samples are human+mouse,TRUE,TRUE,Homo sapiens,GSE174376,GSM5390456,3p_v2,fastq,SRR14854525;SRR14854526,NA,SRX11173038,SRP319643,NA,SAMN19763858,NA,NA,"Dyer et al, Dev Cell, 2022",10.1016/j.devcel.2022.04.003,https://pubmed.ncbi.nlm.nih.gov/35483358/,Illumina NovaSeq 6000,NA,NA
Dyer 2022,SJRHB010928_R1,A single-cell/nucleus atlas of pediatric rhabdomyosarcoma,muscle,tumor,cell,NA,NA,NA,some samples are human+mouse,TRUE,TRUE,Homo sapiens,GSE174376,GSM5390460,3p_v3,fastq,SRR14854533;SRR14854534,NA,SRX11173042,SRP319643,NA,SAMN19763854,NA,NA,"Dyer et al, Dev Cell, 2022",10.1016/j.devcel.2022.04.003,https://pubmed.ncbi.nlm.nih.gov/35483358/,Illumina NovaSeq 6000,NA,NA
Dyer 2022,SJRHB012_S,A single-cell/nucleus atlas of pediatric rhabdomyosarcoma,muscle,tumor,cell,NA,NA,NA,some samples are human+mouse,TRUE,TRUE,Homo sapiens,GSE174376,GSM5390463,3p_v3,fastq,SRR14854543;SRR14854544;SRR14854552;SRR14854553,NA,SRX11173046,SRP319643,NA,SAMN19763851,NA,NA,"Dyer et al, Dev Cell, 2022",10.1016/j.devcel.2022.04.003,https://pubmed.ncbi.nlm.nih.gov/35483358/,Illumina NovaSeq 6000,NA,NA
Dyer 2022,SJRHB031320_D1_sn,A single-cell/nucleus atlas of pediatric rhabdomyosarcoma,muscle,tumor,cell,NA,NA,NA,some samples are human+mouse,TRUE,TRUE,Homo sapiens,GSE174376,GSM5390474,3p_v3,fastq,SRR14854576;SRR14854577,NA,SRX11173057,SRP319643,NA,SAMN19763865,NA,NA,"Dyer et al, Dev Cell, 2022",10.1016/j.devcel.2022.04.003,https://pubmed.ncbi.nlm.nih.gov/35483358/,Illumina NovaSeq 6000,NA,NA
Dyer 2022,SJRHB000026_X1,A single-cell/nucleus atlas of pediatric rhabdomyosarcoma,muscle,xenograft,cell,NA,NA,NA,Orthotopic patient-derived xenograft,TRUE,TRUE,Homo sapiens,GSE174376,GSM5390475,3p_v2,fastq,SRR14854578;SRR14854579;SRR14854580;SRR14854581;SRR14854582;SRR14854583;SRR14854584;SRR14854585;SRR14854586;SRR14854587;SRR14854588;SRR14854589;SRR14854590;SRR14854591;SRR14854592;SRR14854593,NA,SRX11173058,SRP319643,NA,SAMN19763864,NA,NA,NA,NA,NA,Illumina NovaSeq 6000,NA,NA
Dyer 2022,SJRHB000026_X2,A single-cell/nucleus atlas of pediatric rhabdomyosarcoma,muscle,xenograft,cell,NA,NA,NA,Orthotopic patient-derived xenograft,TRUE,TRUE,Homo sapiens,GSE174376,GSM5390476,3p_v2,fastq,SRR14854594,NA,SRX11173059,SRP319643,NA,SAMN19763889,NA,NA,NA,NA,NA,Illumina NovaSeq 6000,NA,NA
Dyer 2022,SJRHB010927_X1,A single-cell/nucleus atlas of pediatric rhabdomyosarcoma,muscle,xenograft,cell,NA,NA,NA,Orthotopic patient-derived xenograft,TRUE,TRUE,Homo sapiens,GSE174376,GSM5390477,3p_v2,fastq,SRR14854595;SRR14854596,NA,SRX11173060,SRP319643,NA,SAMN19763888,NA,NA,NA,NA,NA,Illumina NovaSeq 6000,NA,NA
Dyer 2022,SJRHB010928_X1,A single-cell/nucleus atlas of pediatric rhabdomyosarcoma,muscle,xenograft,cell,NA,NA,NA,Orthotopic patient-derived xenograft,TRUE,TRUE,Homo sapiens,GSE174376,GSM5390478,3p_v2,fastq,SRR14854597;SRR14854598,NA,SRX11173061,SRP319643,NA,SAMN19763887,NA,NA,NA,NA,NA,Illumina NovaSeq 6000,NA,NA
Dyer 2022,SJRHB011_X,A single-cell/nucleus atlas of pediatric rhabdomyosarcoma,muscle,xenograft,cell,NA,NA,NA,Orthotopic patient-derived xenograft,TRUE,TRUE,Homo sapiens,GSE174376,GSM5390479,3p_v2,fastq,SRR14854599;SRR14854600,NA,SRX11173062,SRP319643,NA,SAMN19763886,NA,NA,NA,NA,NA,Illumina NovaSeq 6000,NA,NA
Dyer 2022,SJRHB012_Y,A single-cell/nucleus atlas of pediatric rhabdomyosarcoma,muscle,xenograft,cell,NA,NA,NA,Orthotopic patient-derived xenograft,TRUE,TRUE,Homo sapiens,GSE174376,GSM5390480,3p_v2,fastq,SRR14854601;SRR14854602,NA,SRX11173063,SRP319643,NA,SAMN19763830,NA,NA,NA,NA,NA,Illumina NovaSeq 6000,NA,NA
Dyer 2022,SJRHB012_Z,A single-cell/nucleus atlas of pediatric rhabdomyosarcoma,muscle,xenograft,cell,NA,NA,NA,Orthotopic patient-derived xenograft,TRUE,TRUE,Homo sapiens,GSE174376,GSM5390481,3p_v2,fastq,SRR14854603,NA,SRX11173064,SRP319643,NA,SAMN19763828,NA,NA,NA,NA,NA,Illumina NovaSeq 6000,NA,NA
Dyer 2022,SJRHB012405_X1,A single-cell/nucleus atlas of pediatric rhabdomyosarcoma,muscle,xenograft,cell,NA,NA,NA,Orthotopic patient-derived xenograft,TRUE,TRUE,Homo sapiens,GSE174376,GSM5390482,3p_v2,fastq,SRR14854604;SRR14854605,NA,SRX11173065,SRP319643,NA,SAMN19763826,NA,NA,NA,10.1016/j.devcel.2022.04.003,https://pubmed.ncbi.nlm.nih.gov/35483358/,Illumina NovaSeq 6000,NA,NA
Dyer 2022,SJRHB013758_X1,A single-cell/nucleus atlas of pediatric rhabdomyosarcoma,muscle,xenograft,cell,NA,NA,NA,Orthotopic patient-derived xenograft,TRUE,TRUE,Homo sapiens,GSE174376,GSM5390483,3p_v2,fastq,SRR14854606;SRR14854607,NA,SRX11173066,SRP319643,NA,SAMN19763824,NA,NA,NA,NA,NA,Illumina NovaSeq 6000,NA,NA
Dyer 2022,SJRHB013758_X2,A single-cell/nucleus atlas of pediatric rhabdomyosarcoma,muscle,xenograft,cell,NA,NA,NA,Orthotopic patient-derived xenograft,TRUE,TRUE,Homo sapiens,GSE174376,GSM5390484,3p_v2,fastq,SRR14854608;SRR14854609,NA,SRX11173067,SRP319643,NA,SAMN19763823,NA,NA,NA,10.1016/j.devcel.2022.04.003,https://pubmed.ncbi.nlm.nih.gov/35483358/,Illumina NovaSeq 6000,NA,NA
Dyer 2022,SJRHB049189_X1,A single-cell/nucleus atlas of pediatric rhabdomyosarcoma,muscle,xenograft,cell,NA,NA,NA,Orthotopic patient-derived xenograft,TRUE,TRUE,Homo sapiens,GSE174376,GSM5390485,3p_v2,fastq,SRR14854610;SRR14854611,NA,SRX11173068,SRP319643,NA,SAMN19763822,NA,NA,NA,10.1016/j.devcel.2022.04.003,https://pubmed.ncbi.nlm.nih.gov/35483358/,Illumina NovaSeq 6000,NA,NA
Dyer 2022,SJRHB030680_X1,A single-cell/nucleus atlas of pediatric rhabdomyosarcoma,muscle,xenograft,cell,NA,NA,NA,Orthotopic patient-derived xenograft,TRUE,TRUE,Homo sapiens,GSE174376,GSM5390486,3p_v2,fastq,SRR14854612;SRR14854613,NA,SRX11173069,SRP319643,NA,SAMN19763821,NA,NA,NA,10.1016/j.devcel.2022.04.003,https://pubmed.ncbi.nlm.nih.gov/35483358/,Illumina NovaSeq 6000,NA,NA
Dyer 2022,SJRHB010468_X1,A single-cell/nucleus atlas of pediatric rhabdomyosarcoma,muscle,xenograft,cell,NA,NA,NA,Orthotopic patient-derived xenograft,TRUE,TRUE,Homo sapiens,GSE174376,GSM5390487,3p_v2,fastq,SRR14854614;SRR14854615,NA,SRX11173070,SRP319643,NA,SAMN19763820,NA,NA,NA,10.1016/j.devcel.2022.04.003,https://pubmed.ncbi.nlm.nih.gov/35483358/,Illumina NovaSeq 6000,NA,NA
Dyer 2022,SJRHB013757_X1,A single-cell/nucleus atlas of pediatric rhabdomyosarcoma,muscle,xenograft,cell,NA,NA,NA,Orthotopic patient-derived xenograft,TRUE,TRUE,Homo sapiens,GSE174376,GSM5390488,3p_v2,fastq,SRR14854616;SRR14854617;SRR14854618;SRR14854619,NA,SRX11173071,SRP319643,NA,SAMN19763819,NA,NA,NA,10.1016/j.devcel.2022.04.003,https://pubmed.ncbi.nlm.nih.gov/35483358/,Illumina NovaSeq 6000,NA,NA
Dyer 2022,SJRHB013759_X14,A single-cell/nucleus atlas of pediatric rhabdomyosarcoma,muscle,xenograft,cell,NA,NA,NA,Orthotopic patient-derived xenograft,TRUE,TRUE,Homo sapiens,GSE174376,GSM5390489,3p_v2,fastq,SRR14854620;SRR14854621;SRR14854622;SRR14854623;SRR14854624;SRR14854625;SRR14854626;SRR14854627,NA,SRX11173072,SRP319643,NA,SAMN19763818,NA,NA,NA,NA,NA,Illumina NovaSeq 6000,NA,NA
Dyer 2022,SJRHB013759_X15,A single-cell/nucleus atlas of pediatric rhabdomyosarcoma,muscle,xenograft,cell,NA,NA,NA,Orthotopic patient-derived xenograft,TRUE,TRUE,Homo sapiens,GSE174376,GSM5390490,3p_v2,fastq,SRR14854628;SRR14854629;SRR14854630;SRR14854631;SRR14854632;SRR14854633;SRR14854634;SRR14854635,NA,SRX11173073,SRP319643,NA,SAMN19763817,NA,NA,NA,NA,NA,Illumina NovaSeq 6000,NA,NA
Dyer 2022,SJRHB046156_X1,A single-cell/nucleus atlas of pediatric rhabdomyosarcoma,muscle,xenograft,cell,NA,NA,NA,Orthotopic patient-derived xenograft,TRUE,TRUE,Homo sapiens,GSE174376,GSM5390491,3p_v2,fastq,SRR14854636;SRR14854637,NA,SRX11173074,SRP319643,NA,SAMN19763816,NA,NA,NA,10.1016/j.devcel.2022.04.003,https://pubmed.ncbi.nlm.nih.gov/35483358/,Illumina NovaSeq 6000,NA,NA
Dyer 2022,SJRHB031320_X1,A single-cell/nucleus atlas of pediatric rhabdomyosarcoma,muscle,xenograft,cell,NA,NA,NA,Orthotopic patient-derived xenograft,TRUE,TRUE,Homo sapiens,GSE174376,GSM5390492,3p_v2,fastq,SRR14854638;SRR14854639,NA,SRX11173075,SRP319643,NA,SAMN19763815,NA,NA,NA,10.1016/j.devcel.2022.04.003,https://pubmed.ncbi.nlm.nih.gov/35483358/,Illumina NovaSeq 6000,NA,NA
Dyer 2022,SJRHB030680_X1_organoid,A single-cell/nucleus atlas of pediatric rhabdomyosarcoma,muscle,organoid,cell,NA,NA,NA,Organoid,TRUE,TRUE,Homo sapiens,GSE174376,GSM5390515,3p_v3,fastq,SRR14854694;SRR14854693,NA,SRX11173098,SRP319643,NA,SAMN19763794,NA,NA,NA,NA,NA,Illumina NovaSeq 6000,NA,NA
Dyer 2022,SJRHB00026_X1_treat_day0,A single-cell/nucleus atlas of pediatric rhabdomyosarcoma,muscle,xenograft,cell,NA,NA,NA,Orthotopic patient-derived xenograft,TRUE,TRUE,Homo sapiens,GSE174376,GSM5390516,3p_v3,fastq,SRR14854695;SRR14854696,NA,SRX11173099,SRP319643,NA,SAMN19763793,NA,NA,NA,10.1016/j.devcel.2022.04.003,https://pubmed.ncbi.nlm.nih.gov/35483358/,Illumina NovaSeq 6000,NA,NA
Dyer 2022,SJRHB00026_X1_treat_day3,A single-cell/nucleus atlas of pediatric rhabdomyosarcoma,muscle,xenograft,cell,NA,NA,NA,Orthotopic patient-derived xenograft,TRUE,TRUE,Homo sapiens,GSE174376,GSM5390517,3p_v2,fastq,SRR14854697;SRR14854698,NA,SRX11173100,SRP319643,NA,SAMN19763792,NA,NA,NA,10.1016/j.devcel.2022.04.003,https://pubmed.ncbi.nlm.nih.gov/35483358/,Illumina NovaSeq 6000,NA,NA
Dyer 2022,SJRHB00026_X1_treat_day28,A single-cell/nucleus atlas of pediatric rhabdomyosarcoma,muscle,xenograft,cell,NA,NA,NA,Orthotopic patient-derived xenograft,TRUE,TRUE,Homo sapiens,GSE174376,GSM5390518,3p_v2,fastq,SRR14854699;SRR14854700,NA,SRX11173101,SRP319643,NA,SAMN19763791,NA,NA,NA,10.1016/j.devcel.2022.04.003,https://pubmed.ncbi.nlm.nih.gov/35483358/,Illumina NovaSeq 6000,NA,NA
Potluri 2022,Arom1,NA,muscle,lower abdominal muscle,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE174594,GSM5320243,3p_v3,fastq,SRR14574608;SRR14574609;SRR14574610;SRR14574611;SRR14574612,NA,NA,NA,NA,SAMN19239056,NA,NA,"Potluri et al, JCI Insight, 2022",10.1172/jci.insight.152011,https://pubmed.ncbi.nlm.nih.gov/35439171/,NA,NA,NA
Potluri 2022,Arom2,NA,muscle,lower abdominal muscle,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE174594,GSM5320244,3p_v3,fastq,SRR14574613;SRR14574614;SRR14574615;SRR14574616;SRR14574617,NA,NA,NA,NA,SAMN19239055,NA,NA,"Potluri et al, JCI Insight, 2022",10.1172/jci.insight.152011,https://pubmed.ncbi.nlm.nih.gov/35439171/,NA,NA,NA
Potluri 2022,Arom3,NA,muscle,lower abdominal muscle,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE174594,GSM5320245,3p_v3,fastq,SRR14574618;SRR14574619;SRR14574620;SRR14574621;SRR14574622,NA,NA,NA,NA,SAMN19239054,NA,NA,"Potluri et al, JCI Insight, 2022",10.1172/jci.insight.152011,https://pubmed.ncbi.nlm.nih.gov/35439171/,NA,NA,NA
Potluri 2022,WT1,NA,muscle,lower abdominal muscle,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE174594,GSM5320246,3p_v3,fastq,SRR14574623;SRR14574624;SRR14574625;SRR14574626;SRR14574627,NA,NA,NA,NA,SAMN19239053,NA,NA,"Potluri et al, JCI Insight, 2022",10.1172/jci.insight.152011,https://pubmed.ncbi.nlm.nih.gov/35439171/,NA,NA,NA
Potluri 2022,WT2,NA,muscle,lower abdominal muscle,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE174594,GSM5320247,3p_v3,fastq,SRR14574628;SRR14574629;SRR14574630;SRR14574631;SRR14574632,NA,NA,NA,NA,SAMN19239052,NA,NA,"Potluri et al, JCI Insight, 2022",10.1172/jci.insight.152011,https://pubmed.ncbi.nlm.nih.gov/35439171/,NA,NA,NA
Potluri 2022,WT3,NA,muscle,lower abdominal muscle,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE174594,GSM5320248,3p_v3,fastq,SRR14574633;SRR14574634;SRR14574635;SRR14574636;SRR14574637,NA,NA,NA,NA,SAMN19239051,NA,NA,"Potluri et al, JCI Insight, 2022",10.1172/jci.insight.152011,https://pubmed.ncbi.nlm.nih.gov/35439171/,NA,NA,NA
Uapinyoying 2022,Wild type FAPs 1,NA,muscle,fibro/adipogenic progenitors,cell,female,NA,NA,NA,TRUE,FALSE,Mus musculus,GSE182293,GSM5526267,3p_v3,fastq,SRR15502447,NA,SRX11801760,NA,NA,SAMN20839456,NA,NA,NA,NA,NA,NA,NA,NA
Uapinyoying 2022,Wild type FAPs 2,NA,muscle,fibro/adipogenic progenitors,cell,female,NA,NA,NA,TRUE,FALSE,Mus musculus,GSE182293,GSM5526268,3p_v3,fastq,SRR15502448,NA,SRX11801761,NA,NA,SAMN20839459,NA,NA,NA,NA,NA,NA,NA,NA
Uapinyoying 2022,Wild type FAPs 3,NA,muscle,fibro/adipogenic progenitors,cell,female,NA,NA,NA,TRUE,FALSE,Mus musculus,GSE182293,GSM5526269,3p_v3,fastq,SRR15502449,NA,SRX11801762,NA,NA,SAMN20839460,NA,NA,NA,NA,NA,NA,NA,NA
Uapinyoying 2022,Wild type FAPs 4,NA,muscle,fibro/adipogenic progenitors,cell,female,NA,NA,NA,TRUE,FALSE,Mus musculus,GSE182293,GSM5526270,3p_v3,fastq,SRR15502450,NA,SRX11801763,NA,NA,SAMN20839462,NA,NA,NA,NA,NA,NA,NA,NA
Uapinyoying 2022,Dysferlin KO FAPs 1,NA,muscle,fibro/adipogenic progenitors,cell,female,NA,NA,NA,TRUE,FALSE,Mus musculus,GSE182293,GSM5526271,3p_v3,fastq,SRR15502451,NA,SRX11801764,NA,NA,SAMN20839463,NA,NA,NA,NA,NA,NA,NA,NA
Uapinyoying 2022,Dysferlin KO FAPs 2,NA,muscle,fibro/adipogenic progenitors,cell,female,NA,NA,NA,TRUE,FALSE,Mus musculus,GSE182293,GSM5526272,3p_v3,fastq,SRR15502452,NA,SRX11801765,NA,NA,SAMN20839464,NA,NA,NA,NA,NA,NA,NA,NA
Uapinyoying 2022,Dysferlin KO FAPs 3,NA,muscle,fibro/adipogenic progenitors,cell,female,NA,NA,NA,TRUE,FALSE,Mus musculus,GSE182293,GSM5526273,3p_v3,fastq,SRR15502453,NA,SRX11801766,NA,NA,SAMN20839465,NA,NA,NA,NA,NA,NA,NA,NA
Uapinyoying 2022,Dysferlin KO FAPs 4,NA,muscle,fibro/adipogenic progenitors,cell,female,NA,NA,NA,TRUE,FALSE,Mus musculus,GSE182293,GSM5526274,3p_v3,fastq,SRR15502454,NA,SRX11801767,NA,NA,SAMN20839466,NA,NA,NA,NA,NA,NA,NA,NA
Yang J 2022,Single-cell sedentary standard (chow) diet rep1 [SC1.SM],NA,muscle,triceps,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE183288,GSM5554992,3p_v3,fastq,SRR15702809;SRR15702810,NA,SRX11998668,NA,NA,SRX11998668,NA,NA,NA,10.1016/j.cmet.2022.09.004,https://pubmed.ncbi.nlm.nih.gov/36198295/,NA,NA,NA
Yang J 2022,Single-cell sedentary standard (chow) diet rep2 [SC2.SM],NA,muscle,triceps,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE183288,GSM5554993,3p_v3,fastq,SRR15702811;SRR15702812,NA,SRX11998669,NA,NA,SRX11998669,NA,NA,NA,10.1016/j.cmet.2022.09.004,https://pubmed.ncbi.nlm.nih.gov/36198295/,NA,NA,NA
Yang J 2022,Single-cell sedentary standard (chow) diet rep3 [SC3.SM],NA,muscle,triceps,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE183288,GSM5554994,3p_v3,fastq,SRR15702813;SRR15702814,NA,SRX11998670,NA,NA,SRX11998670,NA,NA,NA,10.1016/j.cmet.2022.09.004,https://pubmed.ncbi.nlm.nih.gov/36198295/,NA,NA,NA
Yang J 2022,Single-cell training standard (chow) diet rep1 [TC1.SM],NA,muscle,triceps,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE183288,GSM5554995,3p_v3,fastq,SRR15702815;SRR15702816,NA,SRX11998671,NA,NA,SRX11998671,NA,NA,NA,10.1016/j.cmet.2022.09.004,https://pubmed.ncbi.nlm.nih.gov/36198295/,NA,NA,NA
Yang J 2022,Single-cell training standard (chow) diet rep2 [TC2.SM],NA,muscle,triceps,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE183288,GSM5554996,3p_v3,fastq,SRR15702817;SRR15702818,NA,SRX11998672,NA,NA,SRX11998672,NA,NA,NA,10.1016/j.cmet.2022.09.004,https://pubmed.ncbi.nlm.nih.gov/36198295/,NA,NA,NA
Yang J 2022,Single-cell training standard (chow) diet rep3 [TC3.SM],NA,muscle,triceps,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE183288,GSM5554997,3p_v3,fastq,SRR15702819;SRR15702820,NA,SRX11998673,NA,NA,SRX11998673,NA,NA,NA,10.1016/j.cmet.2022.09.004,https://pubmed.ncbi.nlm.nih.gov/36198295/,NA,NA,NA
Yang J 2022,Single-cell training standard (chow) diet rep4 [TC4.SM],NA,muscle,triceps,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE183288,GSM5554998,3p_v3,fastq,SRR15702821;SRR15702822,NA,SRX11998674,NA,NA,SRX11998674,NA,NA,NA,10.1016/j.cmet.2022.09.004,https://pubmed.ncbi.nlm.nih.gov/36198295/,NA,NA,NA
Yang J 2022,Single-cell sedentary high-fat diet rep1 [SH1.SM],NA,muscle,triceps,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE183288,GSM5554999,3p_v3,fastq,SRR15702823;SRR15702824,NA,SRX11998675,NA,NA,SRX11998675,NA,NA,NA,10.1016/j.cmet.2022.09.004,https://pubmed.ncbi.nlm.nih.gov/36198295/,NA,NA,NA
Yang J 2022,Single-cell sedentary high-fat diet rep2 [SH2.SM],NA,muscle,triceps,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE183288,GSM5555000,3p_v3,fastq,SRR15702825;SRR15702826,NA,SRX11998676,NA,NA,SRX11998676,NA,NA,NA,10.1016/j.cmet.2022.09.004,https://pubmed.ncbi.nlm.nih.gov/36198295/,NA,NA,NA
Yang J 2022,Single-cell sedentary high-fat diet rep3 [SH3.SM],NA,muscle,triceps,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE183288,GSM5555001,3p_v3,fastq,SRR15702827;SRR15702828,NA,SRX11998677,NA,NA,SRX11998677,NA,NA,NA,10.1016/j.cmet.2022.09.004,https://pubmed.ncbi.nlm.nih.gov/36198295/,NA,NA,NA
Yang J 2022,Single-cell training high-fat diet rep1 [TH1.SM],NA,muscle,triceps,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE183288,GSM5555002,3p_v3,fastq,SRR15702829;SRR15702830,NA,SRX11998678,NA,NA,SRX11998678,NA,NA,NA,10.1016/j.cmet.2022.09.004,https://pubmed.ncbi.nlm.nih.gov/36198295/,NA,NA,NA
Yang J 2022,Single-cell training high-fat diet rep2 [TH2.SM],NA,muscle,triceps,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE183288,GSM5555003,3p_v3,fastq,SRR15702831;SRR15702832,NA,SRX11998679,NA,NA,SRX11998679,NA,NA,NA,10.1016/j.cmet.2022.09.004,https://pubmed.ncbi.nlm.nih.gov/36198295/,NA,NA,NA
Yang J 2022,Single-cell training high-fat diet rep3 [TH3.SM],NA,muscle,triceps,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE183288,GSM5555004,3p_v3,fastq,SRR15702833;SRR15702834,NA,SRX11998680,NA,NA,SRX11998680,NA,NA,NA,10.1016/j.cmet.2022.09.004,https://pubmed.ncbi.nlm.nih.gov/36198295/,NA,NA,NA
Yang J 2022,Single-cell training high-fat diet rep4 [TH4.SM],NA,muscle,triceps,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE183288,GSM5555005,3p_v3,fastq,SRR15702835;SRR15702836,NA,SRX11998681,NA,NA,SRX11998681,NA,NA,NA,10.1016/j.cmet.2022.09.004,https://pubmed.ncbi.nlm.nih.gov/36198295/,NA,NA,NA
Lyu 2022,bovine satellite cells 1,NA,muscle,muscle stem cell,cell,NA,NA,NA,"Only _2 and _3; no R2 file uploaded according to ffq, but it is there according to SRA_fastq",TRUE,FALSE,Bos taurus,GSE184128,GSM5578326,3p_v3,fastq,SRR15898616,NA,NA,NA,NA,NA,NA,NA,"Lyu et al, Frontiers in Genetics, 2022",10.3389/fgene.2021.742077,https://pubmed.ncbi.nlm.nih.gov/34777469/,NA, Single-cell RNA Sequencing Reveals Heterogeneity of Cultured Bovine Satellite Cells,NA
Lyu 2022,bovine satellite cells 2,NA,muscle,muscle stem cell,cell,NA,NA,NA,"Only _2 and _3; no R2 file uploaded according to ffq, but it is there according to SRA_fastq",TRUE,FALSE,Bos taurus,GSE184128,GSM5578327,3p_v3,fastq,SRR15898617,NA,NA,NA,NA,NA,NA,NA,"Lyu et al, Frontiers in Genetics, 2022",10.3389/fgene.2021.742077,https://pubmed.ncbi.nlm.nih.gov/34777469/,NA,NA,NA
Wu YF 2022,TA - Mobile scRNA-seq,NA,muscle,tibialis anterior,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE185560,GSM5618381,3p_v3,fastq,SRR16249204;SRR16249205,NA,SRX12528966,NA,NA,SAMN22160568,NA,NA,NA,10.1113/JP282867,https://pubmed.ncbi.nlm.nih.gov/35318675/,NA,NA,NA
Wu YF 2022,TA - Immobile scRNA-seq,NA,muscle,tibialis anterior,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE185560,GSM5618382,3p_v3,fastq,SRR16249202;SRR16249203,NA,SRX12528967,NA,NA,SAMN22160567,NA,NA,NA,10.1113/JP282867,https://pubmed.ncbi.nlm.nih.gov/35318675/,NA,NA,NA
Fujimaki 2022,Gastrocnemius,NA,muscle,gastrocnemius,nucleus,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE185678,GSM5621535,3p_v3.1,fastq,SRR16292879,NA,NA,NA,NA,NA,NA,NA,NA,10.1038/s42255-022-00533-9,https://pubmed.ncbi.nlm.nih.gov/35228746/,HiSeq X Ten,NA,NA
Fujimaki 2022,Plantaris,NA,muscle,plantaris,nucleus,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE185678,GSM5621536,3p_v3.1,fastq,SRR16292880,NA,NA,NA,NA,NA,NA,NA,NA,10.1038/s42255-022-00533-9,https://pubmed.ncbi.nlm.nih.gov/35228746/,HiSeq X Ten,NA,NA
Nie 2021,runx2b+/+ scRNA-seq,150x150,muscle,tail,NA,NA,NA,NA,150bp R1,TRUE,TRUE,Danio rerio,GSE186957,GSM5664292,NA,fastq,SRR16681976,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Nie 2021,runx2b-/- scRNA-seq,150x150,muscle,tail,NA,NA,NA,NA,150bp R1,TRUE,TRUE,Danio rerio,GSE186957,GSM5664293,NA,fastq,SRR16681977,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Nie 2021,runx2b-/- scRNA-seq,NA,muscle,tail,NA,NA,NA,NA,150bp R1,TRUE,TRUE,Danio rerio,GSE186957,GSM5664293,NA,fastq,SRR16681977,NA,SRX12882565,SRP344071,SRS10825217,SAMN22822661,NA,NA,unpublished,NA,unpublished,Illumina NovaSeq 6000,Single-cell transcriptomes and runx2b-/- mutants reveal the genetic signatures of intermuscular bone formation in teleosts,"Purpose: Intermuscular bones (IBs) are hard spicules, mainly existing in the myosepta of recent vertebrates. This evolutionary trait has puzzled biologists and consumers, and the molecular basis of IB development remains unclear. The goals of this study are to acquire characteristic single-cell maps of gene expression landscapes and lineages and to elucidate the differentiation trajectory of cell clusters related to IB formation and obtain the key regulated gene of IB formation. Methods: The scRNA-seq profiles of 60 dpf wild-type zebrafish and 60 dpf runx2b-/- zebrafish were generated, using the 10X Genomics Chromium system. The bulk RNA-seq profiles of 60 dpf wild-type zebrafish and 60 dpf runx2b-/- zebrafish were generated, using mirVana miRNA ISOlation Kit. The scRNA-seq data were filted and clsutered by the Seurat package. The cell differentiation trajectorie was constructed, using Monocle analysis. Runx2b knockdown was preformed by RNA interference and runx2b was inducted by neuropeptide substance P. qRTPCR validation was performed using SYBR Green assays. The mutant zebrafish lines were constructed, using cripsr cas9 technology.The Phenotypic observation was perfomed by Hematoxylin and Eosin (HE), Alizarin red, masson trichrome staining and mico-CT. The nutritent content was also obtained including fatty acid content and anio acid content. Results: we reveal that teleost fish IBs originate from tendons in the skeletal muscle and that the differentiation trajectory from tendon progenitors and defined runx2b as the key rugulated gene of IB formaiton, using cripsr cas9 technology. Conclusions: This study is the first to reveal that teleost fish IBs originate from tendons in the skeletal muscle and that the differentiation trajectory from tendon progenitors to the osteoblast lineage is key for IB formation. Large-scale gene function analysis using CRISPR-Cas9 identified the decisive role of runx2b in IB formation. The loss of runx2b significantly restricted osteoblast differentiation and inhibited IB formation, which potentially provides a basis for breeding strains of fish without IBs to improve the safe consumption and economic value of many aquaculture species and in this way, boost the proportion of fish for the supply of animal protein worldwide (Fig. 6). For this reason, we needed to verify that the content of fatty acid in the runx2b-/- mutant was higher than that in runx2b+/+ fish, as well as the expression of key genes related to IBs in the runx2b-/- and runx2b+/+ strains obtained by scRNA-seq data. This study also provides materials and directions for further study to clarify the specific regulatory mechanism of IB formation and will help to discover more specific genetic resources that can be used for IB trait improvement in fish. Overall design: the scRNA-seq and bulk-seq profiles of 60 dpf wild-type zebrafish and 60 dpf runx2b-/- zebrafish"
Wang J 2021,2D expanded cells,2D expanded CD56+ myogenic cells,muscle,cultured primary cells,cell,NA,NA,NA,NA,TRUE,FALSE,Homo sapiens,GSE188215,GSM5672476,3p_v3,fastq,SRR16774171,NA,SRX12973435,SRP344609,SRS10914287,SAMN22892805,NA,NA,NA,10.1038/s42003-021-02059-4,https://pubmed.ncbi.nlm.nih.gov/33953320/,DNBSEQ-G400,Three-dimensional tissue-engineered human skeletal muscle model of satellite cell quiescence,"In vivo, satellite cells (SCs) are essential for skeletal muscle repair. However, in vitro investigation of SC function is challenged by isolation-induced SC activation, loss of the native quiescent state, and differentiation to myoblasts. This study applies  tissue-engineered human skeletal muscle to track myoblast deactivation to 3D-SCs, which bear a quiescent phenotype, as well as examine melittin-induced injury response. Overall design: CD56+ sorted cells from human muscle were expanded for 5 passages (2D) and used to generate 3D engineered muscle (myobundles). After 4 days of 3D growth conditions, myobundles were differentiated for 3 days (d3), 9 days (d9), or melittin-injured at d7 and sampled 2 days post injury (i2) and 5 days post injury (i5). In the myobundle samples (d3,d9,i2,i5),  cells were dissociated from the myobundles before being subjected to single cell RNA-sequencing (scRNA-seq) using the 10x Genomics Chromium technology."
Wang J 2021,3-day differentiated myobundles,dissociated 3D engineered tissue (myobundle),muscle,cultured primary cells,cell,NA,NA,NA,NA,TRUE,FALSE,Homo sapiens,GSE188215,GSM5672477,3p_v3,fastq,SRR16774172,NA,SRX12973436,SRP344609,SRS10914288,SAMN22892807,NA,NA,NA,10.1038/s42003-021-02059-4,https://pubmed.ncbi.nlm.nih.gov/33953320/,DNBSEQ-G400,Three-dimensional tissue-engineered human skeletal muscle model of satellite cell quiescence,"In vivo, satellite cells (SCs) are essential for skeletal muscle repair. However, in vitro investigation of SC function is challenged by isolation-induced SC activation, loss of the native quiescent state, and differentiation to myoblasts. This study applies  tissue-engineered human skeletal muscle to track myoblast deactivation to 3D-SCs, which bear a quiescent phenotype, as well as examine melittin-induced injury response. Overall design: CD56+ sorted cells from human muscle were expanded for 5 passages (2D) and used to generate 3D engineered muscle (myobundles). After 4 days of 3D growth conditions, myobundles were differentiated for 3 days (d3), 9 days (d9), or melittin-injured at d7 and sampled 2 days post injury (i2) and 5 days post injury (i5). In the myobundle samples (d3,d9,i2,i5),  cells were dissociated from the myobundles before being subjected to single cell RNA-sequencing (scRNA-seq) using the 10x Genomics Chromium technology."
Wang J 2021,9-day differentiated myobundles,dissociated 3D engineered tissue (myobundle),muscle,cultured primary cells,cell,NA,NA,NA,NA,TRUE,FALSE,Homo sapiens,GSE188215,GSM5672478,3p_v3,fastq,SRR16774173,NA,SRX12973437,SRP344609,SRS10914289,SAMN22892809,NA,NA,NA,10.1038/s42003-021-02059-4,https://pubmed.ncbi.nlm.nih.gov/33953320/,DNBSEQ-G400,Three-dimensional tissue-engineered human skeletal muscle model of satellite cell quiescence,"In vivo, satellite cells (SCs) are essential for skeletal muscle repair. However, in vitro investigation of SC function is challenged by isolation-induced SC activation, loss of the native quiescent state, and differentiation to myoblasts. This study applies  tissue-engineered human skeletal muscle to track myoblast deactivation to 3D-SCs, which bear a quiescent phenotype, as well as examine melittin-induced injury response. Overall design: CD56+ sorted cells from human muscle were expanded for 5 passages (2D) and used to generate 3D engineered muscle (myobundles). After 4 days of 3D growth conditions, myobundles were differentiated for 3 days (d3), 9 days (d9), or melittin-injured at d7 and sampled 2 days post injury (i2) and 5 days post injury (i5). In the myobundle samples (d3,d9,i2,i5),  cells were dissociated from the myobundles before being subjected to single cell RNA-sequencing (scRNA-seq) using the 10x Genomics Chromium technology."
Wang J 2021,2 days post injury of 7-day differentiated myobundles,dissociated 3D engineered tissue (myobundle),muscle,cultured primary cells,cell,NA,NA,NA,NA,TRUE,FALSE,Homo sapiens,GSE188215,GSM5672479,3p_v3,fastq,SRR16774174,NA,SRX12973438,SRP344609,SRS10914290,SAMN22892811,NA,NA,NA,10.1038/s42003-021-02059-4,https://pubmed.ncbi.nlm.nih.gov/33953320/,DNBSEQ-G400,Three-dimensional tissue-engineered human skeletal muscle model of satellite cell quiescence,"In vivo, satellite cells (SCs) are essential for skeletal muscle repair. However, in vitro investigation of SC function is challenged by isolation-induced SC activation, loss of the native quiescent state, and differentiation to myoblasts. This study applies  tissue-engineered human skeletal muscle to track myoblast deactivation to 3D-SCs, which bear a quiescent phenotype, as well as examine melittin-induced injury response. Overall design: CD56+ sorted cells from human muscle were expanded for 5 passages (2D) and used to generate 3D engineered muscle (myobundles). After 4 days of 3D growth conditions, myobundles were differentiated for 3 days (d3), 9 days (d9), or melittin-injured at d7 and sampled 2 days post injury (i2) and 5 days post injury (i5). In the myobundle samples (d3,d9,i2,i5),  cells were dissociated from the myobundles before being subjected to single cell RNA-sequencing (scRNA-seq) using the 10x Genomics Chromium technology."
Wang J 2021,5 days post injury of 7-day differentiated myobundles,dissociated 3D engineered tissue (myobundle),muscle,cultured primary cells,cell,NA,NA,NA,NA,TRUE,FALSE,Homo sapiens,GSE188215,GSM5672480,3p_v3,fastq,SRR16774175,NA,SRX12973439,SRP344609,SRS10914291,SAMN22892813,NA,NA,NA,10.1038/s42003-021-02059-4,https://pubmed.ncbi.nlm.nih.gov/33953320/,DNBSEQ-G400,Three-dimensional tissue-engineered human skeletal muscle model of satellite cell quiescence,"In vivo, satellite cells (SCs) are essential for skeletal muscle repair. However, in vitro investigation of SC function is challenged by isolation-induced SC activation, loss of the native quiescent state, and differentiation to myoblasts. This study applies  tissue-engineered human skeletal muscle to track myoblast deactivation to 3D-SCs, which bear a quiescent phenotype, as well as examine melittin-induced injury response. Overall design: CD56+ sorted cells from human muscle were expanded for 5 passages (2D) and used to generate 3D engineered muscle (myobundles). After 4 days of 3D growth conditions, myobundles were differentiated for 3 days (d3), 9 days (d9), or melittin-injured at d7 and sampled 2 days post injury (i2) and 5 days post injury (i5). In the myobundle samples (d3,d9,i2,i5),  cells were dissociated from the myobundles before being subjected to single cell RNA-sequencing (scRNA-seq) using the 10x Genomics Chromium technology."
Guo 2022,SRSF2f/f/Myf5-Cre/tdT,NA,muscle,embryonic trunk and limbs,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE189088,GSM5694401,3p_v3.1,fastq,SRR16974736;SRR16974737;SRR16974738;SRR16974739,NA,NA,NA,NA,SAMN23282117,NA,NA,NA,10.1002/advs.202105775,https://pubmed.ncbi.nlm.nih.gov/35460187/,NA,NA,NA
Guo 2022,SRSF2f/w/Myf5-Cre/tdT,NA,muscle,embryonic trunk and limbs,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE189088,GSM5694402,3p_v3.1,fastq,SRR16974740;SRR16974741;SRR16974742;SRR16974743,NA,NA,NA,NA,SAMN23282118,NA,NA,NA,10.1002/advs.202105775,https://pubmed.ncbi.nlm.nih.gov/35460187/,NA,NA,NA
Yoo 2022,"FAPs, Bap1, WT",NA,muscle,fibro/adipogenic progenitors,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE190426,GSM5723635,3p_v3,fastq,SRR17167452,NA,SRX13351347,NA,NA,SAMN23773681,NA,NA,NA,10.1172/jci.insight.158380,https://pubmed.ncbi.nlm.nih.gov/35603786/,NA,NA,NA
Yoo 2022,"FAPs, Bap1, cKO",NA,muscle,fibro/adipogenic progenitors,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE190426,GSM5723636,3p_v3,fastq,SRR17167453,NA,SRX13351348,NA,NA,SAMN23773682,NA,NA,NA,10.1172/jci.insight.158380,https://pubmed.ncbi.nlm.nih.gov/35603786/,NA,NA,NA
Oskolkov 2022,"Skeletal muscle cells, GAC021",NA,muscle,vastus lateralis,cell,NA,NA,NA,Reads from each sequencing run are split across separate SRR IDs?,TRUE,TRUE,Homo sapiens,GSE190489 ,GSM5724579,3p_v2,fastq,SRR21931094,NA,NA,NA,NA,SAMN23794932,NA,NA,NA,NA,NA,NA,NA,NA
Oskolkov 2022,"Skeletal muscle cells, GAC022",NA,muscle,vastus lateralis,cell,NA,NA,NA,Reads from each sequencing run are split across separate SRR IDs?,TRUE,TRUE,Pan troglodytes,GSE190489 ,GSM5724580,3p_v2,fastq,SRR21931095,NA,NA,NA,NA,SAMN23794933,NA,NA,NA,NA,NA,NA,NA,NA
Kulkarni 2022,Old_muscle_1,NA,muscle,gastrocnemius,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE194386,GSM5834903,3p_v2,fastq,SRR17747992,NA,SRX13910428,NA,NA,SAMN25247584,NA,NA,NA,10.1093/gigascience/giac126,https://pubmed.ncbi.nlm.nih.gov/36691728/,NA,NA,NA
Kulkarni 2022,Old_muscle_2,NA,muscle,gastrocnemius,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE194386,GSM5834905,3p_v2,fastq,SRR17747990,NA,SRX13910430,NA,NA,SAMN25247582,NA,NA,NA,10.1093/gigascience/giac126,https://pubmed.ncbi.nlm.nih.gov/36691728/,NA,NA,NA
Kulkarni 2022,Old_muscle_3,NA,muscle,gastrocnemius,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE194386,GSM5834907,3p_v2,fastq,SRR17747988,NA,SRX13910432,NA,NA,SAMN25247580,NA,NA,NA,10.1093/gigascience/giac126,https://pubmed.ncbi.nlm.nih.gov/36691728/,NA,NA,NA
Kulkarni 2022,Old_muscle_4,NA,muscle,gastrocnemius,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE194386,GSM5834909,3p_v2,fastq,SRR17747986,NA,SRX13910434,NA,NA,SAMN25247578,NA,NA,NA,10.1093/gigascience/giac126,https://pubmed.ncbi.nlm.nih.gov/36691728/,NA,NA,NA
Kulkarni 2022,Metformin-treated_muscle_1,NA,muscle,gastrocnemius,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE194386,GSM5834911,3p_v2,fastq,SRR17747984,NA,SRX13910436,NA,NA,SAMN25247576,NA,NA,NA,10.1093/gigascience/giac126,https://pubmed.ncbi.nlm.nih.gov/36691728/,NA,NA,NA
Kulkarni 2022,Metformin-treated_muscle_2,NA,muscle,gastrocnemius,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE194386,GSM5834913,3p_v2,fastq,SRR17747982,NA,SRX13910438,NA,NA,SAMN25247574,NA,NA,NA,10.1093/gigascience/giac126,https://pubmed.ncbi.nlm.nih.gov/36691728/,NA,NA,NA
Kulkarni 2022,Metformin-treated_muscle_3,NA,muscle,gastrocnemius,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE194386,GSM5834915,3p_v2,fastq,SRR17747980,NA,SRX13910440,NA,NA,SAMN25247572,NA,NA,NA,10.1093/gigascience/giac126,https://pubmed.ncbi.nlm.nih.gov/36691728/,NA,NA,NA
Kulkarni 2022,Metformin-treated_muscle_4,NA,muscle,gastrocnemius,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE194386,GSM5834917,3p_v2,fastq,SRR17747978,NA,SRX13910442,NA,NA,SAMN25247570,NA,NA,NA,10.1093/gigascience/giac126,https://pubmed.ncbi.nlm.nih.gov/36691728/,NA,NA,NA
Kulkarni 2022,Young_muscle_1,NA,muscle,gastrocnemius,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE194386,GSM5834919,3p_v2,fastq,SRR17747976,NA,SRX13910444,NA,NA,SAMN25247568,NA,NA,NA,10.1093/gigascience/giac126,https://pubmed.ncbi.nlm.nih.gov/36691728/,NA,NA,NA
Kulkarni 2022,Young_muscle_2,NA,muscle,gastrocnemius,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE194386,GSM5834921,3p_v2,fastq,SRR17747974,NA,SRX13910446,NA,NA,SAMN25247566,NA,NA,NA,10.1093/gigascience/giac126,https://pubmed.ncbi.nlm.nih.gov/36691728/,NA,NA,NA
Kulkarni 2022,Young_muscle_3,NA,muscle,gastrocnemius,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE194386,GSM5834923,3p_v2,fastq,SRR17747972,NA,SRX13910448,NA,NA,SAMN25247564,NA,NA,NA,10.1093/gigascience/giac126,https://pubmed.ncbi.nlm.nih.gov/36691728/,NA,NA,NA
Kulkarni 2022,Young_muscle_4,NA,muscle,gastrocnemius,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE194386,GSM5834925,3p_v2,fastq,SRR17747970,NA,SRX13910450,NA,NA,SAMN25247562,NA,NA,NA,10.1093/gigascience/giac126,https://pubmed.ncbi.nlm.nih.gov/36691728/,NA,NA,NA
Krasniewski 2022,Macrophage #1 Old,NA,muscle,macrophage,cell,NA,NA,NA,NA,TRUE,FALSE,Mus musculus,GSE195507,GSM5839574,3p_v3,bam,SRR17772821,NA,SRX13935281,NA,NA,SAMN25286223,NA,NA,"Krasniewski et al, eLife, 2022",10.7554/eLife.77974,https://pubmed.ncbi.nlm.nih.gov/36259488/,NA,NA,NA
Krasniewski 2022,Macrophage #1 Young,NA,muscle,macrophage,cell,NA,NA,NA,NA,TRUE,FALSE,Mus musculus,GSE195507,GSM5839575,3p_v3,bam,SRR17772820,NA,SRX13935282,NA,NA,SAMN25286222,NA,NA,"Krasniewski et al, eLife, 2022",10.7554/eLife.77974,https://pubmed.ncbi.nlm.nih.gov/36259488/,NA,NA,NA
Krasniewski 2022,Macrophage #2 Old,NA,muscle,macrophage,cell,NA,NA,NA,NA,TRUE,FALSE,Mus musculus,GSE195507,GSM5839576,3p_v3,bam,SRR17772819,NA,SRX13935283,NA,NA,SAMN25286221,NA,NA,"Krasniewski et al, eLife, 2022",10.7554/eLife.77974,https://pubmed.ncbi.nlm.nih.gov/36259488/,NA,NA,NA
Krasniewski 2022,Macrophage #2 Young,NA,muscle,macrophage,cell,NA,NA,NA,NA,TRUE,FALSE,Mus musculus,GSE195507,GSM5839577,3p_v3,bam,SRR17772818,NA,SRX13935284,NA,NA,SAMN25286220,NA,NA,"Krasniewski et al, eLife, 2022",10.7554/eLife.77974,https://pubmed.ncbi.nlm.nih.gov/36259488/,NA,NA,NA
Krasniewski 2022,Macrophage #3 Old,NA,muscle,macrophage,cell,NA,NA,NA,NA,TRUE,FALSE,Mus musculus,GSE195507,GSM5839578,3p_v3,bam,SRR17772817,NA,SRX13935285,NA,NA,SAMN25286219,NA,NA,"Krasniewski et al, eLife, 2022",10.7554/eLife.77974,https://pubmed.ncbi.nlm.nih.gov/36259488/,NA,NA,NA
Krasniewski 2022,Macrophage #3 Young,NA,muscle,macrophage,cell,NA,NA,NA,NA,TRUE,FALSE,Mus musculus,GSE195507,GSM5839579,3p_v3,bam,SRR17772816,NA,SRX13935286,NA,NA,SAMN25286218,NA,NA,"Krasniewski et al, eLife, 2022",10.7554/eLife.77974,https://pubmed.ncbi.nlm.nih.gov/36259488/,NA,NA,NA
Wei 2022,20082 rhabdomyosarcoma primary patient sample,NA,muscle,tumor,cell,NA,NA,NA,NA,TRUE,FALSE,Homo sapiens,GSE195709,GSM5848673,3p_v3,fastq,SRR17818982;SRR17818983;SRR17818984;SRR17818985,NA,NA,NA,NA,NA,NA,NA,NA,10.1038/s43018-022-00414-w,https://pubmed.ncbi.nlm.nih.gov/35982179/,NA,NA,NA
Wei 2022,20696 rhabdomyosarcoma primary patient sample,NA,muscle,tumor,cell,NA,NA,NA,NA,TRUE,FALSE,Homo sapiens,GSE195709,GSM5848674,3p_v3,fastq,SRR17818978;SRR17818979;SRR17818980;SRR17818981,NA,NA,NA,NA,NA,NA,NA,NA,10.1038/s43018-022-00414-w,https://pubmed.ncbi.nlm.nih.gov/35982179/,NA,NA,NA
Wei 2022,21202 rhabdomyosarcoma primary patient sample,NA,muscle,tumor,cell,NA,NA,NA,NA,TRUE,FALSE,Homo sapiens,GSE195709,GSM5848675,3p_v3,fastq,SRR17818974;SRR17818975;SRR17818976;SRR17818977,NA,NA,NA,NA,NA,NA,NA,NA,10.1038/s43018-022-00414-w,https://pubmed.ncbi.nlm.nih.gov/35982179/,NA,NA,NA
Wei 2022,29806 rhabdomyosarcoma primary patient sample,NA,muscle,tumor,cell,NA,NA,NA,NA,TRUE,FALSE,Homo sapiens,GSE195709,GSM5848676,3p_v3,fastq,SRR17818970;SRR17818971;SRR17818972;SRR17818973,NA,NA,NA,NA,NA,NA,NA,NA,10.1038/s43018-022-00414-w,https://pubmed.ncbi.nlm.nih.gov/35982179/,NA,NA,NA
Wei 2022,RD cell line,NA,muscle,cell line,cell,NA,NA,NA,runtime issue w/ STAR,TRUE,FALSE,Homo sapiens,GSE195709,GSM5848677,3p_v2,fastq,SRR17818966;SRR17818967;SRR17818968;SRR17818969,NA,NA,NA,NA,NA,NA,NA,NA,10.1038/s43018-022-00414-w,https://pubmed.ncbi.nlm.nih.gov/35982179/,NA,NA,NA
Wei 2022,RD cell line with LARRY barcodes with Regular medium at first time point,NA,muscle,cell line,cell,NA,NA,NA,NA,TRUE,FALSE,Homo sapiens,GSE195709,GSM5848678,3p_v3,fastq,SRR17818962;SRR17818963;SRR17818964;SRR17818965,NA,NA,NA,NA,NA,NA,NA,NA,10.1038/s43018-022-00414-w,https://pubmed.ncbi.nlm.nih.gov/35982179/,NA,NA,NA
Wei 2022,RD cell line with LARRY barcodes with Regular medium at second time point,NA,muscle,cell line,cell,NA,NA,NA,NA,TRUE,FALSE,Homo sapiens,GSE195709,GSM5848679,3p_v3,fastq,SRR17818958;SRR17818959;SRR17818960;SRR17818961,NA,NA,NA,NA,NA,NA,NA,NA,10.1038/s43018-022-00414-w,https://pubmed.ncbi.nlm.nih.gov/35982179/,NA,NA,NA
Wei 2022,RD cell line with LARRY barcodes with Differentiation medium at second time point,NA,muscle,cell line,cell,NA,NA,NA,NA,TRUE,FALSE,Homo sapiens,GSE195709,GSM5848680,3p_v3,fastq,SRR17818954;SRR17818955;SRR17818956;SRR17818957,NA,NA,NA,NA,NA,NA,NA,NA,10.1038/s43018-022-00414-w,https://pubmed.ncbi.nlm.nih.gov/35982179/,NA,NA,NA
Wei 2022,RD cell line with LARRY barcodes after washing out Differentiation medium at third time point,NA,muscle,cell line,cell,NA,NA,NA,NA,TRUE,FALSE,Homo sapiens,GSE195709,GSM5848681,3p_v3,fastq,SRR17818942;SRR17818943;SRR17818944;SRR17818945,NA,NA,NA,NA,NA,NA,NA,NA,10.1038/s43018-022-00414-w,https://pubmed.ncbi.nlm.nih.gov/35982179/,NA,NA,NA
Wei 2022,MAST111 PDX sample,NA,muscle,xenograft,cell,NA,NA,NA,NA,TRUE,TRUE,Homo sapiens,GSE195709,GSM5848682,3p_v3,fastq,SRR17818946;SRR17818947;SRR17818948;SRR17818949;SRR17818950;SRR17818951;SRR17818952;SRR17818953,NA,NA,NA,NA,NA,NA,NA,NA,10.1038/s43018-022-00414-w,https://pubmed.ncbi.nlm.nih.gov/35982179/,NA,NA,NA
Wei 2022,MAST118 PDX sample,NA,muscle,xenograft,cell,NA,NA,NA,NA,TRUE,TRUE,Homo sapiens,GSE195709,GSM5848683,3p_v3,fastq,SRR17818938;SRR17818939;SRR17818940;SRR17818941,NA,NA,NA,NA,NA,NA,NA,NA,10.1038/s43018-022-00414-w,https://pubmed.ncbi.nlm.nih.gov/35982179/,NA,NA,NA
Wei 2022,MAST139 PDX sample,NA,muscle,xenograft,cell,NA,NA,NA,NA,TRUE,TRUE,Homo sapiens,GSE195709,GSM5848684,3p_v3,fastq,SRR17818924;SRR17818925;SRR17818926;SRR17818927;SRR17818928;SRR17818929;SRR17818930;SRR17818931;SRR17818932;SRR17818933;SRR17818934;SRR17818935,NA,NA,NA,NA,NA,NA,NA,NA,10.1038/s43018-022-00414-w,https://pubmed.ncbi.nlm.nih.gov/35982179/,NA,NA,NA
Wei 2022,MAST139-SC PDX sample,NA,muscle,xenograft,cell,NA,NA,NA,NA,TRUE,TRUE,Homo sapiens,GSE195709,GSM5848685,3p_v3,fastq,SRR17818908;SRR17818909;SRR17818910;SRR17818911,NA,NA,NA,NA,NA,NA,NA,NA,10.1038/s43018-022-00414-w,https://pubmed.ncbi.nlm.nih.gov/35982179/,NA,NA,NA
Wei 2022,MAST39 PDX sample,NA,muscle,xenograft,cell,NA,NA,NA,NA,TRUE,TRUE,Homo sapiens,GSE195709,GSM5848686,3p_v2,fastq,SRR17818912;SRR17818913;SRR17818914;SRR17818915;SRR17818916;SRR17818917;SRR17818918;SRR17818919;SRR17818920;SRR17818921;SRR17818922;SRR17818923;SRR17818936;SRR17818937,NA,NA,NA,NA,NA,NA,NA,NA,10.1038/s43018-022-00414-w,https://pubmed.ncbi.nlm.nih.gov/35982179/,NA,NA,NA
Wei 2022,MAST85-r1 PDX sample,NA,muscle,xenograft,cell,NA,NA,NA,NA,TRUE,TRUE,Homo sapiens,GSE195709,GSM5848687,3p_v3,fastq,SRR17818904;SRR17818905;SRR17818906;SRR17818907,NA,NA,NA,NA,NA,NA,NA,NA,10.1038/s43018-022-00414-w,https://pubmed.ncbi.nlm.nih.gov/35982179/,NA,NA,NA
Wei 2022,MAST85-r2 PDX sample,NA,muscle,xenograft,cell,NA,NA,NA,NA,TRUE,TRUE,Homo sapiens,GSE195709,GSM5848688,3p_v3,fastq,SRR17818892;SRR17818893;SRR17818894;SRR17818895;SRR17818896;SRR17818897;SRR17818898;SRR17818899;SRR17818900;SRR17818901;SRR17818902;SRR17818903,NA,NA,NA,NA,NA,NA,NA,NA,10.1038/s43018-022-00414-w,https://pubmed.ncbi.nlm.nih.gov/35982179/,NA,NA,NA
Wei 2022,MAST85-r2-SC PDX sample,NA,muscle,xenograft,cell,NA,NA,NA,NA,TRUE,TRUE,Homo sapiens,GSE195709,GSM5848689,3p_v3,fastq,SRR17818876;SRR17818877;SRR17818878;SRR17818879;SRR17818880;SRR17818881;SRR17818882;SRR17818883;SRR17818884;SRR17818885;SRR17818886;SRR17818887;SRR17818888;SRR17818889;SRR17818890;SRR17818891,NA,NA,NA,NA,NA,NA,NA,NA,10.1038/s43018-022-00414-w,https://pubmed.ncbi.nlm.nih.gov/35982179/,NA,NA,NA
Wei 2022,MAST95 PDX sample,NA,muscle,xenograft,cell,NA,NA,NA,NA,TRUE,TRUE,Homo sapiens,GSE195709,GSM5848690,3p_v2,fastq,SRR17818864;SRR17818865;SRR17818866;SRR17818867;SRR17818868;SRR17818869;SRR17818870;SRR17818871;SRR17818872;SRR17818873;SRR17818874;SRR17818875,NA,NA,NA,NA,NA,NA,NA,NA,10.1038/s43018-022-00414-w,https://pubmed.ncbi.nlm.nih.gov/35982179/,NA,NA,NA
Wei 2022,MSK72117 PDX sample,NA,muscle,xenograft,cell,NA,NA,NA,NA,TRUE,TRUE,Homo sapiens,GSE195709,GSM5848691,3p_v3,fastq,SRR17818860;SRR17818861;SRR17818862;SRR17818863,NA,NA,NA,NA,NA,NA,NA,NA,10.1038/s43018-022-00414-w,https://pubmed.ncbi.nlm.nih.gov/35982179/,NA,NA,NA
Wei 2022,MSK72117-SC PDX sample,NA,muscle,xenograft,cell,NA,NA,NA,NA,TRUE,TRUE,Homo sapiens,GSE195709,GSM5848692,3p_v3,fastq,SRR17818859;SRR17818860;SRR17818861;SRR17818862,NA,NA,NA,NA,NA,NA,NA,NA,10.1038/s43018-022-00414-w,https://pubmed.ncbi.nlm.nih.gov/35982179/,NA,NA,NA
Wei 2022,MSK74711 PDX sample,NA,muscle,xenograft,cell,NA,NA,NA,NA,TRUE,TRUE,Homo sapiens,GSE195709,GSM5848693,3p_v3,fastq,SRR17818836;SRR17818837;SRR17818838;SRR17818839,NA,NA,NA,NA,NA,NA,NA,NA,10.1038/s43018-022-00414-w,https://pubmed.ncbi.nlm.nih.gov/35982179/,NA,NA,NA
Wei 2022,MSK82489 PDX sample,NA,muscle,xenograft,cell,NA,NA,NA,NA,TRUE,TRUE,Homo sapiens,GSE195709,GSM5848694,3p_v3,fastq,SRR17818840;SRR17818841;SRR17818842;SRR17818843;SRR17818844;SRR17818845;SRR17818846;SRR17818847;SRR17818848;SRR17818849;SRR17818850;SRR17818851;SRR17818852;SRR17818853;SRR17818854;SRR17818855,NA,NA,NA,NA,NA,NA,NA,NA,10.1038/s43018-022-00414-w,https://pubmed.ncbi.nlm.nih.gov/35982179/,NA,NA,NA
Hanna 2022,muscle_Treg_D3_scRNAseq_counts,NA,muscle,hindlimb,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE196337,GSM5872768,3p_v2,fastq,SRR17936867;SRR17936868,NA,NA,NA,NA,SAMN25752027,NA,NA,NA,10.1016/j.immuni.2023.01.033,https://pubmed.ncbi.nlm.nih.gov/36822206/,NA,NA,NA
Hanna 2022,muscle_Treg_D3_VMNA_vs_Vehicle_Mafko_vs_Mafwt_scRNAseq,NA,muscle,hindlimb,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE196337,GSM5872769,3p_v2,fastq,SRR17936869;SRR17936870,NA,NA,NA,NA,SAMN25752028,NA,NA,NA,10.1016/j.immuni.2023.01.033,https://pubmed.ncbi.nlm.nih.gov/36822206/,NA,NA,NA
Hanna 2022,muscle_colon_Treg_D3_scRNAseq_scTcr,NA,muscle,hindlimb,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE196337,GSM5872770,5p_v3,fastq,SRR17936871;SRR17936872;SRR17936873;SRR17936874;SRR17936875;SRR17936876;SRR17936877;SRR17936878;SRR17936879;SRR17936880;SRR17936881;SRR17936882;SRR17936883;SRR17936884;SRR17936885;SRR17936886;SRR17936887;SRR17936888;SRR17936889;SRR17936890;SRR17936891;SRR17936892;SRR17936893;SRR17936894;SRR17936895;SRR17936896;SRR17936897;SRR17936898,NA,NA,NA,NA,NA,NA,NA,NA,10.1016/j.immuni.2023.01.033,https://pubmed.ncbi.nlm.nih.gov/36822206/,NA,NA,NA
Chen 2022,scRNA-Seq of muscle: adult male cynomolgus monkey,NA,muscle,NA,cell,NA,NA,NA,NA,TRUE,TRUE,Macaca fascicularis,GSE196794,GSM5901087,3p_v3.1,fastq,SRR18039370,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Taglietti 2022,scRNAseq DIA WT 12months,NA,muscle,NA,cell,NA,NA,NA,NA,TRUE,TRUE,Rattus norvegicus,GSE198237,GSM5941720,3p_v3.1,fastq,SRR18278844;SRR18278845;SRR18278845;SRR18278847,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Taglietti 2022,scRNAseq DIA DMD 12months,NA,muscle,NA,cell,NA,NA,NA,NA,TRUE,TRUE,Rattus norvegicus,GSE198237,GSM5941721,3p_v3.1,fastq,SRR18278840;SRR18278841;SRR18278842;SRR18278843,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Kang 2022,NORM,NA,muscle,NA,NA,NA,NA,NA,NA,TRUE,TRUE,Gallus gallus,GSE200516,GSM6035364,NA,fastq,SRR18689889,NA,SRX14790887,NA,NA,SAMN27482453,NA,NA,NA,NA,NA,NA,NA,NA
Kang 2022,WB,NA,muscle,NA,NA,NA,NA,NA,NA,TRUE,TRUE,Gallus gallus,GSE200516,GSM6035365,NA,fastq,SRR18689890,NA,SRX14790886,NA,NA,SAMN27482454,NA,NA,NA,NA,NA,NA,NA,NA
Feng 2022,Control_soft palate1,NA,muscle,pharynx,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE203035,GSM6152840,3p_v2,fastq,SRR19214015;SRR19214016,NA,SRX15278070,NA,NA,SAMN28409024,NA,NA,NA,10.7554/eLife.80405,https://pubmed.ncbi.nlm.nih.gov/36542062/,NA,NA,NA
Feng 2022,Control_soft palate2,NA,muscle,pharynx,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE203035,GSM6152841,3p_v2,fastq,SRR19214013;SRR19214014,NA,SRX15278071,NA,NA,SAMN28409023,NA,NA,NA,10.7554/eLife.80405,https://pubmed.ncbi.nlm.nih.gov/36542062/,NA,NA,NA
Feng 2022,Mutant_soft palate,NA,muscle,pharynx,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE203035,GSM6152842,3p_v2,fastq,SRR19214011;SRR19214012,NA,SRX15278072,NA,NA,SAMN28409022,NA,NA,NA,10.7554/eLife.80405,https://pubmed.ncbi.nlm.nih.gov/36542062/,NA,NA,NA
Yang BA 2022,"Young, Injured Day 5, replicate 1",NA,muscle,tibialis anterior,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE205395,GSM6211369,3p_v3,bam,SRR19524910,NA,SRX15577168,NA,NA,SAMN28843023,NA,NA,NA,10.1111/acel.13789,https://pubmed.ncbi.nlm.nih.gov/36727578/,NA,NA,NA
Yang BA 2022,"Aged, Injured Day 5, replicate 1",NA,muscle,tibialis anterior,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE205395,GSM6211371,3p_v3,bam,SRR19524912,NA,SRX15577166,NA,NA,SAMN28843025,NA,NA,NA,10.1111/acel.13789,https://pubmed.ncbi.nlm.nih.gov/36727578/,NA,NA,NA
Cutler 2022,"Adult, 4 days post-injury rep1_1",NA,muscle,tibialis anterior,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE205690,GSM6217408,3p_v2,fastq,SRR19581905,NA,SRX15633726,NA,NA,SAMN28922314,NA,NA,NA,10.1016/j.isci.2022.104444,https://pubmed.ncbi.nlm.nih.gov/35733848/,NA,NA,NA
Cutler 2022,"Adult, 4 days post-injury rep1_3",NA,muscle,tibialis anterior,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE205690,GSM6217410,3p_v2,fastq,SRR19581907,NA,SRX15633724,NA,NA,SAMN28922316,NA,NA,NA,10.1016/j.isci.2022.104444,https://pubmed.ncbi.nlm.nih.gov/35733848/,NA,NA,NA
Cutler 2022,"Adult, 4 days post-injury rep1_4",NA,muscle,tibialis anterior,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE205690,GSM6217411,3p_v2,fastq,SRR19581908,NA,SRX15633723,NA,NA,SAMN28922317,NA,NA,NA,10.1016/j.isci.2022.104444,https://pubmed.ncbi.nlm.nih.gov/35733848/,NA,NA,NA
Cutler 2022,"Adult, 4 days post-injury rep2_1",NA,muscle,tibialis anterior,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE205690,GSM6217412,3p_v2,fastq,SRR19581909,NA,SRX15633722,NA,NA,SAMN28922318,NA,NA,NA,10.1016/j.isci.2022.104444,https://pubmed.ncbi.nlm.nih.gov/35733848/,NA,NA,NA
Cutler 2022,"Adult, 4 days post-injury rep2_2",NA,muscle,tibialis anterior,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE205690,GSM6217413,3p_v2,fastq,SRR19581910,NA,SRX15633721,NA,NA,SAMN28922319,NA,NA,NA,10.1016/j.isci.2022.104444,https://pubmed.ncbi.nlm.nih.gov/35733848/,NA,NA,NA
Cutler 2022,"Adult, 4 days post-injury rep2_3",NA,muscle,tibialis anterior,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE205690,GSM6217414,3p_v2,fastq,SRR19581911,NA,SRX15633720,NA,NA,SAMN28922320,NA,NA,NA,10.1016/j.isci.2022.104444,https://pubmed.ncbi.nlm.nih.gov/35733848/,NA,NA,NA
Cutler 2022,"Adult, 4 days post-injury rep2_4",NA,muscle,tibialis anterior,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE205690,GSM6217415,3p_v2,fastq,SRR19581912,NA,SRX15633719,NA,NA,SAMN28922321,NA,NA,NA,10.1016/j.isci.2022.104444,https://pubmed.ncbi.nlm.nih.gov/35733848/,NA,NA,NA
Cutler 2022,"Adult, 7 days post-injury rep1_1",NA,muscle,tibialis anterior,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE205690,GSM6217416,3p_v2,fastq,SRR19581913,NA,SRX15633717,NA,NA,SAMN28922323,NA,NA,NA,10.1016/j.isci.2022.104444,https://pubmed.ncbi.nlm.nih.gov/35733848/,NA,NA,NA
Cutler 2022,"Adult, 7 days post-injury rep1_2",NA,muscle,tibialis anterior,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE205690,GSM6217417,3p_v2,fastq,SRR19581914,NA,SRX15633715,NA,NA,SAMN28922325,NA,NA,NA,10.1016/j.isci.2022.104444,https://pubmed.ncbi.nlm.nih.gov/35733848/,NA,NA,NA
Cutler 2022,"Adult, 7 days post-injury rep1_3",NA,muscle,tibialis anterior,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE205690,GSM6217418,3p_v2,fastq,SRR19581915,NA,SRX15633714,NA,NA,SAMN28922326,NA,NA,NA,10.1016/j.isci.2022.104444,https://pubmed.ncbi.nlm.nih.gov/35733848/,NA,NA,NA
Cutler 2022,"Adult, 7 days post-injury rep1_4",NA,muscle,tibialis anterior,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE205690,GSM6217419,3p_v2,fastq,SRR19581916,NA,SRX15633716,NA,NA,SAMN28922324,NA,NA,NA,10.1016/j.isci.2022.104444,https://pubmed.ncbi.nlm.nih.gov/35733848/,NA,NA,NA
Cutler 2022,"Adult, 7 days post-injury rep2_1",NA,muscle,tibialis anterior,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE205690,GSM6217420,3p_v2,fastq,SRR19581917,NA,SRX15633718,NA,NA,SAMN28922322,NA,NA,NA,10.1016/j.isci.2022.104444,https://pubmed.ncbi.nlm.nih.gov/35733848/,NA,NA,NA
Cutler 2022,"Adult, 7 days post-injury rep2_2",NA,muscle,tibialis anterior,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE205690,GSM6217421,3p_v2,fastq,SRR19581918,NA,SRX15633713,NA,NA,SAMN28922327,NA,NA,NA,10.1016/j.isci.2022.104444,https://pubmed.ncbi.nlm.nih.gov/35733848/,NA,NA,NA
Cutler 2022,"Adult, 7 days post-injury rep2_3",NA,muscle,tibialis anterior,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE205690,GSM6217422,3p_v2,fastq,SRR19581919,NA,SRX15633712,NA,NA,SAMN28922328,NA,NA,NA,10.1016/j.isci.2022.104444,https://pubmed.ncbi.nlm.nih.gov/35733848/,NA,NA,NA
Cutler 2022,"Adult, 7 days post-injury rep2_4",NA,muscle,tibialis anterior,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE205690,GSM6217423,3p_v2,fastq,SRR19581920,NA,SRX15633711,NA,NA,SAMN28922329,NA,NA,NA,10.1016/j.isci.2022.104444,https://pubmed.ncbi.nlm.nih.gov/35733848/,NA,NA,NA
Cutler 2022,"Adult, uninjured, rep1_1",NA,muscle,tibialis anterior,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE205690,GSM6217424,3p_v2,fastq,SRR19581921,NA,SRX15633710,NA,NA,SAMN28922330,NA,NA,NA,10.1016/j.isci.2022.104444,https://pubmed.ncbi.nlm.nih.gov/35733848/,NA,NA,NA
Cutler 2022,"Adult, uninjured, rep1_2",NA,muscle,tibialis anterior,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE205690,GSM6217425,3p_v2,fastq,SRR19581922,NA,SRX15633708,NA,NA,SAMN28922332,NA,NA,NA,10.1016/j.isci.2022.104444,https://pubmed.ncbi.nlm.nih.gov/35733848/,NA,NA,NA
Cutler 2022,"Adult, uninjured, rep1_3",NA,muscle,tibialis anterior,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE205690,GSM6217426,3p_v2,fastq,SRR19581923,NA,SRX15633706,NA,NA,SAMN28922334,NA,NA,NA,10.1016/j.isci.2022.104444,https://pubmed.ncbi.nlm.nih.gov/35733848/,NA,NA,NA
Cutler 2022,"Adult, uninjured, rep1_4",NA,muscle,tibialis anterior,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE205690,GSM6217427,3p_v2,fastq,SRR19581924,NA,SRX15633705,NA,NA,SAMN28922335,NA,NA,NA,10.1016/j.isci.2022.104444,https://pubmed.ncbi.nlm.nih.gov/35733848/,NA,NA,NA
Cutler 2022,"Adult, uninjured, rep2_1",NA,muscle,tibialis anterior,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE205690,GSM6217428,3p_v2,fastq,SRR19581925,NA,SRX15633707,NA,NA,SAMN28922333,NA,NA,NA,10.1016/j.isci.2022.104444,https://pubmed.ncbi.nlm.nih.gov/35733848/,NA,NA,NA
Cutler 2022,"Adult, uninjured, rep2_2",NA,muscle,tibialis anterior,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE205690,GSM6217429,3p_v2,fastq,SRR19581926,NA,SRX15633709,NA,NA,SAMN28922331,NA,NA,NA,10.1016/j.isci.2022.104444,https://pubmed.ncbi.nlm.nih.gov/35733848/,NA,NA,NA
Cutler 2022,"Adult, uninjured, rep2_4",NA,muscle,tibialis anterior,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE205690,GSM6217431,3p_v2,fastq,SRR19581928,NA,SRX15633703,NA,NA,SAMN28922337,NA,NA,NA,10.1016/j.isci.2022.104444,https://pubmed.ncbi.nlm.nih.gov/35733848/,NA,NA,NA
Yaghi 2022,Uninjured MmSCs,NA,muscle,MSCs,cell,NA,NA,NA,NA,TRUE,FALSE,Mus musculus,GSE205737,GSM6222433,5p_v3,fastq,SRR19591789,NA,SRX15643445,NA,NA,SAMN28928460,NA,NA,NA,NA,NA,NA,NA,NA
Yaghi 2022,Day half post-CTX MmSCs,NA,muscle,MSCs,cell,NA,NA,NA,NA,TRUE,FALSE,Mus musculus,GSE205737,GSM6222434,5p_v3,fastq,SRR19591788,NA,SRX15643446,NA,NA,SAMN28928459,NA,NA,NA,NA,NA,NA,NA,NA
Yaghi 2022,Day 1 post-CTX MmSCs,NA,muscle,MSCs,cell,NA,NA,NA,NA,TRUE,FALSE,Mus musculus,GSE205737,GSM6222435,5p_v3,fastq,SRR19591787,NA,SRX15643447,NA,NA,SAMN28928458,NA,NA,NA,NA,NA,NA,NA,NA
Yaghi 2022,Day 3 post-CTX MmSCs,NA,muscle,MSCs,cell,NA,NA,NA,NA,TRUE,FALSE,Mus musculus,GSE205737,GSM6222436,5p_v3,fastq,SRR19591786,NA,SRX15643448,NA,NA,SAMN28928457,NA,NA,NA,NA,NA,NA,NA,NA
Yaghi 2022,Day 7 post-CTX MmSCs,NA,muscle,MSCs,cell,NA,NA,NA,NA,TRUE,FALSE,Mus musculus,GSE205737,GSM6222437,5p_v3,fastq,SRR19591785,NA,SRX15643449,NA,NA,SAMN28928456,NA,NA,NA,NA,NA,NA,NA,NA
Yaghi 2022,Day 14 post-CTX MmSCs,NA,muscle,MSCs,cell,NA,NA,NA,NA,TRUE,FALSE,Mus musculus,GSE205737,GSM6222438,5p_v3,fastq,SRR19591784,NA,SRX15643450,NA,NA,SAMN28928455,NA,NA,NA,NA,NA,NA,NA,NA
Babaeijandaghi 2022,FR121_macrophages,NA,muscle,tibialis anterior,cell,NA,NA,NA,NA,TRUE,FALSE,Mus musculus,GSE212371,GSM6528917,3p_v3,fastq,SRR21356441;SRR21356442;SRR21356443;SRR21356444,NA,SRX17362182,NA,NA,SAMN30603395,NA,NA,NA,10.1073/pnas.2209976119,https://pubmed.ncbi.nlm.nih.gov/36279473/,NA,NA,NA
Saleh 2022,"Skeletal Muscle, Wt-NSG, 8Wk, replicate 1",NA,muscle,gastrocnemius,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE213925,GSM6596509,3p_v3,fastq,SRR21675544;SRR21675545,NA,SRX17673874,NA,NA,NA,NA,NA,"Saleh et al, iScience, 2022",10.1016/j.isci.2022.105415,https://pubmed.ncbi.nlm.nih.gov/36388984/,Illumina NovaSeq 6000,NA,NA
Saleh 2022,"Skeletal Muscle, Wt-NSG, 8Wk, replicate 2",NA,muscle,gastrocnemius,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE213925,GSM6596510,3p_v3,fastq,SRR21675543,NA,SRX17673875,NA,NA,NA,NA,NA,"Saleh et al, iScience, 2022",10.1016/j.isci.2022.105415,https://pubmed.ncbi.nlm.nih.gov/36388984/,Illumina NovaSeq 6000,NA,NA
Saleh 2022,"Skeletal Muscle, mdx-NSG, 8Wk, replicate 1",NA,muscle,gastrocnemius,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE213925,GSM6596511,3p_v3,fastq,SRR21675541;SRR21675542,NA,SRX17673876,NA,NA,NA,NA,NA,"Saleh et al, iScience, 2022",10.1016/j.isci.2022.105415,https://pubmed.ncbi.nlm.nih.gov/36388984/,Illumina NovaSeq 6000,NA,NA
Saleh 2022,"Skeletal Muscle, mdx-NSG, 8Wk, replicate 2",NA,muscle,gastrocnemius,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE213925,GSM6596512,3p_v3,fastq,SRR21675540,NA,SRX17673877,NA,NA,NA,NA,NA,"Saleh et al, iScience, 2022",10.1016/j.isci.2022.105415,https://pubmed.ncbi.nlm.nih.gov/36388984/,Illumina NovaSeq 6000,NA,NA
Saleh 2022,"Skeletal Muscle, mdxD2-NSG, 8Wk, replicate 1",NA,muscle,gastrocnemius,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE213925,GSM6596513,3p_v3,fastq,SRR21675538;SRR21675539,NA,SRX17673878,NA,NA,NA,NA,NA,"Saleh et al, iScience, 2022",10.1016/j.isci.2022.105415,https://pubmed.ncbi.nlm.nih.gov/36388984/,Illumina NovaSeq 6000,NA,NA
Saleh 2022,"Skeletal Muscle, mdxD2-NSG, 8Wk, replicate 2",NA,muscle,gastrocnemius,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE213925,GSM6596514,3p_v3,fastq,SRR21675537,NA,SRX17673879,NA,NA,NA,NA,NA,"Saleh et al, iScience, 2022",10.1016/j.isci.2022.105415,https://pubmed.ncbi.nlm.nih.gov/36388984/,Illumina NovaSeq 6000,NA,NA
Lovric 2022,Skeletal muscle Sample 1 pre exercise,NA,muscle,vastus lateralis,cell,NA,NA,NA,NA,TRUE,TRUE,Homo sapiens,GSE214544,GSM6611295,3p_v3,fastq,SRR21770067;SRR21770068,NA,SRX17765051,SRP400455,NA,SAMN31109470,NA,NA,"Lovric et al, Communications Biology, 2022",10.1038/s42003-022-04088-z,https://pubmed.ncbi.nlm.nih.gov/36273106/,NA,NA,NA
Lovric 2022,Skeletal muscle Sample 1 post exercise,NA,muscle,vastus lateralis,cell,NA,NA,NA,NA,TRUE,TRUE,Homo sapiens,GSE214544,GSM6611296,3p_v3,fastq,SRR21770065;SRR21770066,NA,SRX17765052,SRP400455,NA,SAMN31109469,NA,NA,"Lovric et al, Communications Biology, 2022",10.1038/s42003-022-04088-z,https://pubmed.ncbi.nlm.nih.gov/36273106/,NA,NA,NA
Lovric 2022,Skeletal muscle Sample 2 pre exercise,NA,muscle,vastus lateralis,cell,NA,NA,NA,NA,TRUE,TRUE,Homo sapiens,GSE214544,GSM6611297,3p_v3,fastq,SRR21770063;SRR21770064,NA,SRX17765053,SRP400455,NA,SAMN31109468,NA,NA,"Lovric et al, Communications Biology, 2022",10.1038/s42003-022-04088-z,https://pubmed.ncbi.nlm.nih.gov/36273106/,NA,NA,NA
Lovric 2022,Skeletal muscle Sample 2 post exercise,NA,muscle,vastus lateralis,cell,NA,NA,NA,NA,TRUE,TRUE,Homo sapiens,GSE214544,GSM6611298,3p_v3,fastq,SRR21770061;SRR21770062,NA,SRX17765054,SRP400455,NA,SAMN31109467,NA,NA,"Lovric et al, Communications Biology, 2022",10.1038/s42003-022-04088-z,https://pubmed.ncbi.nlm.nih.gov/36273106/,NA,NA,NA
Lovric 2022,Skeletal muscle Sample 3 pre exercise,NA,muscle,vastus lateralis,cell,NA,NA,NA,NA,TRUE,TRUE,Homo sapiens,GSE214544,GSM6611299,3p_v3,fastq,SRR21770059;SRR21770060,NA,SRX17765055,SRP400455,NA,SAMN31109466,NA,NA,"Lovric et al, Communications Biology, 2022",10.1038/s42003-022-04088-z,https://pubmed.ncbi.nlm.nih.gov/36273106/,NA,NA,NA
Lovric 2022,Skeletal muscle Sample 3 post exercise,NA,muscle,vastus lateralis,cell,NA,NA,NA,NA,TRUE,TRUE,Homo sapiens,GSE214544,GSM6611300,3p_v3,fastq,SRR21770057;SRR21770058,NA,SRX17765056,SRP400455,NA,SAMN31109465,NA,NA,"Lovric et al, Communications Biology, 2022",10.1038/s42003-022-04088-z,https://pubmed.ncbi.nlm.nih.gov/36273106/,NA,NA,NA
Lovric 2022,Skeletal muscle Sample 3 pre exercise (deep-seq),NA,muscle,vastus lateralis,cell,NA,NA,NA,NA,TRUE,TRUE,Homo sapiens,GSE214544,GSM6611301,3p_v3,fastq,SRR21770055;SRR21770056,NA,SRX17765057,SRP400455,NA,SAMN31109464,NA,NA,"Lovric et al, Communications Biology, 2022",10.1038/s42003-022-04088-z,https://pubmed.ncbi.nlm.nih.gov/36273106/,NA,NA,NA
Lovric 2022,Skeletal muscle Sample 3 post exercise (deep-seq),NA,muscle,vastus lateralis,cell,NA,NA,NA,NA,TRUE,TRUE,Homo sapiens,GSE214544,GSM6611302,3p_v3,fastq,SRR21770053;SRR21770054,NA,SRX17765058,SRP400455,NA,SAMN31109463,NA,NA,"Lovric et al, Communications Biology, 2022",10.1038/s42003-022-04088-z,https://pubmed.ncbi.nlm.nih.gov/36273106/,NA,NA,NA
Young 2022,"M. musculus, TA, CTX, scRNA-seq",NA,muscle,tibialis anterior,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE214892,GSM6617505,3p_v3,bam,SRR21820102,NA,SRX17809340,NA,NA,SAMN31170310,NA,NA,"Young et al, The FASEB Journal, 2022",10.1096/fj.202200289RR,https://pubmed.ncbi.nlm.nih.gov/36190443/,NA,NA,NA
Young 2022,"M. musculus, TA, PBS, scRNA-seq",NA,muscle,tibialis anterior,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE214892,GSM6617506,3p_v3,bam,SRR21820101,NA,SRX17809341,NA,NA,SAMN31170309,NA,NA,"Young et al, The FASEB Journal, 2022",10.1096/fj.202200289RR,https://pubmed.ncbi.nlm.nih.gov/36190443/,NA,NA,NA
Wakelin 2022,"human, Semitendinosus, 01, scRNA-seq",NA,muscle,MSCs,cell,NA,NA,NA,NA,TRUE,FALSE,Homo sapiens,GSE216544,GSM6678961,3p_v3,bam,SRR22035235,NA,NA,NA,NA,SAMN31440538,NA,NA,NA,10.1152/ajpcell.00364.2022,https://pubmed.ncbi.nlm.nih.gov/36342160/,NA,NA,NA
Van Deusen 2023a,mdx control 1,NA,muscle,gastrocnemius,nucleus,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE227510,GSM7101938,3p_v3,bam,SRR23881537,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Van Deusen 2023a,mdx control 2,NA,muscle,gastrocnemius,nucleus,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE227510,GSM7101939,3p_v3,bam,SRR23881538,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Van Deusen 2023a,mdx control 3,NA,muscle,gastrocnemius,nucleus,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE227510,GSM7101940,3p_v3,bam,SRR23881539,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Van Deusen 2023a,mdx treated 1,NA,muscle,gastrocnemius,nucleus,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE227510,GSM7101941,3p_v3,bam,SRR23881540,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Van Deusen 2023a,mdx treated 2,NA,muscle,gastrocnemius,nucleus,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE227510,GSM7101942,3p_v3,bam,SRR23881541,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Van Deusen 2023a,mdx treated 3,NA,muscle,gastrocnemius,nucleus,NA,NA,NA,download issues,FALSE,TRUE,Mus musculus,GSE227510,GSM7101943,3p_v3,bam,SRR23881542,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Van Deusen 2023a,wt control 1,NA,muscle,gastrocnemius,nucleus,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE227510,GSM7101944,3p_v3,bam,SRR23881543,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Van Deusen 2023a,wt control 2,NA,muscle,gastrocnemius,nucleus,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE227510,GSM7101945,3p_v3,bam,SRR23881544,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Sun 2023,OC-Muscle,NA,muscle,NA,NA,NA,NA,NA,no methods released at the time of recording,TRUE,TRUE,Mus musculus,PRJCA009794,CRX456249,3p_v3,ngdc_fastq,CRR516186,https://download.cncb.ac.cn/gsa2/CRA007207/CRR516186_f1_fastq.gz https://download.cncb.ac.cn/gsa2/CRA007207/CRR516186_r2.fastq.gz,CRX456249,PRJCA009794,SAMC801326,NA,NA,NA,NA,NA,NA,NA,NA,NA
Sun 2023,OE-Muscle,NA,muscle,NA,NA,NA,NA,NA,no methods released at the time of recording,TRUE,TRUE,Mus musculus,PRJCA009794,CRX456250,3p_v3,ngdc_fastq,CRR516187,https://download.cncb.ac.cn/gsa2/CRA007207/CRR516187_f1_fastq.gz https://download.cncb.ac.cn/gsa2/CRA007207/CRR516187_r2.fastq.gz,CRX456250,PRJCA009794,SAMC801327,NA,NA,NA,NA,NA,NA,NA,NA,NA
Sun 2023,YC-Muscle,NA,muscle,NA,NA,NA,NA,NA,no methods released at the time of recording,TRUE,TRUE,Mus musculus,PRJCA009794,CRX456251,3p_v3,ngdc_fastq,CRR516188,https://download.cncb.ac.cn/gsa2/CRA007207/CRR516188_f1_fastq.gz https://download.cncb.ac.cn/gsa2/CRA007207/CRR516188_r2.fastq.gz,CRX456251,PRJCA009794,SAMC801328,NA,NA,NA,NA,NA,NA,NA,NA,NA
Sun 2023,YE-Muscle,NA,muscle,NA,NA,NA,NA,NA,no methods released at the time of recording,TRUE,TRUE,Mus musculus,PRJCA009794,CRX456252,3p_v3,ngdc_fastq,CRR516189,https://download.cncb.ac.cn/gsa2/CRA007207/CRR516189_f1_fastq.gz https://download.cncb.ac.cn/gsa2/CRA007207/CRR516189_r2.fastq.gz,CRX456252,PRJCA009794,SAMC801329,NA,NA,NA,NA,NA,NA,NA,NA,NA
Sun 2023,Muscle-OC-1,NA,muscle,NA,NA,NA,NA,NA,no methods released at the time of recording,TRUE,TRUE,Mus musculus,PRJCA009794,CRX469819,3p_v3,ngdc_fastq,CRR529941,https://download.cncb.ac.cn/gsa2/CRA007207/CRR529941_f1_fastq.gz https://download.cncb.ac.cn/gsa2/CRA007207/CRR529941_r2.fastq.gz,CRX469819,PRJCA009794,SAMC816738,NA,NA,NA,NA,NA,NA,NA,NA,NA
Sun 2023,Muscle-OC-2,NA,muscle,NA,NA,NA,NA,NA,no methods released at the time of recording,TRUE,TRUE,Mus musculus,PRJCA009794,CRX469820,3p_v3,ngdc_fastq,CRR529942,https://download.cncb.ac.cn/gsa2/CRA007207/CRR529942_f1_fastq.gz https://download.cncb.ac.cn/gsa2/CRA007207/CRR529942_r2.fastq.gz,CRX469820,PRJCA009794,SAMC816739,NA,NA,NA,NA,NA,NA,NA,NA,NA
Sun 2023,Muscle-OC-3,NA,muscle,NA,NA,NA,NA,NA,no methods released at the time of recording,TRUE,TRUE,Mus musculus,PRJCA009794,CRX469821,3p_v3,ngdc_fastq,CRR529943,https://download.cncb.ac.cn/gsa2/CRA007207/CRR529943_f1_fastq.gz https://download.cncb.ac.cn/gsa2/CRA007207/CRR529943_r2.fastq.gz,CRX469821,PRJCA009794,SAMC816740,NA,NA,NA,NA,NA,NA,NA,NA,NA
Sun 2023,Muscle-OE-1,NA,muscle,NA,NA,NA,NA,NA,no methods released at the time of recording,TRUE,TRUE,Mus musculus,PRJCA009794,CRX469822,3p_v3,ngdc_fastq,CRR529944,https://download.cncb.ac.cn/gsa2/CRA007207/CRR529944_f1_fastq.gz https://download.cncb.ac.cn/gsa2/CRA007207/CRR529944_r2.fastq.gz,CRX469822,PRJCA009794,SAMC816741,NA,NA,NA,NA,NA,NA,NA,NA,NA
Sun 2023,Muscle-OE-2,NA,muscle,NA,NA,NA,NA,NA,no methods released at the time of recording,TRUE,TRUE,Mus musculus,PRJCA009794,CRX469823,3p_v3,ngdc_fastq,CRR529945,https://download.cncb.ac.cn/gsa2/CRA007207/CRR529945_f1_fastq.gz https://download.cncb.ac.cn/gsa2/CRA007207/CRR529945_r2.fastq.gz,CRX469823,PRJCA009794,SAMC816742,NA,NA,NA,NA,NA,NA,NA,NA,NA
Sun 2023,Muscle-OE-3,NA,muscle,NA,NA,NA,NA,NA,no methods released at the time of recording,TRUE,TRUE,Mus musculus,PRJCA009794,CRX469824,3p_v3,ngdc_fastq,CRR529946,https://download.cncb.ac.cn/gsa2/CRA007207/CRR529946_f1_fastq.gz https://download.cncb.ac.cn/gsa2/CRA007207/CRR529946_r2.fastq.gz,CRX469824,PRJCA009794,SAMC816743,NA,NA,NA,NA,NA,NA,NA,NA,NA
Sun 2023,Muscle-YC-1,NA,muscle,NA,NA,NA,NA,NA,no methods released at the time of recording,TRUE,TRUE,Mus musculus,PRJCA009794,CRX469825,3p_v3,ngdc_fastq,CRR529947,https://download.cncb.ac.cn/gsa2/CRA007207/CRR529947_f1_fastq.gz https://download.cncb.ac.cn/gsa2/CRA007207/CRR529947_r2.fastq.gz,CRX469825,PRJCA009794,SAMC816744,NA,NA,NA,NA,NA,NA,NA,NA,NA
Sun 2023,Muscle-YC-2,NA,muscle,NA,NA,NA,NA,NA,no methods released at the time of recording,TRUE,TRUE,Mus musculus,PRJCA009794,CRX469826,3p_v3,ngdc_fastq,CRR529948,https://download.cncb.ac.cn/gsa2/CRA007207/CRR529948_f1_fastq.gz https://download.cncb.ac.cn/gsa2/CRA007207/CRR529948_r2.fastq.gz,CRX469826,PRJCA009794,SAMC816745,NA,NA,NA,NA,NA,NA,NA,NA,NA
Sun 2023,Muscle-YC-3,NA,muscle,NA,NA,NA,NA,NA,no methods released at the time of recording,TRUE,TRUE,Mus musculus,PRJCA009794,CRX469827,3p_v3,ngdc_fastq,CRR529949,https://download.cncb.ac.cn/gsa2/CRA007207/CRR529949_f1_fastq.gz https://download.cncb.ac.cn/gsa2/CRA007207/CRR529949_r2.fastq.gz,CRX469827,PRJCA009794,SAMC816746,NA,NA,NA,NA,NA,NA,NA,NA,NA
Sun 2023,Muscle-YE-1,NA,muscle,NA,NA,NA,NA,NA,no methods released at the time of recording,TRUE,TRUE,Mus musculus,PRJCA009794,CRX469828,3p_v3,ngdc_fastq,CRR529950,https://download.cncb.ac.cn/gsa2/CRA007207/CRR529950_f1_fastq.gz https://download.cncb.ac.cn/gsa2/CRA007207/CRR529950_r2.fastq.gz,CRX469828,PRJCA009794,SAMC816747,NA,NA,NA,NA,NA,NA,NA,NA,NA
Sun 2023,Muscle-YE-2,NA,muscle,NA,NA,NA,NA,NA,no methods released at the time of recording,TRUE,TRUE,Mus musculus,PRJCA009794,CRX469829,3p_v3,ngdc_fastq,CRR529951,https://download.cncb.ac.cn/gsa2/CRA007207/CRR529951_f1_fastq.gz https://download.cncb.ac.cn/gsa2/CRA007207/CRR529951_r2.fastq.gz,CRX469829,PRJCA009794,SAMC816748,NA,NA,NA,NA,NA,NA,NA,NA,NA
Sun 2023,Muscle-YE-3,NA,muscle,NA,NA,NA,NA,NA,no methods released at the time of recording,TRUE,TRUE,Mus musculus,PRJCA009794,CRX469830,3p_v3,ngdc_fastq,CRR529952,https://download.cncb.ac.cn/gsa2/CRA007207/CRR529952_f1_fastq.gz https://download.cncb.ac.cn/gsa2/CRA007207/CRR529952_r2.fastq.gz,CRX469830,PRJCA009794,SAMC816749,NA,NA,NA,NA,NA,NA,NA,NA,NA
Liang 2020,DBDB_CD8T,10x scRNA-Seq of Cd8+ T cells from the ischemic muscles of Lepr db/db,muscle,hindlimb,cell,NA,NA,NA,not on GEO- Used SRA IDs instead,TRUE,TRUE,Mus musculus,SRP242500,SRX7575054,3p_v2,fastq,SRR10906902,NA,SRX7575054,SRP242500,SRS6009742,SAMN13495621,NA,NA,"Liang et al, Theranostics, 2020",10.7150/thno.40663,https://pubmed.ncbi.nlm.nih.gov/32226549/,Illumina HiSeq 2500,CD8+ T-cell plasticity regulates vascular regeneration in type-2 diabetes,"The subsets of CD8+ T-cells regulating tissue repair and regeneration have not been studied. To delineate the heterogeneity of CD8+ T-cells in non-lymphoid tissues of Lepr db/+ and Lepr db/db mice, we performed large-scale, droplet-based single-cell transcriptomic profiling. We purified about ~ 1,000 CD45+CD3+CD8+ T-cells from the ischemic muscles of Lepr db/+ and Lepr db/db, respectively, at day 7 after injury. After filtering, we obtained 934 and 768 cells from Lepr db/+ and Lepr db/db, respectively; and performed unsupervised analysis."
Liang 2020,DBM_CD8T,10x scRNA-Seq of Cd8+ T cells from the ischemic muscles of Lepr db/+,muscle,hindlimb,cell,NA,NA,NA,not on GEO- Used SRA IDs instead,TRUE,TRUE,Mus musculus,SRP242500,SRX7575055,3p_v2,fastq,SRR10906901,NA,SRX7575055,SRP242500,SRS6009743,SAMN13495620,NA,NA,"Liang et al, Theranostics, 2020",10.7150/thno.40663,https://pubmed.ncbi.nlm.nih.gov/32226549/,Illumina HiSeq 2500,CD8+ T-cell plasticity regulates vascular regeneration in type-2 diabetes,"The subsets of CD8+ T-cells regulating tissue repair and regeneration have not been studied. To delineate the heterogeneity of CD8+ T-cells in non-lymphoid tissues of Lepr db/+ and Lepr db/db mice, we performed large-scale, droplet-based single-cell transcriptomic profiling. We purified about ~ 1,000 CD45+CD3+CD8+ T-cells from the ischemic muscles of Lepr db/+ and Lepr db/db, respectively, at day 7 after injury. After filtering, we obtained 934 and 768 cells from Lepr db/+ and Lepr db/db, respectively; and performed unsupervised analysis."
Proetti 2021,scCTR_4,NA,muscle,NA,cell,NA,NA,NA,not on GEO- Used SRA IDs instead,TRUE,TRUE,Mus musculus,SRP257509,SRX8142653,3p_v3.1,fastq,SRR11574465,NA,SRX8142653,SRP257509,SRS6505604,NA,NA,https://www.ncbi.nlm.nih.gov/Traces/study/?acc=SRP257509&o=acc_s%3Aa,"Proietti et al, JCI Insights, 2021",10.1172/jci.insight.143469,https://pubmed.ncbi.nlm.nih.gov/33661767/,Illumina NovaSeq 6000,Role of ITGA7 positive muscle derived cells in denervation,Single Cells RNA-seq analysis of ITGA7 positive cells derived from denervated muscle
Proetti 2021,scCTR_3,NA,muscle,NA,cell,NA,NA,NA,not on GEO- Used SRA IDs instead,TRUE,TRUE,Mus musculus,SRP257509,SRX8142654,3p_v3.1,fastq,SRR11574464,NA,SRX8142654,SRP257509,SRS6505605,NA,NA,https://www.ncbi.nlm.nih.gov/Traces/study/?acc=SRP257509&o=acc_s%3Aa,"Proietti et al, JCI Insights, 2021",10.1172/jci.insight.143469,https://pubmed.ncbi.nlm.nih.gov/33661767/,Illumina NovaSeq 6000,Role of ITGA7 positive muscle derived cells in denervation,Single Cells RNA-seq analysis of ITGA7 positive cells derived from denervated muscle
Proetti 2021,scCTR_2,NA,muscle,NA,cell,NA,NA,NA,not on GEO- Used SRA IDs instead,TRUE,TRUE,Mus musculus,SRP257509,SRX8142655,3p_v3.1,fastq,SRR11574463,NA,SRX8142655,SRP257509,SRS6505605,NA,NA,https://www.ncbi.nlm.nih.gov/Traces/study/?acc=SRP257509&o=acc_s%3Aa,"Proietti et al, JCI Insights, 2021",10.1172/jci.insight.143469,https://pubmed.ncbi.nlm.nih.gov/33661767/,Illumina NovaSeq 6000,Role of ITGA7 positive muscle derived cells in denervation,Single Cells RNA-seq analysis of ITGA7 positive cells derived from denervated muscle
Proetti 2021,scCTR_1,NA,muscle,NA,cell,NA,NA,NA,not on GEO- Used SRA IDs instead,TRUE,TRUE,Mus musculus,SRP257509,SRX8142656,3p_v3.1,fastq,SRR11574462,NA,SRX8142656,SRP257509,SRS6505605,NA,NA,https://www.ncbi.nlm.nih.gov/Traces/study/?acc=SRP257509&o=acc_s%3Aa,"Proietti et al, JCI Insights, 2021",10.1172/jci.insight.143469,https://pubmed.ncbi.nlm.nih.gov/33661767/,Illumina NovaSeq 6000,Role of ITGA7 positive muscle derived cells in denervation,Single Cells RNA-seq analysis of ITGA7 positive cells derived from denervated muscle
Proetti 2021,scDEN_4,NA,muscle,NA,cell,NA,NA,NA,not on GEO- Used SRA IDs instead,TRUE,TRUE,Mus musculus,SRP257509,SRX8142657,3p_v3.1,fastq,SRR11574461,NA,SRX8142657,SRP257509,SRS6505604,NA,NA,https://www.ncbi.nlm.nih.gov/Traces/study/?acc=SRP257509&o=acc_s%3Aa,"Proietti et al, JCI Insights, 2021",10.1172/jci.insight.143469,https://pubmed.ncbi.nlm.nih.gov/33661767/,Illumina NovaSeq 6000,Role of ITGA7 positive muscle derived cells in denervation,Single Cells RNA-seq analysis of ITGA7 positive cells derived from denervated muscle
Proetti 2021,scDEN_3,NA,muscle,NA,cell,NA,NA,NA,not on GEO- Used SRA IDs instead,TRUE,TRUE,Mus musculus,SRP257509,SRX8142658,3p_v3.1,fastq,SRR11574460,NA,SRX8142658,SRP257509,SRS6505604,NA,NA,https://www.ncbi.nlm.nih.gov/Traces/study/?acc=SRP257509&o=acc_s%3Aa,"Proietti et al, JCI Insights, 2021",10.1172/jci.insight.143469,https://pubmed.ncbi.nlm.nih.gov/33661767/,Illumina NovaSeq 6000,Role of ITGA7 positive muscle derived cells in denervation,Single Cells RNA-seq analysis of ITGA7 positive cells derived from denervated muscle
Proetti 2021,scDEN_2,NA,muscle,NA,cell,NA,NA,NA,not on GEO- Used SRA IDs instead,TRUE,TRUE,Mus musculus,SRP257509,SRX8142659,3p_v3.1,fastq,SRR11574459,NA,SRX8142659,SRP257509,SRS6505604,NA,NA,https://www.ncbi.nlm.nih.gov/Traces/study/?acc=SRP257509&o=acc_s%3Aa,"Proietti et al, JCI Insights, 2021",10.1172/jci.insight.143469,https://pubmed.ncbi.nlm.nih.gov/33661767/,Illumina NovaSeq 6000,Role of ITGA7 positive muscle derived cells in denervation,Single Cells RNA-seq analysis of ITGA7 positive cells derived from denervated muscle
Proetti 2021,scDEN_1,NA,muscle,NA,cell,NA,NA,NA,not on GEO- Used SRA IDs instead,TRUE,TRUE,Mus musculus,SRP257509,SRX8142660,3p_v3.1,fastq,SRR11574458,NA,SRX8142660,SRP257509,SRS6505605,NA,NA,https://www.ncbi.nlm.nih.gov/Traces/study/?acc=SRP257509&o=acc_s%3Aa,"Proietti et al, JCI Insights, 2021",10.1172/jci.insight.143469,https://pubmed.ncbi.nlm.nih.gov/33661767/,Illumina NovaSeq 6000,Role of ITGA7 positive muscle derived cells in denervation,Single Cells RNA-seq analysis of ITGA7 positive cells derived from denervated muscle
Cho DS 2020,Muscle 1 day_scRNA-seq,NA,muscle,NA,cell,NA,NA,NA,not on GEO- Used SRA IDs instead,TRUE,TRUE,Mus musculus,SRP257517,SRX8142724,3p_v2,fastq,SRR11574540,NA,SRX8142724,SRP257517,NA,NA,NA,NA,NA,10.1002/jcsm.12596,https://pubmed.ncbi.nlm.nih.gov/32643301/,NA,NA,NA
Cho DS 2020,Muscle 1 month_scRNA-seq,NA,muscle,NA,cell,NA,NA,NA,not on GEO- Used SRA IDs instead,TRUE,TRUE,Mus musculus,SRP257517,SRX8142725,3p_v2,fastq,SRR11574539,NA,SRX8142725,SRP257517,NA,NA,NA,NA,NA,10.1002/jcsm.12596,https://pubmed.ncbi.nlm.nih.gov/32643301/,NA,NA,NA
Cho DS 2020,Muscle control_scRNA-seq,NA,muscle,NA,cell,NA,NA,NA,not on GEO- Used SRA IDs instead,TRUE,TRUE,Mus musculus,SRP257517,SRX8142726,3p_v2,fastq,SRR11574541,NA,SRX8142726,SRP257517,NA,NA,NA,NA,NA,10.1002/jcsm.12596,https://pubmed.ncbi.nlm.nih.gov/32643301/,NA,NA,NA
Scripture-Adams 2022,"C57BL/10 tibialis anterior, sample 3",NA,muscle,tibialis anterior,nucleus,NA,NA,NA,not on GEO- Used SRA IDs instead,TRUE,TRUE,Mus musculus,SRP342930,SRX12757373,3p_v3.1,fastq,SRR16555251,NA,SRX12757373,SRP342930,SRS10704689 ,SAMN22349692,NA,NA,"Scripture-Adams et al, Communications Biology, 2022",10.1038/s42003-022-03938-0,https://pubmed.ncbi.nlm.nih.gov/36123393/,NA,NA,NA
Scripture-Adams 2022,"C57BL/10 tibialis anterior, sample 2",NA,muscle,tibialis anterior,nucleus,NA,NA,NA,not on GEO- Used SRA IDs instead,TRUE,TRUE,Mus musculus,SRP342930,SRX12757374,3p_v3.1,fastq,SRR16555250,NA,SRX12757374,SRP342930,SRS10704690 ,SAMN22349691,NA,NA,"Scripture-Adams et al, Communications Biology, 2022",10.1038/s42003-022-03938-0,https://pubmed.ncbi.nlm.nih.gov/36123393/,NA,NA,NA
Scripture-Adams 2022,"mdx e23AON tibialis anterior, sample 1",NA,muscle,tibialis anterior,nucleus,NA,NA,NA,not on GEO- Used SRA IDs instead,TRUE,TRUE,Mus musculus,SRP342930,SRX12757375,3p_v3.1,fastq,SRR16555249,NA,SRX12757375,SRP342930,SRS10704694 ,SAMN22349690,NA,NA,"Scripture-Adams et al, Communications Biology, 2022",10.1038/s42003-022-03938-0,https://pubmed.ncbi.nlm.nih.gov/36123393/,NA,NA,NA
Scripture-Adams 2022,"C57BL/10 tibialis anterior, sample 1",NA,muscle,tibialis anterior,nucleus,NA,NA,NA,not on GEO- Used SRA IDs instead,TRUE,TRUE,Mus musculus,SRP342930,SRX12757376,3p_v3.1,fastq,SRR16555248,NA,SRX12757376,SRP342930,SRS10704693 ,SAMN22349689,NA,NA,"Scripture-Adams et al, Communications Biology, 2022",10.1038/s42003-022-03938-0,https://pubmed.ncbi.nlm.nih.gov/36123393/,NA,NA,NA
Scripture-Adams 2022,"mdx tibialis anterior, sample 4",NA,muscle,tibialis anterior,nucleus,NA,NA,NA,not on GEO- Used SRA IDs instead,TRUE,TRUE,Mus musculus,SRP342930,SRX12757377,3p_v3.1,fastq,SRR16555247,NA,SRX12757377,SRP342930,SRS10704692 ,SAMN22349688,NA,NA,"Scripture-Adams et al, Communications Biology, 2022",10.1038/s42003-022-03938-0,https://pubmed.ncbi.nlm.nih.gov/36123393/,NA,NA,NA
Scripture-Adams 2022,"mdx tibialis anterior, sample 3",NA,muscle,tibialis anterior,nucleus,NA,NA,NA,not on GEO- Used SRA IDs instead,TRUE,TRUE,Mus musculus,SRP342930,SRX12757378,3p_v3.1,fastq,SRR16555246,NA,SRX12757378,SRP342930,SRS10704691 ,SAMN22349687 ,NA,NA,"Scripture-Adams et al, Communications Biology, 2022",10.1038/s42003-022-03938-0,https://pubmed.ncbi.nlm.nih.gov/36123393/,NA,NA,NA
Scripture-Adams 2022,"mdx tibialis anterior, sample 2",NA,muscle,tibialis anterior,nucleus,NA,NA,NA,not on GEO- Used SRA IDs instead,TRUE,TRUE,Mus musculus,SRP342930,SRX12757379,3p_v3.1,fastq,SRR16555245,NA,SRX12757379,SRP342930,SRS10704695 ,SAMN22349686,NA,NA,"Scripture-Adams et al, Communications Biology, 2022",10.1038/s42003-022-03938-0,https://pubmed.ncbi.nlm.nih.gov/36123393/,NA,NA,NA
Scripture-Adams 2022,"mdx tibialis anterior, sample 1",NA,muscle,tibialis anterior,nucleus,NA,NA,NA,not on GEO- Used SRA IDs instead,TRUE,TRUE,Mus musculus,SRP342930,SRX12757380,3p_v3.1,fastq,SRR16555244,NA,SRX12757380,SRP342930,SRS10704696 ,SAMN22349685 ,NA,NA,"Scripture-Adams et al, Communications Biology, 2022",10.1038/s42003-022-03938-0,https://pubmed.ncbi.nlm.nih.gov/36123393/,NA,NA,NA
Scripture-Adams 2022,"mdx e23AON tibialis anterior, sample 3",NA,muscle,tibialis anterior,nucleus,NA,NA,NA,not on GEO- Used SRA IDs instead,TRUE,TRUE,Mus musculus,SRP342930,SRX12757381,3p_v3.1,fastq,SRR16555243,NA,SRX12757381,SRP342930,SRS10704697 ,SAMN22349683,NA,NA,"Scripture-Adams et al, Communications Biology, 2022",10.1038/s42003-022-03938-0,https://pubmed.ncbi.nlm.nih.gov/36123393/,NA,NA,NA
Scripture-Adams 2022,"mdx e23AON tibialis anterior, sample 4",NA,muscle,tibialis anterior,nucleus,NA,NA,NA,not on GEO- Used SRA IDs instead,TRUE,TRUE,Mus musculus,SRP342930,SRX12757382,3p_v3.1,fastq,SRR16555242,NA,SRX12757382,SRP342930,SRS10704699 ,SAMN22349684 ,NA,NA,"Scripture-Adams et al, Communications Biology, 2022",10.1038/s42003-022-03938-0,https://pubmed.ncbi.nlm.nih.gov/36123393/,NA,NA,NA
Scripture-Adams 2022,"mdx e23AON tibialis anterior, sample 2",NA,muscle,tibialis anterior,nucleus,NA,NA,NA,not on GEO- Used SRA IDs instead,TRUE,TRUE,Mus musculus,SRP342930,SRX12757383,3p_v3.1,fastq,SRR16555241;SRR16555242,NA,SRX12757383,SRP342930,SRS10704698 ,SAMN22349682 ,NA,NA,"Scripture-Adams et al, Communications Biology, 2022",10.1038/s42003-022-03938-0,https://pubmed.ncbi.nlm.nih.gov/36123393/,NA,NA,NA
Scripture-Adams 2022,"Healthy Control Vastus lateralis, sample 2",NA,muscle,vastus lateralis,nucleus,NA,NA,NA,not on GEO- Used SRA IDs instead,TRUE,TRUE,Homo sapiens,SRP342931,SRX12757384,3p_v3.1,fastq,SRR16555256,NA,SRX12757384,SRP342931,SRS10704700 ,SAMN22357909 ,NA,NA,"Scripture-Adams et al, Communications Biology, 2022",10.1038/s42003-022-03938-0,https://pubmed.ncbi.nlm.nih.gov/36123393/,NA,NA,NA
Scripture-Adams 2022,"Healthy Control Vastus lateralis, sample 1",NA,muscle,vastus lateralis,nucleus,NA,NA,NA,not on GEO- Used SRA IDs instead,TRUE,TRUE,Homo sapiens,SRP342931,SRX12757385,3p_v3.1,fastq,SRR16555255,NA,SRX12757385,SRP342931,SRS10704701 ,SAMN22357908 ,NA,NA,"Scripture-Adams et al, Communications Biology, 2022",10.1038/s42003-022-03938-0,https://pubmed.ncbi.nlm.nih.gov/36123393/,NA,NA,NA
Scripture-Adams 2022,"Duchenne Vastus lateralis, sample 3",NA,muscle,vastus lateralis,nucleus,NA,NA,NA,not on GEO- Used SRA IDs instead,TRUE,TRUE,Homo sapiens,SRP342931,SRX12757386,3p_v3.1,fastq,SRR16555254;SRR16596797,NA,SRX12757386,SRP342931,SRS10704702 ,SAMN22357907 ,NA,NA,"Scripture-Adams et al, Communications Biology, 2022",10.1038/s42003-022-03938-0,https://pubmed.ncbi.nlm.nih.gov/36123393/,NA,NA,NA
Scripture-Adams 2022,"Duchenne Vastus lateralis, sample 2",NA,muscle,vastus lateralis,nucleus,NA,NA,NA,not on GEO- Used SRA IDs instead,TRUE,TRUE,Homo sapiens,SRP342931,SRX12757387,3p_v3.1,fastq,SRR16555253,NA,SRX12757387,SRP342931,SRS10704703 ,SAMN22357906 ,NA,NA,"Scripture-Adams et al, Communications Biology, 2022",10.1038/s42003-022-03938-0,https://pubmed.ncbi.nlm.nih.gov/36123393/,NA,NA,NA
Scripture-Adams 2022,"Duchenne Vastus lateralis, sample 1",NA,muscle,vastus lateralis,nucleus,NA,NA,NA,not on GEO- Used SRA IDs instead,TRUE,TRUE,Homo sapiens,SRP342931,SRX12757388,3p_v3.1,fastq,SRR16555252,NA,SRX12757388,SRP342931,SRS10704704 ,SAMN22357905 ,NA,NA,"Scripture-Adams et al, Communications Biology, 2022",10.1038/s42003-022-03938-0,https://pubmed.ncbi.nlm.nih.gov/36123393/,NA,NA,NA
Gitler 2020,replicate1_male_female,NA,spinal cord,NA,nucleus,NA,NA,NA,Error R1 missing_fastq provided,TRUE,TRUE,Mus musculus,GSE161621,GSM4911289,3p_v3,NA,SRR13073639;SRR13073640;SRR13073641;SRR13073642,NA,SRX9520787,SRP292908,SRS7728003,SAMN16816776,NA,NA,NA,10.1038/s41593-020-00795-0,https://pubmed.ncbi.nlm.nih.gov/33589834/,NextSeq 550,Single-cell transcriptomic analysis of the adult mouse spinal cord reveals fundamental molecular diversity of autonomic and skeletal motor neurons,"To characterize the diversity of cholinergic neurons in the spinal cord, we performed single-nucleus RNA sequencing on cholinergic-enriched pools of nuclei from the adult mouse. Overall design: Enrichment: Nuclei were enriched by fluorescence-activated nuclei sorting (FANS) of GFP+ cholinergic nuclei from reporter mice. Barcoding: Nuclei were loaded into a 10X Chromium device and barcoded via oligo-dT reverse transcription using the V3 chemistry. Library prep: Libraries were prepared by PCR and size-exclusion according to published 10X protocols. Sequencing: Libraries were sequenced using NextSeq 550 high-throughput, 150-cycle kits and NovaSeq 100-cycle kits."
Gitler 2020,replicate2a_male_female,NA,spinal cord,NA,nucleus,NA,NA,NA,Error R1 missing_fastq provided,TRUE,TRUE,Mus musculus,GSE161621,GSM4911290,3p_v3,NA,SRR13073643;SRR13073644;SRR13073645;SRR13073646,NA,SRX9520788,SRP292908,SRS7728002,SAMN16816775,NA,NA,NA,10.1038/s41593-020-00795-0,https://pubmed.ncbi.nlm.nih.gov/33589834/,NextSeq 550,Single-cell transcriptomic analysis of the adult mouse spinal cord reveals fundamental molecular diversity of autonomic and skeletal motor neurons,"To characterize the diversity of cholinergic neurons in the spinal cord, we performed single-nucleus RNA sequencing on cholinergic-enriched pools of nuclei from the adult mouse. Overall design: Enrichment: Nuclei were enriched by fluorescence-activated nuclei sorting (FANS) of GFP+ cholinergic nuclei from reporter mice. Barcoding: Nuclei were loaded into a 10X Chromium device and barcoded via oligo-dT reverse transcription using the V3 chemistry. Library prep: Libraries were prepared by PCR and size-exclusion according to published 10X protocols. Sequencing: Libraries were sequenced using NextSeq 550 high-throughput, 150-cycle kits and NovaSeq 100-cycle kits."
Gitler 2020,replicate2b_male_female,NA,spinal cord,NA,nucleus,NA,NA,NA,Error R1 missing_fastq provided,TRUE,TRUE,Mus musculus,GSE161621,GSM4911291,3p_v3,NA,SRR13073647;SRR13073648;SRR13073649;SRR13073650,NA,SRX9520789,SRP292908,SRS7728004,SAMN16816774,NA,NA,NA,10.1038/s41593-020-00795-0,https://pubmed.ncbi.nlm.nih.gov/33589834/,NextSeq 550,Single-cell transcriptomic analysis of the adult mouse spinal cord reveals fundamental molecular diversity of autonomic and skeletal motor neurons,"To characterize the diversity of cholinergic neurons in the spinal cord, we performed single-nucleus RNA sequencing on cholinergic-enriched pools of nuclei from the adult mouse. Overall design: Enrichment: Nuclei were enriched by fluorescence-activated nuclei sorting (FANS) of GFP+ cholinergic nuclei from reporter mice. Barcoding: Nuclei were loaded into a 10X Chromium device and barcoded via oligo-dT reverse transcription using the V3 chemistry. Library prep: Libraries were prepared by PCR and size-exclusion according to published 10X protocols. Sequencing: Libraries were sequenced using NextSeq 550 high-throughput, 150-cycle kits and NovaSeq 100-cycle kits."
Gitler 2020,replicate3_female,NA,spinal cord,NA,nucleus,NA,NA,NA,Error R1 missing_fastq provided,TRUE,TRUE,Mus musculus,GSE161621,GSM4911292,3p_v3,NA,SRR13073651;SRR13073652;SRR13073653;SRR13073654,NA,SRX9520790,SRP292908,SRS7728005,SAMN16816773,NA,NA,NA,10.1038/s41593-020-00795-0,https://pubmed.ncbi.nlm.nih.gov/33589834/,NextSeq 550,Single-cell transcriptomic analysis of the adult mouse spinal cord reveals fundamental molecular diversity of autonomic and skeletal motor neurons,"To characterize the diversity of cholinergic neurons in the spinal cord, we performed single-nucleus RNA sequencing on cholinergic-enriched pools of nuclei from the adult mouse. Overall design: Enrichment: Nuclei were enriched by fluorescence-activated nuclei sorting (FANS) of GFP+ cholinergic nuclei from reporter mice. Barcoding: Nuclei were loaded into a 10X Chromium device and barcoded via oligo-dT reverse transcription using the V3 chemistry. Library prep: Libraries were prepared by PCR and size-exclusion according to published 10X protocols. Sequencing: Libraries were sequenced using NextSeq 550 high-throughput, 150-cycle kits and NovaSeq 100-cycle kits."
Gitler 2020,replicate4_male,NA,spinal cord,NA,nucleus,NA,NA,NA,Error R1 missing_fastq provided,TRUE,TRUE,Mus musculus,GSE161621,GSM4911293,3p_v3,NA,SRR13073655;SRR13073656;SRR13073657;SRR13073658,NA,SRX9520791,SRP292908,SRS7728006,SAMN16816772,NA,NA,NA,10.1038/s41593-020-00795-0,https://pubmed.ncbi.nlm.nih.gov/33589834/,NextSeq 550,Single-cell transcriptomic analysis of the adult mouse spinal cord reveals fundamental molecular diversity of autonomic and skeletal motor neurons,"To characterize the diversity of cholinergic neurons in the spinal cord, we performed single-nucleus RNA sequencing on cholinergic-enriched pools of nuclei from the adult mouse. Overall design: Enrichment: Nuclei were enriched by fluorescence-activated nuclei sorting (FANS) of GFP+ cholinergic nuclei from reporter mice. Barcoding: Nuclei were loaded into a 10X Chromium device and barcoded via oligo-dT reverse transcription using the V3 chemistry. Library prep: Libraries were prepared by PCR and size-exclusion according to published 10X protocols. Sequencing: Libraries were sequenced using NextSeq 550 high-throughput, 150-cycle kits and NovaSeq 100-cycle kits."
Gitler 2020,replicate5_female,NA,spinal cord,NA,nucleus,NA,NA,NA,Error R1 missing_fastq provided,TRUE,TRUE,Mus musculus,GSE161621,GSM4911294,3p_v3,NA,SRR13073659,NA,SRX9520792,SRP292908,SRS7728007,SAMN16816771,NA,NA,NA,10.1038/s41593-020-00795-0,https://pubmed.ncbi.nlm.nih.gov/33589834/,Illumina NovaSeq 6000,Single-cell transcriptomic analysis of the adult mouse spinal cord reveals fundamental molecular diversity of autonomic and skeletal motor neurons,"To characterize the diversity of cholinergic neurons in the spinal cord, we performed single-nucleus RNA sequencing on cholinergic-enriched pools of nuclei from the adult mouse. Overall design: Enrichment: Nuclei were enriched by fluorescence-activated nuclei sorting (FANS) of GFP+ cholinergic nuclei from reporter mice. Barcoding: Nuclei were loaded into a 10X Chromium device and barcoded via oligo-dT reverse transcription using the V3 chemistry. Library prep: Libraries were prepared by PCR and size-exclusion according to published 10X protocols. Sequencing: Libraries were sequenced using NextSeq 550 high-throughput, 150-cycle kits and NovaSeq 100-cycle kits."
Alkaslasi 2021,Cervical_M+F_rep1,pooled male and female; Cervical spinal cord,spinal cord,NA,NA,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE167597,GSM5111192,3p_v3,bam,SRR13790640,NA,SRX10175665,SRP308350,SRS8324677,SAMN18063059,NA,NA,"Alkaslasi et al, Nature Communications, 2021",10.1038/s41467-021-22691-2,https://pubmed.ncbi.nlm.nih.gov/33931636/,Illumina HiSeq 2500,Single nucleus RNA-sequencing defines unexpected diversity of cholinergic neuron types in the adult mouse spinal cord,"We developed a targeted single nucleus RNA sequencing approach to enrich and transcriptomically characterize cholinergic neurons of the adult mouse spinal cord. Our data expose markers for known classes of cholinergic neurons and their extremely rich diversity. Visceral/preganglionic motor neurons could be divided into more than a dozen transcriptomic classes with anatomically restricted localization along the spinal cord. The complexity of the skeletal motor neurons was also reflected in our analysis with alpha, gamma, and a third subtype clearly distinguished. We further identified previously unrecognized subtypes of cholinergic interneurons. Overall design: Cholinergic nuclei were enriched by FACS sorting of GFP+ nuclei from nuclear reporter mice and barcoded using 10X Genomics Chromium Single Cell Processor. Samples were run on an Illumina HiSeq2500."
Alkaslasi 2021,Thoracic_M+F_rep1,pooled male and female; Thoracic spinal cord,spinal cord,NA,NA,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE167597,GSM5111193,3p_v3,bam,SRR13790641,NA,SRX10175666,SRP308350,SRS8324679,SAMN18063058,NA,NA,"Alkaslasi et al, Nature Communications, 2021",10.1038/s41467-021-22691-2,https://pubmed.ncbi.nlm.nih.gov/33931636/,Illumina HiSeq 2500,Single nucleus RNA-sequencing defines unexpected diversity of cholinergic neuron types in the adult mouse spinal cord,"We developed a targeted single nucleus RNA sequencing approach to enrich and transcriptomically characterize cholinergic neurons of the adult mouse spinal cord. Our data expose markers for known classes of cholinergic neurons and their extremely rich diversity. Visceral/preganglionic motor neurons could be divided into more than a dozen transcriptomic classes with anatomically restricted localization along the spinal cord. The complexity of the skeletal motor neurons was also reflected in our analysis with alpha, gamma, and a third subtype clearly distinguished. We further identified previously unrecognized subtypes of cholinergic interneurons. Overall design: Cholinergic nuclei were enriched by FACS sorting of GFP+ nuclei from nuclear reporter mice and barcoded using 10X Genomics Chromium Single Cell Processor. Samples were run on an Illumina HiSeq2500."
Alkaslasi 2021,Lumbar/Sacral_M+F_rep1,pooled male and female; Lumbar and sacral spinal cord,spinal cord,NA,NA,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE167597,GSM5111194,3p_v3,bam,SRR13790642,NA,SRX10175667,SRP308350,SRS8324678,SAMN18063057,NA,NA,"Alkaslasi et al, Nature Communications, 2021",10.1038/s41467-021-22691-2,https://pubmed.ncbi.nlm.nih.gov/33931636/,Illumina HiSeq 2500,Single nucleus RNA-sequencing defines unexpected diversity of cholinergic neuron types in the adult mouse spinal cord,"We developed a targeted single nucleus RNA sequencing approach to enrich and transcriptomically characterize cholinergic neurons of the adult mouse spinal cord. Our data expose markers for known classes of cholinergic neurons and their extremely rich diversity. Visceral/preganglionic motor neurons could be divided into more than a dozen transcriptomic classes with anatomically restricted localization along the spinal cord. The complexity of the skeletal motor neurons was also reflected in our analysis with alpha, gamma, and a third subtype clearly distinguished. We further identified previously unrecognized subtypes of cholinergic interneurons. Overall design: Cholinergic nuclei were enriched by FACS sorting of GFP+ nuclei from nuclear reporter mice and barcoded using 10X Genomics Chromium Single Cell Processor. Samples were run on an Illumina HiSeq2500."
Alkaslasi 2021,Cervical_M_rep2,male; Cervical spinal cord,spinal cord,NA,NA,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE167597,GSM5111195,3p_v3,bam,SRR13790643,NA,SRX10175668,SRP308350,SRS8324680,SAMN18063056,NA,NA,"Alkaslasi et al, Nature Communications, 2021",10.1038/s41467-021-22691-2,https://pubmed.ncbi.nlm.nih.gov/33931636/,Illumina HiSeq 2500,Single nucleus RNA-sequencing defines unexpected diversity of cholinergic neuron types in the adult mouse spinal cord,"We developed a targeted single nucleus RNA sequencing approach to enrich and transcriptomically characterize cholinergic neurons of the adult mouse spinal cord. Our data expose markers for known classes of cholinergic neurons and their extremely rich diversity. Visceral/preganglionic motor neurons could be divided into more than a dozen transcriptomic classes with anatomically restricted localization along the spinal cord. The complexity of the skeletal motor neurons was also reflected in our analysis with alpha, gamma, and a third subtype clearly distinguished. We further identified previously unrecognized subtypes of cholinergic interneurons. Overall design: Cholinergic nuclei were enriched by FACS sorting of GFP+ nuclei from nuclear reporter mice and barcoded using 10X Genomics Chromium Single Cell Processor. Samples were run on an Illumina HiSeq2500."
Alkaslasi 2021,Thoracic_M_rep2,male; Thoracic spinal cord,spinal cord,NA,NA,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE167597,GSM5111196,3p_v3,bam,SRR13790644,NA,SRX10175669,SRP308350,SRS8324681,SAMN18063055,NA,NA,"Alkaslasi et al, Nature Communications, 2021",10.1038/s41467-021-22691-2,https://pubmed.ncbi.nlm.nih.gov/33931636/,Illumina HiSeq 2500,Single nucleus RNA-sequencing defines unexpected diversity of cholinergic neuron types in the adult mouse spinal cord,"We developed a targeted single nucleus RNA sequencing approach to enrich and transcriptomically characterize cholinergic neurons of the adult mouse spinal cord. Our data expose markers for known classes of cholinergic neurons and their extremely rich diversity. Visceral/preganglionic motor neurons could be divided into more than a dozen transcriptomic classes with anatomically restricted localization along the spinal cord. The complexity of the skeletal motor neurons was also reflected in our analysis with alpha, gamma, and a third subtype clearly distinguished. We further identified previously unrecognized subtypes of cholinergic interneurons. Overall design: Cholinergic nuclei were enriched by FACS sorting of GFP+ nuclei from nuclear reporter mice and barcoded using 10X Genomics Chromium Single Cell Processor. Samples were run on an Illumina HiSeq2500."
Alkaslasi 2021,Lumbar/Sacral_M_rep2,male; Lumbar and sacral spinal cord,spinal cord,NA,NA,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE167597,GSM5111197,3p_v3,bam,SRR13790645,NA,SRX10175670,SRP308350,SRS8324683,SAMN18063054,NA,NA,"Alkaslasi et al, Nature Communications, 2021",10.1038/s41467-021-22691-2,https://pubmed.ncbi.nlm.nih.gov/33931636/,Illumina HiSeq 2500,Single nucleus RNA-sequencing defines unexpected diversity of cholinergic neuron types in the adult mouse spinal cord,"We developed a targeted single nucleus RNA sequencing approach to enrich and transcriptomically characterize cholinergic neurons of the adult mouse spinal cord. Our data expose markers for known classes of cholinergic neurons and their extremely rich diversity. Visceral/preganglionic motor neurons could be divided into more than a dozen transcriptomic classes with anatomically restricted localization along the spinal cord. The complexity of the skeletal motor neurons was also reflected in our analysis with alpha, gamma, and a third subtype clearly distinguished. We further identified previously unrecognized subtypes of cholinergic interneurons. Overall design: Cholinergic nuclei were enriched by FACS sorting of GFP+ nuclei from nuclear reporter mice and barcoded using 10X Genomics Chromium Single Cell Processor. Samples were run on an Illumina HiSeq2500."
Alkaslasi 2021,Cervical_F_rep3,female; Cervical spinal cord,spinal cord,NA,NA,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE167597,GSM5111198,3p_v3,bam,SRR13790646,NA,SRX10175671,SRP308350,SRS8324684,SAMN18063053,NA,NA,"Alkaslasi et al, Nature Communications, 2021",10.1038/s41467-021-22691-2,https://pubmed.ncbi.nlm.nih.gov/33931636/,Illumina HiSeq 2500,Single nucleus RNA-sequencing defines unexpected diversity of cholinergic neuron types in the adult mouse spinal cord,"We developed a targeted single nucleus RNA sequencing approach to enrich and transcriptomically characterize cholinergic neurons of the adult mouse spinal cord. Our data expose markers for known classes of cholinergic neurons and their extremely rich diversity. Visceral/preganglionic motor neurons could be divided into more than a dozen transcriptomic classes with anatomically restricted localization along the spinal cord. The complexity of the skeletal motor neurons was also reflected in our analysis with alpha, gamma, and a third subtype clearly distinguished. We further identified previously unrecognized subtypes of cholinergic interneurons. Overall design: Cholinergic nuclei were enriched by FACS sorting of GFP+ nuclei from nuclear reporter mice and barcoded using 10X Genomics Chromium Single Cell Processor. Samples were run on an Illumina HiSeq2500."
Alkaslasi 2021,Thoracic_F_rep3,female; Thoracic spinal cord,spinal cord,NA,NA,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE167597,GSM5111199,3p_v3,bam,SRR13790647,NA,SRX10175672,SRP308350,SRS8324682,SAMN18063052,NA,NA,"Alkaslasi et al, Nature Communications, 2021",10.1038/s41467-021-22691-2,https://pubmed.ncbi.nlm.nih.gov/33931636/,Illumina HiSeq 2500,Single nucleus RNA-sequencing defines unexpected diversity of cholinergic neuron types in the adult mouse spinal cord,"We developed a targeted single nucleus RNA sequencing approach to enrich and transcriptomically characterize cholinergic neurons of the adult mouse spinal cord. Our data expose markers for known classes of cholinergic neurons and their extremely rich diversity. Visceral/preganglionic motor neurons could be divided into more than a dozen transcriptomic classes with anatomically restricted localization along the spinal cord. The complexity of the skeletal motor neurons was also reflected in our analysis with alpha, gamma, and a third subtype clearly distinguished. We further identified previously unrecognized subtypes of cholinergic interneurons. Overall design: Cholinergic nuclei were enriched by FACS sorting of GFP+ nuclei from nuclear reporter mice and barcoded using 10X Genomics Chromium Single Cell Processor. Samples were run on an Illumina HiSeq2500."
Alkaslasi 2021,Lumbar/Sacral_F_rep3,female; Lumbar and sacral spinal cord,spinal cord,NA,NA,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE167597,GSM5111200,3p_v3,bam,SRR13790648,NA,SRX10175673,SRP308350,SRS8324685,SAMN18063051,NA,NA,"Alkaslasi et al, Nature Communications, 2021",10.1038/s41467-021-22691-2,https://pubmed.ncbi.nlm.nih.gov/33931636/,Illumina HiSeq 2500,Single nucleus RNA-sequencing defines unexpected diversity of cholinergic neuron types in the adult mouse spinal cord,"We developed a targeted single nucleus RNA sequencing approach to enrich and transcriptomically characterize cholinergic neurons of the adult mouse spinal cord. Our data expose markers for known classes of cholinergic neurons and their extremely rich diversity. Visceral/preganglionic motor neurons could be divided into more than a dozen transcriptomic classes with anatomically restricted localization along the spinal cord. The complexity of the skeletal motor neurons was also reflected in our analysis with alpha, gamma, and a third subtype clearly distinguished. We further identified previously unrecognized subtypes of cholinergic interneurons. Overall design: Cholinergic nuclei were enriched by FACS sorting of GFP+ nuclei from nuclear reporter mice and barcoded using 10X Genomics Chromium Single Cell Processor. Samples were run on an Illumina HiSeq2500."
Still 2021,Resting Normal TPCs,NA,tendon,NA,NA,NA,NA,NA,hashed,FALSE,TRUE,Homo sapiens,GSE150482,GSM4551237,3p_v#_HASH,fastq,SRR11784373,NA,SRX8336796,NA,NA,SAMN14911592,NA,NA,NA,NA,https://pubmed.ncbi.nlm.nih.gov/34337559/,NA,NA,NA
Still 2021,Resting Disease TPCs,NA,tendon,NA,NA,NA,NA,NA,hashed,FALSE,TRUE,Homo sapiens,GSE150482,GSM4551238,3p_v#_HASH,fastq,SRR11784374,NA,SRX8336797,NA,NA,SAMN14911591,NA,NA,NA,NA,https://pubmed.ncbi.nlm.nih.gov/34337559/,NA,NA,NA
Still 2021,Stretched Normal TPCs,NA,tendon,NA,NA,NA,NA,NA,hashed,FALSE,TRUE,Homo sapiens,GSE150482,GSM4551239,3p_v#_HASH,fastq,SRR11784375,NA,SRX8336798,NA,NA,SAMN14911590,NA,NA,NA,NA,https://pubmed.ncbi.nlm.nih.gov/34337559/,NA,NA,NA
Still 2021,Stretched Disease TPCs,NA,tendon,NA,NA,NA,NA,NA,hashed,FALSE,TRUE,Homo sapiens,GSE150482,GSM4551240,3p_v#_HASH,fastq,SRR11784376,NA,SRX8336799,NA,NA,SAMN14911589,NA,NA,NA,NA,https://pubmed.ncbi.nlm.nih.gov/34337559/,NA,NA,NA
Yoshimoto 2022,T0-1 single-cells,NA,tendon,NA,NA,NA,NA,NA,CEL-Seq2,FALSE,TRUE,Mus musculus,GSE168451,GSM5140555,CEL-Seq2,fastq,SRR13884949,NA,NA,NA,NA,SAMN18205486,NA,NA,NA,NA,NA,NA,NA,NA
Yoshimoto 2022,T0-2 single-cells,NA,tendon,NA,NA,NA,NA,NA,CEL-Seq2,FALSE,TRUE,Mus musculus,GSE168451,GSM5140556,CEL-Seq2,fastq,SRR13884950,NA,NA,NA,NA,SAMN18205485,NA,NA,NA,NA,NA,NA,NA,NA
Yoshimoto 2022,T0-3 single-cells,NA,tendon,NA,NA,NA,NA,NA,CEL-Seq2,FALSE,TRUE,Mus musculus,GSE168451,GSM5140557,CEL-Seq2,fastq,SRR13884951,NA,NA,NA,NA,SAMN18205482,NA,NA,NA,NA,NA,NA,NA,NA
Yoshimoto 2022,T3-1 single-cells,NA,tendon,NA,NA,NA,NA,NA,CEL-Seq2,FALSE,TRUE,Mus musculus,GSE168451,GSM5140558,CEL-Seq2,fastq,SRR13884952,NA,NA,NA,NA,SAMN18205479,NA,NA,NA,NA,NA,NA,NA,NA
Yoshimoto 2022,T3-2 single-cells,NA,tendon,NA,NA,NA,NA,NA,CEL-Seq2,FALSE,TRUE,Mus musculus,GSE168451,GSM5140559,CEL-Seq2,fastq,SRR13884953,NA,NA,NA,NA,SAMN18205475,NA,NA,NA,NA,NA,NA,NA,NA
Yoshimoto 2022,T3-3 single-cells,NA,tendon,NA,NA,NA,NA,NA,CEL-Seq2,FALSE,TRUE,Mus musculus,GSE168451,GSM5140560,CEL-Seq2,fastq,SRR13884954,NA,NA,NA,NA,SAMN18205474,NA,NA,NA,NA,NA,NA,NA,NA
Yoshimoto 2022,T6-1 single-cells,NA,tendon,NA,NA,NA,NA,NA,CEL-Seq2,FALSE,TRUE,Mus musculus,GSE168451,GSM5140561,CEL-Seq2,fastq,SRR13884955,NA,NA,NA,NA,SAMN18205472,NA,NA,NA,NA,NA,NA,NA,NA
Yoshimoto 2022,T6-2 single-cells,NA,tendon,NA,NA,NA,NA,NA,CEL-Seq2,FALSE,TRUE,Mus musculus,GSE168451,GSM5140562,CEL-Seq2,fastq,SRR13884956,NA,NA,NA,NA,SAMN18205470,NA,NA,NA,NA,NA,NA,NA,NA
Yoshimoto 2022,T6-3 single-cells,NA,tendon,NA,NA,NA,NA,NA,CEL-Seq2,FALSE,TRUE,Mus musculus,GSE168451,GSM5140563,CEL-Seq2,fastq,SRR13884957,NA,NA,NA,NA,SAMN18205468,NA,NA,NA,NA,NA,NA,NA,NA
Yoshimoto 2022,T9-1 single-cells,NA,tendon,NA,NA,NA,NA,NA,CEL-Seq2,FALSE,TRUE,Mus musculus,GSE168451,GSM5140564,CEL-Seq2,fastq,SRR13884958,NA,NA,NA,NA,SAMN18205466,NA,NA,NA,NA,NA,NA,NA,NA
Yoshimoto 2022,T9-2 single-cells,NA,tendon,NA,NA,NA,NA,NA,CEL-Seq2,FALSE,TRUE,Mus musculus,GSE168451,GSM5140565,CEL-Seq2,fastq,SRR13884959,NA,NA,NA,NA,SAMN18205492,NA,NA,NA,NA,NA,NA,NA,NA
Yoshimoto 2022,T9-3 single-cells,NA,tendon,NA,NA,NA,NA,NA,CEL-Seq2,FALSE,TRUE,Mus musculus,GSE168451,GSM5140566,CEL-Seq2,fastq,SRR13884960,NA,NA,NA,NA,SAMN18205491,NA,NA,NA,NA,NA,NA,NA,NA
Fang 2022,Enthesis Gli1 P7,NA,tendon,enthesis,NA,NA,NA,NA,Read count too low,FALSE,TRUE,Mus musculus,GSE182997,GSM5548419,3p_v3,bam,SRR15663755,NA,SRX11960621,NA,NA,SAMN21032473,NA,NA,NA,NA,NA,NA,NA,NA
Fang 2022,Enthesis Gli1 P11,NA,tendon,enthesis,NA,NA,NA,NA,Read count too low,FALSE,TRUE,Mus musculus,GSE182997,GSM5548420,3p_v3,bam,SRR15663756,NA,SRX11960622,NA,NA,SAMN21032474,NA,NA,NA,NA,NA,NA,NA,NA
Fang 2022,Enthesis Gli1 P14,NA,tendon,enthesis,NA,NA,NA,NA,Read count too low,FALSE,TRUE,Mus musculus,GSE182997,GSM5548421,3p_v3,bam,SRR15663757,NA,SRX11960623,NA,NA,SAMN21032475,NA,NA,NA,NA,NA,NA,NA,NA
Fang 2022,Enthesis Gli1 P18,NA,tendon,enthesis,NA,NA,NA,NA,Read count too low,FALSE,TRUE,Mus musculus,GSE182997,GSM5548422,3p_v3,bam,SRR15663758,NA,SRX11960624,NA,NA,SAMN21032476,NA,NA,NA,NA,NA,NA,NA,NA
Fang 2022,Enthesis Gli1 P21,NA,tendon,enthesis,NA,NA,NA,NA,Read count too low,FALSE,TRUE,Mus musculus,GSE182997,GSM5548423,3p_v3,bam,SRR15663759,NA,SRX11960625,NA,NA,SAMN21032477,NA,NA,NA,NA,NA,NA,NA,NA
Fang 2022,Enthesis Gli1 P28,NA,tendon,enthesis,NA,NA,NA,NA,Read count too low,FALSE,TRUE,Mus musculus,GSE182997,GSM5548424,3p_v3,bam,SRR15663760,NA,SRX11960626,NA,NA,SAMN21032478,NA,NA,NA,NA,NA,NA,NA,NA
Fang 2022,Enthesis Gli1 P42,NA,tendon,enthesis,NA,NA,NA,NA,Read count too low,FALSE,TRUE,Mus musculus,GSE182997,GSM5548425,3p_v3,bam,SRR15663761,NA,SRX11960627,NA,NA,SAMN21032479,NA,NA,NA,NA,NA,NA,NA,NA
Barruet 2020,NA,NA,tendon,NA,NA,NA,NA,NA,NA,FALSE,TRUE,Homo sapiens,NA,NA,NA,fastq,NA,NA,NA,NA,NA,NA,NA,NA,"Akbar et al, PNAS, 2021",NA,https://pubmed.ncbi.nlm.nih.gov/34544860/,NA,NA,NA
Xu 2021,NA,NA,tendon,NA,NA,NA,NA,NA,NA,FALSE,TRUE,Mus musculus,NA,NA,NA,fastq,NA,NA,NA,NA,NA,NA,NA,Couldn't find data availability info,"Kendal et al, Sci Rep, 2020",NA,https://pubmed.ncbi.nlm.nih.gov/32883960/,NA,NA,NA
Garcia-Melchor 2021,NA,NA,tendon,NA,NA,NA,NA,NA,NA,FALSE,TRUE,Homo sapiens,NA,NA,NA,fastq,NA,NA,NA,NA,NA,NA,NA,Data available upon request (neal.millar@glasgow.ac.uk),"Garcia-Melchor et al, Ann Rheum Dis, 2021",NA,https://pubmed.ncbi.nlm.nih.gov/33692018/,NA,NA,NA
Sorkin 2020,HODay0replicate1,Day 0 A partial-thickness scald burn injury was administered to animals  cells recruited to injury site at day 0,tendon,NA,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE126060,GSM3589975,3p_v2,bam,SRR10350308,NA,SRX7060062,SRP183505,SRS5575536,SAMN13117879,NA,NA,"Sorkin et al, Nature Communications, 2020",10.1038/s41467-019-14172-4,https://pubmed.ncbi.nlm.nih.gov/32024825/,Illumina HiSeq 4000,Role of myeloid cells in heterotopic ossification (HO) in a burn and incision-induced mouse model,"Despite the high frequency of musculoskeletal extremity trauma, little is known about the dynamics of the initial inflammatory response that can result in pathologic healing. Here, we assess the circulatory monocyte/macrophage recruitment to sites of pathologic extremity wound healing as seen with heterotopic ossification (HO). Using single cell transcriptome analyses at key time points, we identify distinct monocyte/macrophage subpopulations that are recruited to the site of HO formation and contribute to ectopic bone development through varied transforming growth factor-1 (Tgfb1) expression. Monocyte/macrophage specific deletion of Tgfb1 leads to altered function of macrophages and reduced HO. We further identify CD47 as a novel target for Tgfb1 regulation on monocytes/macrophages as CD47 activation leads to decreased expression of Tgfb1 in macrophages and systemic treatment with CD47 activating peptide results in attenuation of canonical TGFB1 signaling and HO. These findings elucidate the critical role of monocytes/macrophage subpopulations in aberrant wound healing and provide a novel therapeutic avenue. Overall design: We have used 10x Genomics to perform single cell sequencing on HO cells"
Sorkin 2020,HODay0replicate2,Day 7 A partial-thickness scald burn injury was administered to animals  cells recruited to injury site at day 7,tendon,NA,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE126060,GSM3589976,3p_v2,bam,SRR10350309,NA,SRX7060063,SRP183505,SRS5575537,SAMN13117878,NA,NA,"Sorkin et al, Nature Communications, 2020",10.1038/s41467-019-14172-4,https://pubmed.ncbi.nlm.nih.gov/32024825/,Illumina HiSeq 4000,Role of myeloid cells in heterotopic ossification (HO) in a burn and incision-induced mouse model,"Despite the high frequency of musculoskeletal extremity trauma, little is known about the dynamics of the initial inflammatory response that can result in pathologic healing. Here, we assess the circulatory monocyte/macrophage recruitment to sites of pathologic extremity wound healing as seen with heterotopic ossification (HO). Using single cell transcriptome analyses at key time points, we identify distinct monocyte/macrophage subpopulations that are recruited to the site of HO formation and contribute to ectopic bone development through varied transforming growth factor-1 (Tgfb1) expression. Monocyte/macrophage specific deletion of Tgfb1 leads to altered function of macrophages and reduced HO. We further identify CD47 as a novel target for Tgfb1 regulation on monocytes/macrophages as CD47 activation leads to decreased expression of Tgfb1 in macrophages and systemic treatment with CD47 activating peptide results in attenuation of canonical TGFB1 signaling and HO. These findings elucidate the critical role of monocytes/macrophage subpopulations in aberrant wound healing and provide a novel therapeutic avenue. Overall design: We have used 10x Genomics to perform single cell sequencing on HO cells"
Sorkin 2020,HODay0replicate3,Day 21 A partial-thickness scald burn injury was administered to animals  cells recruited to injury site at day 21,tendon,NA,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE126060,GSM3589977,3p_v2,bam,SRR10350310,NA,SRX7060064,SRP183505,SRS5575538,SAMN13117877,NA,NA,"Sorkin et al, Nature Communications, 2020",10.1038/s41467-019-14172-4,https://pubmed.ncbi.nlm.nih.gov/32024825/,Illumina HiSeq 4000,Role of myeloid cells in heterotopic ossification (HO) in a burn and incision-induced mouse model,"Despite the high frequency of musculoskeletal extremity trauma, little is known about the dynamics of the initial inflammatory response that can result in pathologic healing. Here, we assess the circulatory monocyte/macrophage recruitment to sites of pathologic extremity wound healing as seen with heterotopic ossification (HO). Using single cell transcriptome analyses at key time points, we identify distinct monocyte/macrophage subpopulations that are recruited to the site of HO formation and contribute to ectopic bone development through varied transforming growth factor-1 (Tgfb1) expression. Monocyte/macrophage specific deletion of Tgfb1 leads to altered function of macrophages and reduced HO. We further identify CD47 as a novel target for Tgfb1 regulation on monocytes/macrophages as CD47 activation leads to decreased expression of Tgfb1 in macrophages and systemic treatment with CD47 activating peptide results in attenuation of canonical TGFB1 signaling and HO. These findings elucidate the critical role of monocytes/macrophage subpopulations in aberrant wound healing and provide a novel therapeutic avenue. Overall design: We have used 10x Genomics to perform single cell sequencing on HO cells"
Sorkin 2020,HODay3replicate1,CD47 treated A partial-thickness scald burn injury was administered to animals; CD47 activating peptide (10mg/kg i.p. daily) treated 3 days prior to injury and 3 days after injury.  cells recruited to injury site,tendon,NA,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE126060,GSM3589978,3p_v2,bam,SRR10350311,NA,SRX7060065,SRP183505,SRS5575539,SAMN13117876,NA,NA,"Sorkin et al, Nature Communications, 2020",10.1038/s41467-019-14172-4,https://pubmed.ncbi.nlm.nih.gov/32024825/,Illumina HiSeq 4000,Role of myeloid cells in heterotopic ossification (HO) in a burn and incision-induced mouse model,"Despite the high frequency of musculoskeletal extremity trauma, little is known about the dynamics of the initial inflammatory response that can result in pathologic healing. Here, we assess the circulatory monocyte/macrophage recruitment to sites of pathologic extremity wound healing as seen with heterotopic ossification (HO). Using single cell transcriptome analyses at key time points, we identify distinct monocyte/macrophage subpopulations that are recruited to the site of HO formation and contribute to ectopic bone development through varied transforming growth factor-1 (Tgfb1) expression. Monocyte/macrophage specific deletion of Tgfb1 leads to altered function of macrophages and reduced HO. We further identify CD47 as a novel target for Tgfb1 regulation on monocytes/macrophages as CD47 activation leads to decreased expression of Tgfb1 in macrophages and systemic treatment with CD47 activating peptide results in attenuation of canonical TGFB1 signaling and HO. These findings elucidate the critical role of monocytes/macrophage subpopulations in aberrant wound healing and provide a novel therapeutic avenue. Overall design: We have used 10x Genomics to perform single cell sequencing on HO cells"
Sorkin 2020,HODay3replicate2,Tenotomy site of a burn/tenotomy mouse A partial-thickness scald burn injury was administered to animals cells recruited to injury site at day 0 ,tendon,NA,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE126060,GSM3589979,3p_v2,bam,SRR8528186,NA,SRX5330770,SRP183505,SRS4325090,SAMN10869541,NA,NA,"Sorkin et al, Nature Communications, 2020",10.1038/s41467-019-14172-4,https://pubmed.ncbi.nlm.nih.gov/32024825/,Illumina HiSeq 4000,Role of myeloid cells in heterotopic ossification (HO) in a burn and incision-induced mouse model,"Despite the high frequency of musculoskeletal extremity trauma, little is known about the dynamics of the initial inflammatory response that can result in pathologic healing. Here, we assess the circulatory monocyte/macrophage recruitment to sites of pathologic extremity wound healing as seen with heterotopic ossification (HO). Using single cell transcriptome analyses at key time points, we identify distinct monocyte/macrophage subpopulations that are recruited to the site of HO formation and contribute to ectopic bone development through varied transforming growth factor-1 (Tgfb1) expression. Monocyte/macrophage specific deletion of Tgfb1 leads to altered function of macrophages and reduced HO. We further identify CD47 as a novel target for Tgfb1 regulation on monocytes/macrophages as CD47 activation leads to decreased expression of Tgfb1 in macrophages and systemic treatment with CD47 activating peptide results in attenuation of canonical TGFB1 signaling and HO. These findings elucidate the critical role of monocytes/macrophage subpopulations in aberrant wound healing and provide a novel therapeutic avenue. Overall design: We have used 10x Genomics to perform single cell sequencing on HO cells"
Sorkin 2020,HODay3replicate3,Tenotomy site of a burn/tenotomy mouse A partial-thickness scald burn injury was administered to animals cells recruited to injury site at day 0 ,tendon,NA,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE126060,GSM3589980,3p_v2,bam,SRR8528187,NA,SRX5330771,SRP183505,SRS4325091,SAMN10869540,NA,NA,"Sorkin et al, Nature Communications, 2020",10.1038/s41467-019-14172-4,https://pubmed.ncbi.nlm.nih.gov/32024825/,Illumina HiSeq 4000,Role of myeloid cells in heterotopic ossification (HO) in a burn and incision-induced mouse model,"Despite the high frequency of musculoskeletal extremity trauma, little is known about the dynamics of the initial inflammatory response that can result in pathologic healing. Here, we assess the circulatory monocyte/macrophage recruitment to sites of pathologic extremity wound healing as seen with heterotopic ossification (HO). Using single cell transcriptome analyses at key time points, we identify distinct monocyte/macrophage subpopulations that are recruited to the site of HO formation and contribute to ectopic bone development through varied transforming growth factor-1 (Tgfb1) expression. Monocyte/macrophage specific deletion of Tgfb1 leads to altered function of macrophages and reduced HO. We further identify CD47 as a novel target for Tgfb1 regulation on monocytes/macrophages as CD47 activation leads to decreased expression of Tgfb1 in macrophages and systemic treatment with CD47 activating peptide results in attenuation of canonical TGFB1 signaling and HO. These findings elucidate the critical role of monocytes/macrophage subpopulations in aberrant wound healing and provide a novel therapeutic avenue. Overall design: We have used 10x Genomics to perform single cell sequencing on HO cells"
Sorkin 2020,HODay7replicate1,Tenotomy site of a burn/tenotomy mouse A partial-thickness scald burn injury was administered to animals cells recruited to injury site at day 0 ,tendon,NA,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE126060,GSM3589981,3p_v2,bam,SRR8528188,NA,SRX5330772,SRP183505,SRS4325092,SAMN10869539,NA,NA,"Sorkin et al, Nature Communications, 2020",10.1038/s41467-019-14172-4,https://pubmed.ncbi.nlm.nih.gov/32024825/,Illumina HiSeq 4000,Role of myeloid cells in heterotopic ossification (HO) in a burn and incision-induced mouse model,"Despite the high frequency of musculoskeletal extremity trauma, little is known about the dynamics of the initial inflammatory response that can result in pathologic healing. Here, we assess the circulatory monocyte/macrophage recruitment to sites of pathologic extremity wound healing as seen with heterotopic ossification (HO). Using single cell transcriptome analyses at key time points, we identify distinct monocyte/macrophage subpopulations that are recruited to the site of HO formation and contribute to ectopic bone development through varied transforming growth factor-1 (Tgfb1) expression. Monocyte/macrophage specific deletion of Tgfb1 leads to altered function of macrophages and reduced HO. We further identify CD47 as a novel target for Tgfb1 regulation on monocytes/macrophages as CD47 activation leads to decreased expression of Tgfb1 in macrophages and systemic treatment with CD47 activating peptide results in attenuation of canonical TGFB1 signaling and HO. These findings elucidate the critical role of monocytes/macrophage subpopulations in aberrant wound healing and provide a novel therapeutic avenue. Overall design: We have used 10x Genomics to perform single cell sequencing on HO cells"
Sorkin 2020,HODay7replicate2,Tenotomy site of a burn/tenotomy mouse A partial-thickness scald burn injury was administered to animals cells recruited to injury site at day 3 ,tendon,NA,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE126060,GSM3589982,3p_v2,bam,SRR8528189,NA,SRX5330773,SRP183505,SRS4325093,SAMN10869538,NA,NA,"Sorkin et al, Nature Communications, 2020",10.1038/s41467-019-14172-4,https://pubmed.ncbi.nlm.nih.gov/32024825/,Illumina HiSeq 4000,Role of myeloid cells in heterotopic ossification (HO) in a burn and incision-induced mouse model,"Despite the high frequency of musculoskeletal extremity trauma, little is known about the dynamics of the initial inflammatory response that can result in pathologic healing. Here, we assess the circulatory monocyte/macrophage recruitment to sites of pathologic extremity wound healing as seen with heterotopic ossification (HO). Using single cell transcriptome analyses at key time points, we identify distinct monocyte/macrophage subpopulations that are recruited to the site of HO formation and contribute to ectopic bone development through varied transforming growth factor-1 (Tgfb1) expression. Monocyte/macrophage specific deletion of Tgfb1 leads to altered function of macrophages and reduced HO. We further identify CD47 as a novel target for Tgfb1 regulation on monocytes/macrophages as CD47 activation leads to decreased expression of Tgfb1 in macrophages and systemic treatment with CD47 activating peptide results in attenuation of canonical TGFB1 signaling and HO. These findings elucidate the critical role of monocytes/macrophage subpopulations in aberrant wound healing and provide a novel therapeutic avenue. Overall design: We have used 10x Genomics to perform single cell sequencing on HO cells"
Sorkin 2020,HODay7replicate3,Tenotomy site of a burn/tenotomy mouse A partial-thickness scald burn injury was administered to animals cells recruited to injury site at day 3 ,tendon,NA,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE126060,GSM3589983,3p_v2,bam,SRR8528190,NA,SRX5330774,SRP183505,SRS4325094,SAMN10869537,NA,NA,"Sorkin et al, Nature Communications, 2020",10.1038/s41467-019-14172-4,https://pubmed.ncbi.nlm.nih.gov/32024825/,Illumina HiSeq 4000,Role of myeloid cells in heterotopic ossification (HO) in a burn and incision-induced mouse model,"Despite the high frequency of musculoskeletal extremity trauma, little is known about the dynamics of the initial inflammatory response that can result in pathologic healing. Here, we assess the circulatory monocyte/macrophage recruitment to sites of pathologic extremity wound healing as seen with heterotopic ossification (HO). Using single cell transcriptome analyses at key time points, we identify distinct monocyte/macrophage subpopulations that are recruited to the site of HO formation and contribute to ectopic bone development through varied transforming growth factor-1 (Tgfb1) expression. Monocyte/macrophage specific deletion of Tgfb1 leads to altered function of macrophages and reduced HO. We further identify CD47 as a novel target for Tgfb1 regulation on monocytes/macrophages as CD47 activation leads to decreased expression of Tgfb1 in macrophages and systemic treatment with CD47 activating peptide results in attenuation of canonical TGFB1 signaling and HO. These findings elucidate the critical role of monocytes/macrophage subpopulations in aberrant wound healing and provide a novel therapeutic avenue. Overall design: We have used 10x Genomics to perform single cell sequencing on HO cells"
Sorkin 2020,HODay21replicate1,Tenotomy site of a burn/tenotomy mouse A partial-thickness scald burn injury was administered to animals cells recruited to injury site at day 3 ,tendon,NA,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE126060,GSM3589984,3p_v2,bam,SRR8528191,NA,SRX5330775,SRP183505,SRS4325095,SAMN10869536,NA,NA,"Sorkin et al, Nature Communications, 2020",10.1038/s41467-019-14172-4,https://pubmed.ncbi.nlm.nih.gov/32024825/,Illumina HiSeq 4000,Role of myeloid cells in heterotopic ossification (HO) in a burn and incision-induced mouse model,"Despite the high frequency of musculoskeletal extremity trauma, little is known about the dynamics of the initial inflammatory response that can result in pathologic healing. Here, we assess the circulatory monocyte/macrophage recruitment to sites of pathologic extremity wound healing as seen with heterotopic ossification (HO). Using single cell transcriptome analyses at key time points, we identify distinct monocyte/macrophage subpopulations that are recruited to the site of HO formation and contribute to ectopic bone development through varied transforming growth factor-1 (Tgfb1) expression. Monocyte/macrophage specific deletion of Tgfb1 leads to altered function of macrophages and reduced HO. We further identify CD47 as a novel target for Tgfb1 regulation on monocytes/macrophages as CD47 activation leads to decreased expression of Tgfb1 in macrophages and systemic treatment with CD47 activating peptide results in attenuation of canonical TGFB1 signaling and HO. These findings elucidate the critical role of monocytes/macrophage subpopulations in aberrant wound healing and provide a novel therapeutic avenue. Overall design: We have used 10x Genomics to perform single cell sequencing on HO cells"
Sorkin 2020,HODay21replicate2,Tenotomy site of a burn/tenotomy mouse A partial-thickness scald burn injury was administered to animals cells recruited to injury site at day 7 ,tendon,NA,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE126060,GSM3589985,3p_v2,bam,SRR8528192,NA,SRX5330776,SRP183505,SRS4325096,SAMN10869535,NA,NA,"Sorkin et al, Nature Communications, 2020",10.1038/s41467-019-14172-4,https://pubmed.ncbi.nlm.nih.gov/32024825/,Illumina HiSeq 4000,Role of myeloid cells in heterotopic ossification (HO) in a burn and incision-induced mouse model,"Despite the high frequency of musculoskeletal extremity trauma, little is known about the dynamics of the initial inflammatory response that can result in pathologic healing. Here, we assess the circulatory monocyte/macrophage recruitment to sites of pathologic extremity wound healing as seen with heterotopic ossification (HO). Using single cell transcriptome analyses at key time points, we identify distinct monocyte/macrophage subpopulations that are recruited to the site of HO formation and contribute to ectopic bone development through varied transforming growth factor-1 (Tgfb1) expression. Monocyte/macrophage specific deletion of Tgfb1 leads to altered function of macrophages and reduced HO. We further identify CD47 as a novel target for Tgfb1 regulation on monocytes/macrophages as CD47 activation leads to decreased expression of Tgfb1 in macrophages and systemic treatment with CD47 activating peptide results in attenuation of canonical TGFB1 signaling and HO. These findings elucidate the critical role of monocytes/macrophage subpopulations in aberrant wound healing and provide a novel therapeutic avenue. Overall design: We have used 10x Genomics to perform single cell sequencing on HO cells"
Sorkin 2020,HODay21replicate3,Tenotomy site of a burn/tenotomy mouse A partial-thickness scald burn injury was administered to animals cells recruited to injury site at day 7 ,tendon,NA,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE126060,GSM3589986,3p_v2,bam,SRR8528193,NA,SRX5330777,SRP183505,SRS4325097,SAMN10869534,NA,NA,"Sorkin et al, Nature Communications, 2020",10.1038/s41467-019-14172-4,https://pubmed.ncbi.nlm.nih.gov/32024825/,Illumina HiSeq 4000,Role of myeloid cells in heterotopic ossification (HO) in a burn and incision-induced mouse model,"Despite the high frequency of musculoskeletal extremity trauma, little is known about the dynamics of the initial inflammatory response that can result in pathologic healing. Here, we assess the circulatory monocyte/macrophage recruitment to sites of pathologic extremity wound healing as seen with heterotopic ossification (HO). Using single cell transcriptome analyses at key time points, we identify distinct monocyte/macrophage subpopulations that are recruited to the site of HO formation and contribute to ectopic bone development through varied transforming growth factor-1 (Tgfb1) expression. Monocyte/macrophage specific deletion of Tgfb1 leads to altered function of macrophages and reduced HO. We further identify CD47 as a novel target for Tgfb1 regulation on monocytes/macrophages as CD47 activation leads to decreased expression of Tgfb1 in macrophages and systemic treatment with CD47 activating peptide results in attenuation of canonical TGFB1 signaling and HO. These findings elucidate the critical role of monocytes/macrophage subpopulations in aberrant wound healing and provide a novel therapeutic avenue. Overall design: We have used 10x Genomics to perform single cell sequencing on HO cells"
Sorkin 2020,HO_CD47_treatedreplicate1,Tenotomy site of a burn/tenotomy mouse A partial-thickness scald burn injury was administered to animals cells recruited to injury site at day 7 ,tendon,NA,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE126060,GSM3589987,3p_v2,bam,SRR8528194,NA,SRX5330778,SRP183505,SRS4325098,SAMN10869533,NA,NA,"Sorkin et al, Nature Communications, 2020",10.1038/s41467-019-14172-4,https://pubmed.ncbi.nlm.nih.gov/32024825/,Illumina HiSeq 4000,Role of myeloid cells in heterotopic ossification (HO) in a burn and incision-induced mouse model,"Despite the high frequency of musculoskeletal extremity trauma, little is known about the dynamics of the initial inflammatory response that can result in pathologic healing. Here, we assess the circulatory monocyte/macrophage recruitment to sites of pathologic extremity wound healing as seen with heterotopic ossification (HO). Using single cell transcriptome analyses at key time points, we identify distinct monocyte/macrophage subpopulations that are recruited to the site of HO formation and contribute to ectopic bone development through varied transforming growth factor-1 (Tgfb1) expression. Monocyte/macrophage specific deletion of Tgfb1 leads to altered function of macrophages and reduced HO. We further identify CD47 as a novel target for Tgfb1 regulation on monocytes/macrophages as CD47 activation leads to decreased expression of Tgfb1 in macrophages and systemic treatment with CD47 activating peptide results in attenuation of canonical TGFB1 signaling and HO. These findings elucidate the critical role of monocytes/macrophage subpopulations in aberrant wound healing and provide a novel therapeutic avenue. Overall design: We have used 10x Genomics to perform single cell sequencing on HO cells"
Sorkin 2020,HO_CD47_treatedreplicate2,Tenotomy site of a burn/tenotomy mouse A partial-thickness scald burn injury was administered to animals cells recruited to injury site at day 21 ,tendon,NA,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE126060,GSM3589988,3p_v2,bam,SRR8528195,NA,SRX5330779,SRP183505,SRS4325099,SAMN10869532,NA,NA,"Sorkin et al, Nature Communications, 2020",10.1038/s41467-019-14172-4,https://pubmed.ncbi.nlm.nih.gov/32024825/,Illumina HiSeq 4000,Role of myeloid cells in heterotopic ossification (HO) in a burn and incision-induced mouse model,"Despite the high frequency of musculoskeletal extremity trauma, little is known about the dynamics of the initial inflammatory response that can result in pathologic healing. Here, we assess the circulatory monocyte/macrophage recruitment to sites of pathologic extremity wound healing as seen with heterotopic ossification (HO). Using single cell transcriptome analyses at key time points, we identify distinct monocyte/macrophage subpopulations that are recruited to the site of HO formation and contribute to ectopic bone development through varied transforming growth factor-1 (Tgfb1) expression. Monocyte/macrophage specific deletion of Tgfb1 leads to altered function of macrophages and reduced HO. We further identify CD47 as a novel target for Tgfb1 regulation on monocytes/macrophages as CD47 activation leads to decreased expression of Tgfb1 in macrophages and systemic treatment with CD47 activating peptide results in attenuation of canonical TGFB1 signaling and HO. These findings elucidate the critical role of monocytes/macrophage subpopulations in aberrant wound healing and provide a novel therapeutic avenue. Overall design: We have used 10x Genomics to perform single cell sequencing on HO cells"
Sorkin 2020,HO_CD47_treatedreplicate3,Tenotomy site of a burn/tenotomy mouse A partial-thickness scald burn injury was administered to animals cells recruited to injury site at day 21 ,tendon,NA,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE126060,GSM3589989,3p_v2,bam,SRR8528196,NA,SRX5330780,SRP183505,SRS4325100,SAMN10869531,NA,NA,"Sorkin et al, Nature Communications, 2020",10.1038/s41467-019-14172-4,https://pubmed.ncbi.nlm.nih.gov/32024825/,Illumina HiSeq 4000,Role of myeloid cells in heterotopic ossification (HO) in a burn and incision-induced mouse model,"Despite the high frequency of musculoskeletal extremity trauma, little is known about the dynamics of the initial inflammatory response that can result in pathologic healing. Here, we assess the circulatory monocyte/macrophage recruitment to sites of pathologic extremity wound healing as seen with heterotopic ossification (HO). Using single cell transcriptome analyses at key time points, we identify distinct monocyte/macrophage subpopulations that are recruited to the site of HO formation and contribute to ectopic bone development through varied transforming growth factor-1 (Tgfb1) expression. Monocyte/macrophage specific deletion of Tgfb1 leads to altered function of macrophages and reduced HO. We further identify CD47 as a novel target for Tgfb1 regulation on monocytes/macrophages as CD47 activation leads to decreased expression of Tgfb1 in macrophages and systemic treatment with CD47 activating peptide results in attenuation of canonical TGFB1 signaling and HO. These findings elucidate the critical role of monocytes/macrophage subpopulations in aberrant wound healing and provide a novel therapeutic avenue. Overall design: We have used 10x Genomics to perform single cell sequencing on HO cells"
Sorkin 2020,HODay0replicate4,Tenotomy site of a burn/tenotomy mouse A partial-thickness scald burn injury was administered to animals cells recruited to injury site at day 21 ,tendon,NA,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE126060,GSM4141558,3p_v2,bam,SRR8528197,NA,SRX5330781,SRP183505,SRS4325101,SAMN10869530,NA,NA,"Sorkin et al, Nature Communications, 2020",10.1038/s41467-019-14172-4,https://pubmed.ncbi.nlm.nih.gov/32024825/,Illumina HiSeq 4000,Role of myeloid cells in heterotopic ossification (HO) in a burn and incision-induced mouse model,"Despite the high frequency of musculoskeletal extremity trauma, little is known about the dynamics of the initial inflammatory response that can result in pathologic healing. Here, we assess the circulatory monocyte/macrophage recruitment to sites of pathologic extremity wound healing as seen with heterotopic ossification (HO). Using single cell transcriptome analyses at key time points, we identify distinct monocyte/macrophage subpopulations that are recruited to the site of HO formation and contribute to ectopic bone development through varied transforming growth factor-1 (Tgfb1) expression. Monocyte/macrophage specific deletion of Tgfb1 leads to altered function of macrophages and reduced HO. We further identify CD47 as a novel target for Tgfb1 regulation on monocytes/macrophages as CD47 activation leads to decreased expression of Tgfb1 in macrophages and systemic treatment with CD47 activating peptide results in attenuation of canonical TGFB1 signaling and HO. These findings elucidate the critical role of monocytes/macrophage subpopulations in aberrant wound healing and provide a novel therapeutic avenue. Overall design: We have used 10x Genomics to perform single cell sequencing on HO cells"
Sorkin 2020,HODay7replicate4,Tenotomy site of a burn/tenotomy mouse A partial-thickness scald burn injury was administered to animals; CD47 activating peptide (10mg/kg i.p. daily) treated 3 days prior to injury and 3 days after injury. cells recruited to injury site at day 7 ,tendon,NA,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE126060,GSM4141559,3p_v2,bam,SRR8528198,NA,SRX5330782,SRP183505,SRS4325102,SAMN10869529,NA,NA,"Sorkin et al, Nature Communications, 2020",10.1038/s41467-019-14172-4,https://pubmed.ncbi.nlm.nih.gov/32024825/,Illumina HiSeq 4000,Role of myeloid cells in heterotopic ossification (HO) in a burn and incision-induced mouse model,"Despite the high frequency of musculoskeletal extremity trauma, little is known about the dynamics of the initial inflammatory response that can result in pathologic healing. Here, we assess the circulatory monocyte/macrophage recruitment to sites of pathologic extremity wound healing as seen with heterotopic ossification (HO). Using single cell transcriptome analyses at key time points, we identify distinct monocyte/macrophage subpopulations that are recruited to the site of HO formation and contribute to ectopic bone development through varied transforming growth factor-1 (Tgfb1) expression. Monocyte/macrophage specific deletion of Tgfb1 leads to altered function of macrophages and reduced HO. We further identify CD47 as a novel target for Tgfb1 regulation on monocytes/macrophages as CD47 activation leads to decreased expression of Tgfb1 in macrophages and systemic treatment with CD47 activating peptide results in attenuation of canonical TGFB1 signaling and HO. These findings elucidate the critical role of monocytes/macrophage subpopulations in aberrant wound healing and provide a novel therapeutic avenue. Overall design: We have used 10x Genomics to perform single cell sequencing on HO cells"
Sorkin 2020,HODay21replicate4,Tenotomy site of a burn/tenotomy mouse A partial-thickness scald burn injury was administered to animals; CD47 activating peptide (10mg/kg i.p. daily) treated 3 days prior to injury and 3 days after injury. cells recruited to injury site at day 7 ,tendon,NA,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE126060,GSM4141560,3p_v2,bam,SRR8528199,NA,SRX5330783,SRP183505,SRS4325103,SAMN10869528,NA,NA,"Sorkin et al, Nature Communications, 2020",10.1038/s41467-019-14172-4,https://pubmed.ncbi.nlm.nih.gov/32024825/,Illumina HiSeq 4000,Role of myeloid cells in heterotopic ossification (HO) in a burn and incision-induced mouse model,"Despite the high frequency of musculoskeletal extremity trauma, little is known about the dynamics of the initial inflammatory response that can result in pathologic healing. Here, we assess the circulatory monocyte/macrophage recruitment to sites of pathologic extremity wound healing as seen with heterotopic ossification (HO). Using single cell transcriptome analyses at key time points, we identify distinct monocyte/macrophage subpopulations that are recruited to the site of HO formation and contribute to ectopic bone development through varied transforming growth factor-1 (Tgfb1) expression. Monocyte/macrophage specific deletion of Tgfb1 leads to altered function of macrophages and reduced HO. We further identify CD47 as a novel target for Tgfb1 regulation on monocytes/macrophages as CD47 activation leads to decreased expression of Tgfb1 in macrophages and systemic treatment with CD47 activating peptide results in attenuation of canonical TGFB1 signaling and HO. These findings elucidate the critical role of monocytes/macrophage subpopulations in aberrant wound healing and provide a novel therapeutic avenue. Overall design: We have used 10x Genomics to perform single cell sequencing on HO cells"
Sorkin 2020,HO_CD47_treatedreplicate4,Tenotomy site of a burn/tenotomy mouse A partial-thickness scald burn injury was administered to animals; CD47 activating peptide (10mg/kg i.p. daily) treated 3 days prior to injury and 3 days after injury. cells recruited to injury site at day 7 ,tendon,NA,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE126060,GSM4141561,3p_v2,bam,SRR8528200,NA,SRX5330784,SRP183505,SRS4325104,SAMN10869527,NA,NA,"Sorkin et al, Nature Communications, 2020",10.1038/s41467-019-14172-4,https://pubmed.ncbi.nlm.nih.gov/32024825/,Illumina HiSeq 4000,Role of myeloid cells in heterotopic ossification (HO) in a burn and incision-induced mouse model,"Despite the high frequency of musculoskeletal extremity trauma, little is known about the dynamics of the initial inflammatory response that can result in pathologic healing. Here, we assess the circulatory monocyte/macrophage recruitment to sites of pathologic extremity wound healing as seen with heterotopic ossification (HO). Using single cell transcriptome analyses at key time points, we identify distinct monocyte/macrophage subpopulations that are recruited to the site of HO formation and contribute to ectopic bone development through varied transforming growth factor-1 (Tgfb1) expression. Monocyte/macrophage specific deletion of Tgfb1 leads to altered function of macrophages and reduced HO. We further identify CD47 as a novel target for Tgfb1 regulation on monocytes/macrophages as CD47 activation leads to decreased expression of Tgfb1 in macrophages and systemic treatment with CD47 activating peptide results in attenuation of canonical TGFB1 signaling and HO. These findings elucidate the critical role of monocytes/macrophage subpopulations in aberrant wound healing and provide a novel therapeutic avenue. Overall design: We have used 10x Genomics to perform single cell sequencing on HO cells"
De Micheli 2020d,BL6_Ach_1,tendon,tendon,achilles,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE138515,GSM4110112,3p_v3,fastq,SRR10239195,NA,SRX6958376,SRP224632,SRS5485200,SAMN12984496,NA,NA,"De Micheli et al, Am J Physiol Cell Physiol, 2020",10.1152/ajpcell.00372.2020,https://pubmed.ncbi.nlm.nih.gov/32877217/,Illumina HiSeq 2500,Single cell transcriptional atlas of mouse Achilles tendons,We report a single cell transcriptome atlas of Achilles tendon from 6-week-old male C57Bl/6 mice using single cell RNA sequencing. Overall design: The overall objective of the study was to generate an atlas of the distinct cell populations in tendon using single cell RNA sequencing.
De Micheli 2020d,BL6_Ach_2,tendon,tendon,achilles,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE138515,GSM4110113,3p_v3,fastq,SRR10239196,NA,SRX6958377,SRP224632,SRS5485201,SAMN12984380,NA,NA,"De Micheli et al, Am J Physiol Cell Physiol, 2020",10.1152/ajpcell.00372.2020,https://pubmed.ncbi.nlm.nih.gov/32877217/,Illumina HiSeq 2500,Single cell transcriptional atlas of mouse Achilles tendons,We report a single cell transcriptome atlas of Achilles tendon from 6-week-old male C57Bl/6 mice using single cell RNA sequencing. Overall design: The overall objective of the study was to generate an atlas of the distinct cell populations in tendon using single cell RNA sequencing.
De Micheli 2020d,BL6_Ach_3,tendon,tendon,achilles,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE138515,GSM4110114,3p_v3,fastq,SRR10239197,NA,SRX6958378,SRP224632,SRS5485202,SAMN12984498,NA,NA,"De Micheli et al, Am J Physiol Cell Physiol, 2020",10.1152/ajpcell.00372.2020,https://pubmed.ncbi.nlm.nih.gov/32877217/,Illumina HiSeq 2500,Single cell transcriptional atlas of mouse Achilles tendons,We report a single cell transcriptome atlas of Achilles tendon from 6-week-old male C57Bl/6 mice using single cell RNA sequencing. Overall design: The overall objective of the study was to generate an atlas of the distinct cell populations in tendon using single cell RNA sequencing.
De Micheli 2020d,BL6_Ach_4,tendon,tendon,achilles,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE138515,GSM4110115,3p_v3,fastq,SRR10239198,NA,SRX6958375,SRP224632,SRS5485199,SAMN12984497,NA,NA,"De Micheli et al, Am J Physiol Cell Physiol, 2020",10.1152/ajpcell.00372.2020,https://pubmed.ncbi.nlm.nih.gov/32877217/,Illumina HiSeq 2500,Single cell transcriptional atlas of mouse Achilles tendons,We report a single cell transcriptome atlas of Achilles tendon from 6-week-old male C57Bl/6 mice using single cell RNA sequencing. Overall design: The overall objective of the study was to generate an atlas of the distinct cell populations in tendon using single cell RNA sequencing.
Nakajima 2021,1_iPS,"Human iPS cell line, 1231A3",tendon,iPSC,cell,NA,NA,NA,NA,TRUE,TRUE,Homo sapiens,GSE156753,GSM4743488,3p_v3,fastq,SRR12507504,NA,SRX8998538,SRP278617,SRS7251319,SAMN15893659,NA,NA,"Najajima et al, Nature Communications, 20021",10.1038/s41467-021-25328-6,https://pubmed.ncbi.nlm.nih.gov/34408142/,Illumina HiSeq 2500,Grafting induced pluripotent stem cells-derived tenocytes contribute to recovery of motor function after Achilles tendon rupture in rat [single cell RNAseq],"Self-renewal of tendons is rare since the vascular formation inside is extremely poor, thus reconstructive surgery using autologous tendons has been often taken place in the case of severe injury. However, the rate of re-injury after surgery is relatively high, and collection of autologous tendons leads muscle weakness which results in prolonged rehabilitation. Here, we introduce the induced pluripotent stem cells (iPSCs)-based technology aiming at developing a new therapeutic option after tendon injury. We derived tenocytes from human iPSCs by recapitulating the normal progression of step-wise narrowing fate decisions in the vertebrate embryo. We used single-cell RNA sequencing to analyze the developmental trajectory of iPSCs-derived tenocytes. Overall design: Single cell rnaseq analysis of the developmental trajectory of iPSC-derived tenocytes"
Nakajima 2021,2_PSM,iPS-derived presomitic mesoderm,tendon,iPSC,cell,NA,NA,NA,NA,TRUE,TRUE,Homo sapiens,GSE156753,GSM4743489,3p_v3,fastq,SRR12507505,NA,SRX8998539,SRP278617,SRS7251320,SAMN15893658,NA,NA,"Najajima et al, Nature Communications, 20021",10.1038/s41467-021-25328-6,https://pubmed.ncbi.nlm.nih.gov/34408142/,Illumina HiSeq 2500,Grafting induced pluripotent stem cells-derived tenocytes contribute to recovery of motor function after Achilles tendon rupture in rat [single cell RNAseq],"Self-renewal of tendons is rare since the vascular formation inside is extremely poor, thus reconstructive surgery using autologous tendons has been often taken place in the case of severe injury. However, the rate of re-injury after surgery is relatively high, and collection of autologous tendons leads muscle weakness which results in prolonged rehabilitation. Here, we introduce the induced pluripotent stem cells (iPSCs)-based technology aiming at developing a new therapeutic option after tendon injury. We derived tenocytes from human iPSCs by recapitulating the normal progression of step-wise narrowing fate decisions in the vertebrate embryo. We used single-cell RNA sequencing to analyze the developmental trajectory of iPSCs-derived tenocytes. Overall design: Single cell rnaseq analysis of the developmental trajectory of iPSC-derived tenocytes"
Nakajima 2021,3_SM,iPS-derived somitic mesoderm,tendon,iPSC,cell,NA,NA,NA,NA,TRUE,TRUE,Homo sapiens,GSE156753,GSM4743490,3p_v3,fastq,SRR12507506,NA,SRX8998540,SRP278617,SRS7251321,SAMN15893657,NA,NA,"Najajima et al, Nature Communications, 20021",10.1038/s41467-021-25328-6,https://pubmed.ncbi.nlm.nih.gov/34408142/,Illumina HiSeq 2500,Grafting induced pluripotent stem cells-derived tenocytes contribute to recovery of motor function after Achilles tendon rupture in rat [single cell RNAseq],"Self-renewal of tendons is rare since the vascular formation inside is extremely poor, thus reconstructive surgery using autologous tendons has been often taken place in the case of severe injury. However, the rate of re-injury after surgery is relatively high, and collection of autologous tendons leads muscle weakness which results in prolonged rehabilitation. Here, we introduce the induced pluripotent stem cells (iPSCs)-based technology aiming at developing a new therapeutic option after tendon injury. We derived tenocytes from human iPSCs by recapitulating the normal progression of step-wise narrowing fate decisions in the vertebrate embryo. We used single-cell RNA sequencing to analyze the developmental trajectory of iPSCs-derived tenocytes. Overall design: Single cell rnaseq analysis of the developmental trajectory of iPSC-derived tenocytes"
Nakajima 2021,4_SCL,iPS-derived sclerotome,tendon,iPSC,cell,NA,NA,NA,NA,TRUE,TRUE,Homo sapiens,GSE156753,GSM4743491,3p_v3,fastq,SRR12507507,NA,SRX8998541,SRP278617,SRS7251322,SAMN15893656,NA,NA,"Najajima et al, Nature Communications, 20021",10.1038/s41467-021-25328-6,https://pubmed.ncbi.nlm.nih.gov/34408142/,Illumina HiSeq 2500,Grafting induced pluripotent stem cells-derived tenocytes contribute to recovery of motor function after Achilles tendon rupture in rat [single cell RNAseq],"Self-renewal of tendons is rare since the vascular formation inside is extremely poor, thus reconstructive surgery using autologous tendons has been often taken place in the case of severe injury. However, the rate of re-injury after surgery is relatively high, and collection of autologous tendons leads muscle weakness which results in prolonged rehabilitation. Here, we introduce the induced pluripotent stem cells (iPSCs)-based technology aiming at developing a new therapeutic option after tendon injury. We derived tenocytes from human iPSCs by recapitulating the normal progression of step-wise narrowing fate decisions in the vertebrate embryo. We used single-cell RNA sequencing to analyze the developmental trajectory of iPSCs-derived tenocytes. Overall design: Single cell rnaseq analysis of the developmental trajectory of iPSC-derived tenocytes"
Nakajima 2021,5_SYN_day2,iPS-derived syndetome,tendon,iPSC,cell,NA,NA,NA,NA,TRUE,TRUE,Homo sapiens,GSE156753,GSM4743492,3p_v3,fastq,SRR12507508,NA,SRX8998542,SRP278617,SRS7251323,SAMN15893654,NA,NA,"Najajima et al, Nature Communications, 20021",10.1038/s41467-021-25328-6,https://pubmed.ncbi.nlm.nih.gov/34408142/,Illumina HiSeq 2500,Grafting induced pluripotent stem cells-derived tenocytes contribute to recovery of motor function after Achilles tendon rupture in rat [single cell RNAseq],"Self-renewal of tendons is rare since the vascular formation inside is extremely poor, thus reconstructive surgery using autologous tendons has been often taken place in the case of severe injury. However, the rate of re-injury after surgery is relatively high, and collection of autologous tendons leads muscle weakness which results in prolonged rehabilitation. Here, we introduce the induced pluripotent stem cells (iPSCs)-based technology aiming at developing a new therapeutic option after tendon injury. We derived tenocytes from human iPSCs by recapitulating the normal progression of step-wise narrowing fate decisions in the vertebrate embryo. We used single-cell RNA sequencing to analyze the developmental trajectory of iPSCs-derived tenocytes. Overall design: Single cell rnaseq analysis of the developmental trajectory of iPSC-derived tenocytes"
Nakajima 2021,6_SYN_day4,iPS-derived syndetome,tendon,iPSC,cell,NA,NA,NA,NA,TRUE,TRUE,Homo sapiens,GSE156753,GSM4743493,3p_v3,fastq,SRR12507509,NA,SRX8998543,SRP278617,SRS7251324,SAMN15893652,NA,NA,"Najajima et al, Nature Communications, 20021",10.1038/s41467-021-25328-6,https://pubmed.ncbi.nlm.nih.gov/34408142/,Illumina HiSeq 2500,Grafting induced pluripotent stem cells-derived tenocytes contribute to recovery of motor function after Achilles tendon rupture in rat [single cell RNAseq],"Self-renewal of tendons is rare since the vascular formation inside is extremely poor, thus reconstructive surgery using autologous tendons has been often taken place in the case of severe injury. However, the rate of re-injury after surgery is relatively high, and collection of autologous tendons leads muscle weakness which results in prolonged rehabilitation. Here, we introduce the induced pluripotent stem cells (iPSCs)-based technology aiming at developing a new therapeutic option after tendon injury. We derived tenocytes from human iPSCs by recapitulating the normal progression of step-wise narrowing fate decisions in the vertebrate embryo. We used single-cell RNA sequencing to analyze the developmental trajectory of iPSCs-derived tenocytes. Overall design: Single cell rnaseq analysis of the developmental trajectory of iPSC-derived tenocytes"
Nakajima 2021,7_SYN_day6,iPS-derived syndetome,tendon,iPSC,cell,NA,NA,NA,NA,TRUE,TRUE,Homo sapiens,GSE156753,GSM4743494,3p_v3,fastq,SRR12507510,NA,SRX8998544,SRP278617,SRS7251325,SAMN15893651,NA,NA,"Najajima et al, Nature Communications, 20021",10.1038/s41467-021-25328-6,https://pubmed.ncbi.nlm.nih.gov/34408142/,Illumina HiSeq 2500,Grafting induced pluripotent stem cells-derived tenocytes contribute to recovery of motor function after Achilles tendon rupture in rat [single cell RNAseq],"Self-renewal of tendons is rare since the vascular formation inside is extremely poor, thus reconstructive surgery using autologous tendons has been often taken place in the case of severe injury. However, the rate of re-injury after surgery is relatively high, and collection of autologous tendons leads muscle weakness which results in prolonged rehabilitation. Here, we introduce the induced pluripotent stem cells (iPSCs)-based technology aiming at developing a new therapeutic option after tendon injury. We derived tenocytes from human iPSCs by recapitulating the normal progression of step-wise narrowing fate decisions in the vertebrate embryo. We used single-cell RNA sequencing to analyze the developmental trajectory of iPSCs-derived tenocytes. Overall design: Single cell rnaseq analysis of the developmental trajectory of iPSC-derived tenocytes"
Nakajima 2021,8_SYN_day8,iPS-derived syndetome,tendon,iPSC,cell,NA,NA,NA,NA,TRUE,TRUE,Homo sapiens,GSE156753,GSM4743495,3p_v3,fastq,SRR12507511,NA,SRX8998545,SRP278617,SRS7251326,SAMN15893650,NA,NA,"Najajima et al, Nature Communications, 20021",10.1038/s41467-021-25328-6,https://pubmed.ncbi.nlm.nih.gov/34408142/,Illumina HiSeq 2500,Grafting induced pluripotent stem cells-derived tenocytes contribute to recovery of motor function after Achilles tendon rupture in rat [single cell RNAseq],"Self-renewal of tendons is rare since the vascular formation inside is extremely poor, thus reconstructive surgery using autologous tendons has been often taken place in the case of severe injury. However, the rate of re-injury after surgery is relatively high, and collection of autologous tendons leads muscle weakness which results in prolonged rehabilitation. Here, we introduce the induced pluripotent stem cells (iPSCs)-based technology aiming at developing a new therapeutic option after tendon injury. We derived tenocytes from human iPSCs by recapitulating the normal progression of step-wise narrowing fate decisions in the vertebrate embryo. We used single-cell RNA sequencing to analyze the developmental trajectory of iPSCs-derived tenocytes. Overall design: Single cell rnaseq analysis of the developmental trajectory of iPSC-derived tenocytes"
Nakajima 2021,9_primary_tenocyte,primary tenocyte,tendon,NA,cell,NA,NA,NA,NA,TRUE,TRUE,Homo sapiens,GSE156753,GSM4743496,3p_v3,fastq,SRR12507512,NA,SRX8998546,SRP278617,SRS7251327,SAMN15893649,NA,NA,"Najajima et al, Nature Communications, 20021",10.1038/s41467-021-25328-6,https://pubmed.ncbi.nlm.nih.gov/34408142/,Illumina HiSeq 2500,Grafting induced pluripotent stem cells-derived tenocytes contribute to recovery of motor function after Achilles tendon rupture in rat [single cell RNAseq],"Self-renewal of tendons is rare since the vascular formation inside is extremely poor, thus reconstructive surgery using autologous tendons has been often taken place in the case of severe injury. However, the rate of re-injury after surgery is relatively high, and collection of autologous tendons leads muscle weakness which results in prolonged rehabilitation. Here, we introduce the induced pluripotent stem cells (iPSCs)-based technology aiming at developing a new therapeutic option after tendon injury. We derived tenocytes from human iPSCs by recapitulating the normal progression of step-wise narrowing fate decisions in the vertebrate embryo. We used single-cell RNA sequencing to analyze the developmental trajectory of iPSCs-derived tenocytes. Overall design: Single cell rnaseq analysis of the developmental trajectory of iPSC-derived tenocytes"
Kult 2021a,E13.5 Sox9+Scx+ attachment progenitors,NA,tendon,NA,cell,NA,NA,NA,issues,TRUE,TRUE,Mus musculus,GSE160090,GSM4859797,3p_v3,fastq,SRR12897911;SRR12897912,NA,NA,NA,NA,NA,NA,NA,"Kult et al, eLife, 2021",10.7554/eLife.55361,https://pubmed.ncbi.nlm.nih.gov/33448926/,NA,NA,NA
Lee 2021,BTS_D7_1,Day 7 post Burn/Tenotomy with sham neurectomy injury site,tendon,achilles,cell,NA,NA,NA,151bp R1; 28bp until poly(T),TRUE,TRUE,Homo sapiens,GSE163446,GSM4979413,3p_v3,fastq,SRR13268672;SRR13268673;SRR13268674;SRR13268675,NA,SRX9698830,SRP298358,SRS7895117,SAMN17106059,NA,NA,"Lee et al, Nature Communications, 2021",10.1038/s41467-021-25143-z,https://pubmed.ncbi.nlm.nih.gov/34400627/,Illumina NovaSeq 6000,scRNA sequencing of cells harvested from the tendon injury site after a severe burn/tenotomy injury with and without sciatic neurectomy,"scRNA sequencing was performed on cells harvested from the injury site of mice that underwent a burn/tenotomy injury with sciatic neurectomy or sham neurectomy (skin incision) to study the role of nerves in the formation of heterotopic ossification and aberrant stem cell differentiation following traumatic injury. Overall design: C57B6 mice received pre-operative treatment with 0.06 mg/kg buprenorphine subcutaneously and were anesthetized with 2% isofluorane inhalation. A 10 mm longitudinal skin incision was made along the medial aspect of the left Achilles tendon. The Achilles tendon was separated from surrounding tissue and dissected at it's midsection. For the sciatic neurectomy, blunt dissection was performed through the biceps femoris to expose the sciatic nerve. The sciatic nerve was transected with reflection and suturing of the proximal nerve stump to the nearby semitendinosus muscle to prevent re-innervation.  As a control, sham nerve injuries consisted of surgical exposure of the sciatic nerve without transection. Incisions were sutured closed with 5-0 Vicryl suture. Tenotomy injury site, consisting of tissue from the Achilles' tendon insertion at the gastrocnemius to the distal tendon enthesis at the calcaneus and surrounding tissue, excluding bone and skin, was harvested 7 days after injury. Tissue samples were digested for 20 minutes in 750U/ml Type 1 Collagenase and 7U/ml Dispase II (Gibco) in Roswell Park Memorial Institute (RPMI) medium at 37C under constant agitation of 160rpm. Digestions were subsequently quenched with 2% FBS in PBS and filtered through 40m sterile strainers. Cells were then washed in 2% FBS in PBS, counted and resuspended at a concentration of 1000-1200 cells/ul. Cell viability was assessed with Trypan blue exclusion on a Countess II (Thermo Fisher Scientific) automated counter and only samples with >85% viability were used for scRNA sequencing. Enough reagent was taken to sequence the transcriptome of 5000 cells according to 10x guidelines. 100,000 remaining cells were used for nuclei isolation according to the 10X Nuclei Isolation for Single Cell ATAC Sequencing protocol (available on their website)."
Lee 2021,BTS_D7_2,Day 7 post Burn/Tenotomy with sham neurectomy injury site,tendon,achilles,cell,NA,NA,NA,151bp R1; 28bp until poly(T),TRUE,TRUE,Homo sapiens,GSE163446,GSM4979414,3p_v3,fastq,SRR13268676;SRR13268677;SRR13268678;SRR13268679,NA,SRX9698831,SRP298358,SRS7895118,SAMN17106058,NA,NA,"Lee et al, Nature Communications, 2021",10.1038/s41467-021-25143-z,https://pubmed.ncbi.nlm.nih.gov/34400627/,Illumina NovaSeq 6000,scRNA sequencing of cells harvested from the tendon injury site after a severe burn/tenotomy injury with and without sciatic neurectomy,"scRNA sequencing was performed on cells harvested from the injury site of mice that underwent a burn/tenotomy injury with sciatic neurectomy or sham neurectomy (skin incision) to study the role of nerves in the formation of heterotopic ossification and aberrant stem cell differentiation following traumatic injury. Overall design: C57B6 mice received pre-operative treatment with 0.06 mg/kg buprenorphine subcutaneously and were anesthetized with 2% isofluorane inhalation. A 10 mm longitudinal skin incision was made along the medial aspect of the left Achilles tendon. The Achilles tendon was separated from surrounding tissue and dissected at it's midsection. For the sciatic neurectomy, blunt dissection was performed through the biceps femoris to expose the sciatic nerve. The sciatic nerve was transected with reflection and suturing of the proximal nerve stump to the nearby semitendinosus muscle to prevent re-innervation.  As a control, sham nerve injuries consisted of surgical exposure of the sciatic nerve without transection. Incisions were sutured closed with 5-0 Vicryl suture. Tenotomy injury site, consisting of tissue from the Achilles' tendon insertion at the gastrocnemius to the distal tendon enthesis at the calcaneus and surrounding tissue, excluding bone and skin, was harvested 7 days after injury. Tissue samples were digested for 20 minutes in 750U/ml Type 1 Collagenase and 7U/ml Dispase II (Gibco) in Roswell Park Memorial Institute (RPMI) medium at 37C under constant agitation of 160rpm. Digestions were subsequently quenched with 2% FBS in PBS and filtered through 40m sterile strainers. Cells were then washed in 2% FBS in PBS, counted and resuspended at a concentration of 1000-1200 cells/ul. Cell viability was assessed with Trypan blue exclusion on a Countess II (Thermo Fisher Scientific) automated counter and only samples with >85% viability were used for scRNA sequencing. Enough reagent was taken to sequence the transcriptome of 5000 cells according to 10x guidelines. 100,000 remaining cells were used for nuclei isolation according to the 10X Nuclei Isolation for Single Cell ATAC Sequencing protocol (available on their website)."
Lee 2021,BTS_D7_3,Day 7 post Burn/Tenotomy with sham neurectomy injury site,tendon,achilles,cell,NA,NA,NA,151bp R1; 28bp until poly(T),TRUE,TRUE,Homo sapiens,GSE163446,GSM4979415,3p_v3,fastq,SRR13268680;SRR13268681;SRR13268682;SRR13268683,NA,SRX9698832,SRP298358,SRS7895119,SAMN17106057,NA,NA,"Lee et al, Nature Communications, 2021",10.1038/s41467-021-25143-z,https://pubmed.ncbi.nlm.nih.gov/34400627/,Illumina NovaSeq 6000,scRNA sequencing of cells harvested from the tendon injury site after a severe burn/tenotomy injury with and without sciatic neurectomy,"scRNA sequencing was performed on cells harvested from the injury site of mice that underwent a burn/tenotomy injury with sciatic neurectomy or sham neurectomy (skin incision) to study the role of nerves in the formation of heterotopic ossification and aberrant stem cell differentiation following traumatic injury. Overall design: C57B6 mice received pre-operative treatment with 0.06 mg/kg buprenorphine subcutaneously and were anesthetized with 2% isofluorane inhalation. A 10 mm longitudinal skin incision was made along the medial aspect of the left Achilles tendon. The Achilles tendon was separated from surrounding tissue and dissected at it's midsection. For the sciatic neurectomy, blunt dissection was performed through the biceps femoris to expose the sciatic nerve. The sciatic nerve was transected with reflection and suturing of the proximal nerve stump to the nearby semitendinosus muscle to prevent re-innervation.  As a control, sham nerve injuries consisted of surgical exposure of the sciatic nerve without transection. Incisions were sutured closed with 5-0 Vicryl suture. Tenotomy injury site, consisting of tissue from the Achilles' tendon insertion at the gastrocnemius to the distal tendon enthesis at the calcaneus and surrounding tissue, excluding bone and skin, was harvested 7 days after injury. Tissue samples were digested for 20 minutes in 750U/ml Type 1 Collagenase and 7U/ml Dispase II (Gibco) in Roswell Park Memorial Institute (RPMI) medium at 37C under constant agitation of 160rpm. Digestions were subsequently quenched with 2% FBS in PBS and filtered through 40m sterile strainers. Cells were then washed in 2% FBS in PBS, counted and resuspended at a concentration of 1000-1200 cells/ul. Cell viability was assessed with Trypan blue exclusion on a Countess II (Thermo Fisher Scientific) automated counter and only samples with >85% viability were used for scRNA sequencing. Enough reagent was taken to sequence the transcriptome of 5000 cells according to 10x guidelines. 100,000 remaining cells were used for nuclei isolation according to the 10X Nuclei Isolation for Single Cell ATAC Sequencing protocol (available on their website)."
Lee 2021,BTN_D7_1,Day 7 post Burn/Tenotomy with neurectomy injury site,tendon,achilles,cell,NA,NA,NA,151bp R1; 28bp until poly(T),TRUE,TRUE,Homo sapiens,GSE163446,GSM4979416,3p_v3,fastq,SRR13268685;SRR13268686;SRR13268687,NA,SRX9698833,SRP298358,SRS7895120,SAMN17106056,NA,NA,"Lee et al, Nature Communications, 2021",10.1038/s41467-021-25143-z,https://pubmed.ncbi.nlm.nih.gov/34400627/,Illumina NovaSeq 6000,scRNA sequencing of cells harvested from the tendon injury site after a severe burn/tenotomy injury with and without sciatic neurectomy,"scRNA sequencing was performed on cells harvested from the injury site of mice that underwent a burn/tenotomy injury with sciatic neurectomy or sham neurectomy (skin incision) to study the role of nerves in the formation of heterotopic ossification and aberrant stem cell differentiation following traumatic injury. Overall design: C57B6 mice received pre-operative treatment with 0.06 mg/kg buprenorphine subcutaneously and were anesthetized with 2% isofluorane inhalation. A 10 mm longitudinal skin incision was made along the medial aspect of the left Achilles tendon. The Achilles tendon was separated from surrounding tissue and dissected at it's midsection. For the sciatic neurectomy, blunt dissection was performed through the biceps femoris to expose the sciatic nerve. The sciatic nerve was transected with reflection and suturing of the proximal nerve stump to the nearby semitendinosus muscle to prevent re-innervation.  As a control, sham nerve injuries consisted of surgical exposure of the sciatic nerve without transection. Incisions were sutured closed with 5-0 Vicryl suture. Tenotomy injury site, consisting of tissue from the Achilles' tendon insertion at the gastrocnemius to the distal tendon enthesis at the calcaneus and surrounding tissue, excluding bone and skin, was harvested 7 days after injury. Tissue samples were digested for 20 minutes in 750U/ml Type 1 Collagenase and 7U/ml Dispase II (Gibco) in Roswell Park Memorial Institute (RPMI) medium at 37C under constant agitation of 160rpm. Digestions were subsequently quenched with 2% FBS in PBS and filtered through 40m sterile strainers. Cells were then washed in 2% FBS in PBS, counted and resuspended at a concentration of 1000-1200 cells/ul. Cell viability was assessed with Trypan blue exclusion on a Countess II (Thermo Fisher Scientific) automated counter and only samples with >85% viability were used for scRNA sequencing. Enough reagent was taken to sequence the transcriptome of 5000 cells according to 10x guidelines. 100,000 remaining cells were used for nuclei isolation according to the 10X Nuclei Isolation for Single Cell ATAC Sequencing protocol (available on their website)."
Lee 2021,BTN_D7_2,Day 7 post Burn/Tenotomy with neurectomy injury site,tendon,achilles,cell,NA,NA,NA,151bp R1; 28bp until poly(T),TRUE,TRUE,Homo sapiens,GSE163446,GSM4979417,3p_v3,fastq,SRR13268688;SRR13268689;SRR13268690;SRR13268691,NA,SRX9698834,SRP298358,SRS7895121,SAMN17106065,NA,NA,"Lee et al, Nature Communications, 2021",10.1038/s41467-021-25143-z,https://pubmed.ncbi.nlm.nih.gov/34400627/,Illumina NovaSeq 6000,scRNA sequencing of cells harvested from the tendon injury site after a severe burn/tenotomy injury with and without sciatic neurectomy,"scRNA sequencing was performed on cells harvested from the injury site of mice that underwent a burn/tenotomy injury with sciatic neurectomy or sham neurectomy (skin incision) to study the role of nerves in the formation of heterotopic ossification and aberrant stem cell differentiation following traumatic injury. Overall design: C57B6 mice received pre-operative treatment with 0.06 mg/kg buprenorphine subcutaneously and were anesthetized with 2% isofluorane inhalation. A 10 mm longitudinal skin incision was made along the medial aspect of the left Achilles tendon. The Achilles tendon was separated from surrounding tissue and dissected at it's midsection. For the sciatic neurectomy, blunt dissection was performed through the biceps femoris to expose the sciatic nerve. The sciatic nerve was transected with reflection and suturing of the proximal nerve stump to the nearby semitendinosus muscle to prevent re-innervation.  As a control, sham nerve injuries consisted of surgical exposure of the sciatic nerve without transection. Incisions were sutured closed with 5-0 Vicryl suture. Tenotomy injury site, consisting of tissue from the Achilles' tendon insertion at the gastrocnemius to the distal tendon enthesis at the calcaneus and surrounding tissue, excluding bone and skin, was harvested 7 days after injury. Tissue samples were digested for 20 minutes in 750U/ml Type 1 Collagenase and 7U/ml Dispase II (Gibco) in Roswell Park Memorial Institute (RPMI) medium at 37C under constant agitation of 160rpm. Digestions were subsequently quenched with 2% FBS in PBS and filtered through 40m sterile strainers. Cells were then washed in 2% FBS in PBS, counted and resuspended at a concentration of 1000-1200 cells/ul. Cell viability was assessed with Trypan blue exclusion on a Countess II (Thermo Fisher Scientific) automated counter and only samples with >85% viability were used for scRNA sequencing. Enough reagent was taken to sequence the transcriptome of 5000 cells according to 10x guidelines. 100,000 remaining cells were used for nuclei isolation according to the 10X Nuclei Isolation for Single Cell ATAC Sequencing protocol (available on their website)."
Lee 2021,BTN_D7_3,Day 7 post Burn/Tenotomy with neurectomy injury site,tendon,achilles,cell,NA,NA,NA,151bp R1; 28bp until poly(T),TRUE,TRUE,Homo sapiens,GSE163446,GSM4979418,3p_v3,fastq,SRR13268692;SRR13268693;SRR13268694;SRR13268695,NA,SRX9698835,SRP298358,SRS7895122,SAMN17106064,NA,NA,"Lee et al, Nature Communications, 2021",10.1038/s41467-021-25143-z,https://pubmed.ncbi.nlm.nih.gov/34400627/,Illumina NovaSeq 6000,scRNA sequencing of cells harvested from the tendon injury site after a severe burn/tenotomy injury with and without sciatic neurectomy,"scRNA sequencing was performed on cells harvested from the injury site of mice that underwent a burn/tenotomy injury with sciatic neurectomy or sham neurectomy (skin incision) to study the role of nerves in the formation of heterotopic ossification and aberrant stem cell differentiation following traumatic injury. Overall design: C57B6 mice received pre-operative treatment with 0.06 mg/kg buprenorphine subcutaneously and were anesthetized with 2% isofluorane inhalation. A 10 mm longitudinal skin incision was made along the medial aspect of the left Achilles tendon. The Achilles tendon was separated from surrounding tissue and dissected at it's midsection. For the sciatic neurectomy, blunt dissection was performed through the biceps femoris to expose the sciatic nerve. The sciatic nerve was transected with reflection and suturing of the proximal nerve stump to the nearby semitendinosus muscle to prevent re-innervation.  As a control, sham nerve injuries consisted of surgical exposure of the sciatic nerve without transection. Incisions were sutured closed with 5-0 Vicryl suture. Tenotomy injury site, consisting of tissue from the Achilles' tendon insertion at the gastrocnemius to the distal tendon enthesis at the calcaneus and surrounding tissue, excluding bone and skin, was harvested 7 days after injury. Tissue samples were digested for 20 minutes in 750U/ml Type 1 Collagenase and 7U/ml Dispase II (Gibco) in Roswell Park Memorial Institute (RPMI) medium at 37C under constant agitation of 160rpm. Digestions were subsequently quenched with 2% FBS in PBS and filtered through 40m sterile strainers. Cells were then washed in 2% FBS in PBS, counted and resuspended at a concentration of 1000-1200 cells/ul. Cell viability was assessed with Trypan blue exclusion on a Countess II (Thermo Fisher Scientific) automated counter and only samples with >85% viability were used for scRNA sequencing. Enough reagent was taken to sequence the transcriptome of 5000 cells according to 10x guidelines. 100,000 remaining cells were used for nuclei isolation according to the 10X Nuclei Isolation for Single Cell ATAC Sequencing protocol (available on their website)."
Fang 2022,Enthesis WT P11,NA,tendon,enthesis,cell,female,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE182997,GSM5548416,3p_v3,bam,SRR15663752,NA,SRX11960618,NA,NA,SAMN21032470,NA,NA,NA,10.1016/j.stem.2022.11.007,https://pubmed.ncbi.nlm.nih.gov/36459968/,NA,NA,NA
Fang 2022,Enthesis WT P18,NA,tendon,enthesis,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE182997,GSM5548417,3p_v3,bam,SRR15663753,NA,SRX11960619,NA,NA,SAMN21032471,NA,NA,NA,10.1016/j.stem.2022.11.007,https://pubmed.ncbi.nlm.nih.gov/36459968/,NA,NA,NA
Fang 2022,Enthesis WT P56,NA,tendon,enthesis,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE182997,GSM5548418,3p_v3,bam,SRR15663754,NA,SRX11960620,NA,NA,SAMN21032472,NA,NA,NA,10.1016/j.stem.2022.11.007,https://pubmed.ncbi.nlm.nih.gov/36459968/,NA,NA,NA
Pagani 2022,Ddr2 slie/slie injured [Day_7_DDR2_sli_injured_S1],NA,tendon,achilles,cell,NA,NA,NA,only getting index reads?,TRUE,TRUE,Mus musculus,GSE212281,GSM6523196,3p_v3,fastq,SRR21307674;SRR21307675,NA,NA,NA,NA,NA,NA,NA,NA,10.1126/sciadv.abq6152,https://pubmed.ncbi.nlm.nih.gov/36542719/,NA,NA,NA
Pagani 2022,Ddr2 slie/slie uninjured [Day_7_DDR2_sli_uninjured_S2],NA,tendon,achilles,cell,NA,NA,NA,only getting index reads?,TRUE,TRUE,Mus musculus,GSE212281,GSM6523197,3p_v3,fastq,SRR21307672;SRR21307673,NA,NA,NA,NA,NA,NA,NA,NA,10.1126/sciadv.abq6152,https://pubmed.ncbi.nlm.nih.gov/36542719/,NA,NA,NA
Pagani 2022,Littermate control injured [Day_7_WT_injured_S3],NA,tendon,achilles,cell,NA,NA,NA,only getting index reads?,TRUE,TRUE,Mus musculus,GSE212281,GSM6523198,3p_v3,fastq,SRR21307670;SRR21307671,NA,NA,NA,NA,NA,NA,NA,NA,10.1126/sciadv.abq6152,https://pubmed.ncbi.nlm.nih.gov/36542719/,NA,NA,NA
Pagani 2022,Littermate control uninjured [Day_7_WT_uninjured_S4],NA,tendon,achilles,cell,NA,NA,NA,only getting index reads?,TRUE,TRUE,Mus musculus,GSE212281,GSM6523199,3p_v3,fastq,SRR21307668;SRR21307669,NA,NA,NA,NA,NA,NA,NA,NA,10.1126/sciadv.abq6152,https://pubmed.ncbi.nlm.nih.gov/36542719/,NA,NA,NA
Korcari 2023,3M Cre+,NA,tendon,flexor digitorus longus,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE214929,GSM6618472,3p_v3,fastq,SRR21831568;SRR21831569,NA,SRX17820727,NA,NA,NA,NA,NA,"Korcari et al, eLife, 2023",10.7554/eLife.84194,https://pubmed.ncbi.nlm.nih.gov/36656751/,NA,NA,NA
Korcari 2023,3M Cre-,NA,tendon,flexor digitorus longus,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE214929,GSM6618473,3p_v3,fastq,SRR21831566;SRR21831567,NA,SRX17820728,NA,NA,NA,NA,NA,"Korcari et al, eLife, 2023",10.7554/eLife.84194,https://pubmed.ncbi.nlm.nih.gov/36656751/,NA,NA,NA
Korcari 2023,21M WT,NA,tendon,flexor digitorus longus,cell,NA,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE214929,GSM6618474,3p_v3,fastq,SRR21831564;SRR21831565,NA,SRX17820729,NA,NA,NA,NA,NA,"Korcari et al, eLife, 2023",10.7554/eLife.84194,https://pubmed.ncbi.nlm.nih.gov/36656751/,NA,NA,NA
Cao 2019,iniG1_rep1,NA,whole,NA,NA,NA,NA,NA,NA,FALSE,TRUE,Ciona intestinalis,GSE131155,GSM3764764,3p_v2,fastq,SRR9050985,NA,SRX5827302,NA,NA,NA,NA,NA,"Cao et al, Nature, 2019",NA,https://pubmed.ncbi.nlm.nih.gov/31292549/,NA,NA,NA
Cao 2019,iniG2_rep2,NA,whole,NA,NA,NA,NA,NA,NA,FALSE,TRUE,Ciona intestinalis,GSE131155,GSM3764765,3p_v2,fastq,SRR9050986,NA,SRX5827303,NA,NA,NA,NA,NA,"Cao et al, Nature, 2019",NA,https://pubmed.ncbi.nlm.nih.gov/31292549/,NA,NA,NA
Cao 2019,midG1_rep1,NA,whole,NA,NA,NA,NA,NA,NA,FALSE,TRUE,Ciona intestinalis,GSE131155,GSM3764766,3p_v2,fastq,SRR9050987,NA,SRX5827304,NA,NA,NA,NA,NA,"Cao et al, Nature, 2019",NA,https://pubmed.ncbi.nlm.nih.gov/31292549/,NA,NA,NA
Cao 2019,midG2_rep2,NA,whole,NA,NA,NA,NA,NA,NA,FALSE,TRUE,Ciona intestinalis,GSE131155,GSM3764767,3p_v2,fastq,SRR9050988,NA,SRX5827305,NA,NA,NA,NA,NA,"Cao et al, Nature, 2019",NA,https://pubmed.ncbi.nlm.nih.gov/31292549/,NA,NA,NA
Cao 2019,earN1_rep1,NA,whole,NA,NA,NA,NA,NA,NA,FALSE,TRUE,Ciona intestinalis,GSE131155,GSM3764768,3p_v2,fastq,SRR9050989,NA,SRX5827306,NA,NA,NA,NA,NA,"Cao et al, Nature, 2019",NA,https://pubmed.ncbi.nlm.nih.gov/31292549/,NA,NA,NA
Cao 2019,earN2_rep2,NA,whole,NA,NA,NA,NA,NA,NA,FALSE,TRUE,Ciona intestinalis,GSE131155,GSM3764769,3p_v2,fastq,SRR9050990,NA,SRX5827307,NA,NA,NA,NA,NA,"Cao et al, Nature, 2019",NA,https://pubmed.ncbi.nlm.nih.gov/31292549/,NA,NA,NA
Cao 2019,latN1_rep1,NA,whole,NA,NA,NA,NA,NA,NA,FALSE,TRUE,Ciona intestinalis,GSE131155,GSM3764770,3p_v2,fastq,SRR9050991,NA,SRX5827308,NA,NA,NA,NA,NA,"Cao et al, Nature, 2019",NA,https://pubmed.ncbi.nlm.nih.gov/31292549/,NA,NA,NA
Cao 2019,latN2_rep2,NA,whole,NA,NA,NA,NA,NA,NA,FALSE,TRUE,Ciona intestinalis,GSE131155,GSM3764771,3p_v2,fastq,SRR9050992,NA,SRX5827309,NA,NA,NA,NA,NA,"Cao et al, Nature, 2019",NA,https://pubmed.ncbi.nlm.nih.gov/31292549/,NA,NA,NA
Cao 2019,iniTI1_rep1,NA,whole,NA,NA,NA,NA,NA,NA,FALSE,TRUE,Ciona intestinalis,GSE131155,GSM3764772,3p_v2,fastq,SRR9050993,NA,SRX5827310,NA,NA,NA,NA,NA,"Cao et al, Nature, 2019",NA,https://pubmed.ncbi.nlm.nih.gov/31292549/,NA,NA,NA
Cao 2019,iniTI2_rep2,NA,whole,NA,NA,NA,NA,NA,NA,FALSE,TRUE,Ciona intestinalis,GSE131155,GSM3764773,3p_v2,fastq,SRR9050994,NA,SRX5827311,NA,NA,NA,NA,NA,"Cao et al, Nature, 2019",NA,https://pubmed.ncbi.nlm.nih.gov/31292549/,NA,NA,NA
Cao 2019,earTI1_rep1,NA,whole,NA,NA,NA,NA,NA,NA,FALSE,TRUE,Ciona intestinalis,GSE131155,GSM3764774,3p_v2,fastq,SRR9050995,NA,SRX5827312,NA,NA,NA,NA,NA,"Cao et al, Nature, 2019",NA,https://pubmed.ncbi.nlm.nih.gov/31292549/,NA,NA,NA
Cao 2019,earTI2_rep2,NA,whole,NA,NA,NA,NA,NA,NA,FALSE,TRUE,Ciona intestinalis,GSE131155,GSM3764775,3p_v2,fastq,SRR9050996,NA,SRX5827313,NA,NA,NA,NA,NA,"Cao et al, Nature, 2019",NA,https://pubmed.ncbi.nlm.nih.gov/31292549/,NA,NA,NA
Cao 2019,midTII1_rep1,NA,whole,NA,NA,NA,NA,NA,NA,FALSE,TRUE,Ciona intestinalis,GSE131155,GSM3764776,3p_v2,fastq,SRR9050997,NA,SRX5827314,NA,NA,NA,NA,NA,"Cao et al, Nature, 2019",NA,https://pubmed.ncbi.nlm.nih.gov/31292549/,NA,NA,NA
Cao 2019,midTII2_rep2,NA,whole,NA,NA,NA,NA,NA,NA,FALSE,TRUE,Ciona intestinalis,GSE131155,GSM3764777,3p_v2,fastq,SRR9050998,NA,SRX5827315,NA,NA,NA,NA,NA,"Cao et al, Nature, 2019",NA,https://pubmed.ncbi.nlm.nih.gov/31292549/,NA,NA,NA
Cao 2019,latTI1a_rep1_tech1,NA,whole,NA,NA,NA,NA,NA,NA,FALSE,TRUE,Ciona intestinalis,GSE131155,GSM3764778,3p_v2,fastq,SRR9050999,NA,SRX5827316,NA,NA,NA,NA,NA,"Cao et al, Nature, 2019",NA,https://pubmed.ncbi.nlm.nih.gov/31292549/,NA,NA,NA
Cao 2019,latTI1b_rep1_tech2,NA,whole,NA,NA,NA,NA,NA,NA,FALSE,TRUE,Ciona intestinalis,GSE131155,GSM3764779,3p_v2,fastq,SRR9051000,NA,SRX5827317,NA,NA,NA,NA,NA,"Cao et al, Nature, 2019",NA,https://pubmed.ncbi.nlm.nih.gov/31292549/,NA,NA,NA
Cao 2019,latTI2_rep2,NA,whole,NA,NA,NA,NA,NA,NA,FALSE,TRUE,Ciona intestinalis,GSE131155,GSM3764780,3p_v2,fastq,SRR9051001,NA,SRX5827318,NA,NA,NA,NA,NA,"Cao et al, Nature, 2019",NA,https://pubmed.ncbi.nlm.nih.gov/31292549/,NA,NA,NA
Cao 2019,latTII1a_rep1_tech1,NA,whole,NA,NA,NA,NA,NA,NA,FALSE,TRUE,Ciona intestinalis,GSE131155,GSM3764781,3p_v2,fastq,SRR9051002,NA,SRX5827319,NA,NA,NA,NA,NA,"Cao et al, Nature, 2019",NA,https://pubmed.ncbi.nlm.nih.gov/31292549/,NA,NA,NA
Cao 2019,latTII1b_rep1_tech2,NA,whole,NA,NA,NA,NA,NA,NA,FALSE,TRUE,Ciona intestinalis,GSE131155,GSM3764782,3p_v2,fastq,SRR9051003,NA,SRX5827320,NA,NA,NA,NA,NA,"Cao et al, Nature, 2019",NA,https://pubmed.ncbi.nlm.nih.gov/31292549/,NA,NA,NA
Cao 2019,latTII2_rep2,NA,whole,NA,NA,NA,NA,NA,NA,FALSE,TRUE,Ciona intestinalis,GSE131155,GSM3764783,3p_v2,fastq,SRR9051004,NA,SRX5827321,NA,NA,NA,NA,NA,"Cao et al, Nature, 2019",NA,https://pubmed.ncbi.nlm.nih.gov/31292549/,NA,NA,NA
Cao 2019,larva1_rep1,NA,whole,NA,NA,NA,NA,NA,NA,FALSE,TRUE,Ciona intestinalis,GSE131155,GSM3764784,3p_v2,fastq,SRR9051005,NA,SRX5827322,NA,NA,NA,NA,NA,"Cao et al, Nature, 2019",NA,https://pubmed.ncbi.nlm.nih.gov/31292549/,NA,NA,NA
Cao 2019,larva2_rep2,NA,whole,NA,NA,NA,NA,NA,NA,FALSE,TRUE,Ciona intestinalis,GSE131155,GSM3764785,3p_v2,fastq,SRR9051006,NA,SRX5827323,NA,NA,NA,NA,NA,"Cao et al, Nature, 2019",NA,https://pubmed.ncbi.nlm.nih.gov/31292549/,NA,NA,NA
Cao 2019,larva3_rep3,NA,whole,NA,NA,NA,NA,NA,need to fix build_ref rule,FALSE,TRUE,Ciona intestinalis,GSE131155,GSM3764786,3p_v2,fastq,SRR9051007,NA,SRX5827324,NA,NA,NA,NA,NA,"Cao et al, Nature, 2019",NA,https://pubmed.ncbi.nlm.nih.gov/31292549/,NA,NA,NA
Ono 2020,Prrx1cre_E115, Prrx1-cre; R26R(tdTomato/+),whole,limb bud,NA,NA,NA,NA,NA,FALSE,TRUE,Mus musculus,GSE144411,GSM4287667,3p_v3,NA,NOT_PUBLIC,NA,NA,NA,NA,SAMN13938142,NA,NA,unpublished,NA,unpublished,NA,NA,NA
Zhao 2021,CT1,From control-diet fed maternal lean mice (CT),whole,embryo,NA,NA,NA,NA,150-by-150 seq lengths; need to update fastq renaming step to accommodate these,FALSE,TRUE,Mus musculus,GSE173994,GSM5284270,3p_v3,NA,SRR14458796,NA,SRX10808926,SRP318759,SRS8894978,SAMN19044146,NA,NA,"Zhao et al, Advanced Science, 2021",NA,https://pubmed.ncbi.nlm.nih.gov/34647690/,Illumina NovaSeq 6000,Transcriptomic analysis of E9.5 mouse embryos,"Obesity impairs the developmental progress and metabolism of the skeletal muscle. Using scRNA-seq, the initial impacts caused by maternal obesity were revealed at the embryonic stage. Overall design: Single-cell transcriptomic profiling of mouse embryos on embryonic 9.5 day."
Zhao 2021,CT2,From control-diet fed maternal lean mice (CT),whole,embryo,NA,NA,NA,NA,150-by-150 seq lengths; need to update fastq renaming step to accommodate these,FALSE,TRUE,Mus musculus,GSE173994,GSM5284271,3p_v3,NA,SRR14458797,NA,SRX10808927,SRP318759,SRS8894977,SAMN19044144,NA,NA,"Zhao et al, Advanced Science, 2021",NA,https://pubmed.ncbi.nlm.nih.gov/34647690/,Illumina NovaSeq 6000,Transcriptomic analysis of E9.5 mouse embryos,"Obesity impairs the developmental progress and metabolism of the skeletal muscle. Using scRNA-seq, the initial impacts caused by maternal obesity were revealed at the embryonic stage. Overall design: Single-cell transcriptomic profiling of mouse embryos on embryonic 9.5 day."
Zhao 2021,HFD1,From high-fat diet fed maternal obese mice (MO),whole,embryo,NA,NA,NA,NA,150-by-150 seq lengths; need to update fastq renaming step to accommodate these,FALSE,TRUE,Mus musculus,GSE173994,GSM5284272,3p_v3,NA,SRR14458798,NA,SRX10808928,SRP318759,SRS8894979,SAMN19044142,NA,NA,"Zhao et al, Advanced Science, 2021",NA,https://pubmed.ncbi.nlm.nih.gov/34647690/,Illumina NovaSeq 6000,Transcriptomic analysis of E9.5 mouse embryos,"Obesity impairs the developmental progress and metabolism of the skeletal muscle. Using scRNA-seq, the initial impacts caused by maternal obesity were revealed at the embryonic stage. Overall design: Single-cell transcriptomic profiling of mouse embryos on embryonic 9.5 day."
Zhao 2021,HFD2,From high-fat diet fed maternal obese mice (MO),whole,embryo,NA,NA,NA,NA,150-by-150 seq lengths; need to update fastq renaming step to accommodate these,FALSE,TRUE,Mus musculus,GSE173994,GSM5284273,3p_v3,NA,SRR14458799,NA,SRX10808929,SRP318759,SRS8894980,SAMN19044141,NA,NA,"Zhao et al, Advanced Science, 2021",NA,https://pubmed.ncbi.nlm.nih.gov/34647690/,Illumina NovaSeq 6000,Transcriptomic analysis of E9.5 mouse embryos,"Obesity impairs the developmental progress and metabolism of the skeletal muscle. Using scRNA-seq, the initial impacts caused by maternal obesity were revealed at the embryonic stage. Overall design: Single-cell transcriptomic profiling of mouse embryos on embryonic 9.5 day."
Alba 2022,"Leg, 0month, uninjured",NA,whole,limb,NA,NA,NA,NA,species not available from Ensembl,FALSE,TRUE,Parhyale hawaiensis,GSE206980,GSM6267524,3p_v3,fastq,SRR19859280;SRR19859281;SRR19859282;SRR19859283,NA,SRX15902842,NA,NA,SAMN29363667,NA,NA,NA,NA,NA,NA,NA,NA
Alba 2022,"Leg, 6months, uninjured",NA,whole,limb,NA,NA,NA,NA,species not available from Ensembl,FALSE,TRUE,Parhyale hawaiensis,GSE206980,GSM6267525,3p_v3,fastq,SRR19859284;SRR19859285;SRR19859286;SRR19859287,NA,SRX15902841,NA,NA,SAMN29363668,NA,NA,NA,NA,NA,NA,NA,NA
Alba 2022,"Leg, 6months, regenerated",NA,whole,limb,NA,NA,NA,NA,species not available from Ensembl,FALSE,TRUE,Parhyale hawaiensis,GSE206980,GSM6267526,3p_v3,fastq,SRR19859288;SRR19859289;SRR19859290;SRR19859291,NA,SRX15902840,NA,NA,SAMN29363669,NA,NA,NA,NA,NA,NA,NA,NA
Alba 2022,"Leg, 2months, uninjured",NA,whole,limb,NA,NA,NA,NA,species not available from Ensembl,FALSE,TRUE,Parhyale hawaiensis,GSE206980,GSM6267527,3p_v3,fastq,SRR19859292;SRR19859293;SRR19859294;SRR19859295,NA,SRX15902839,NA,NA,SAMN29363670,NA,NA,NA,NA,NA,NA,NA,NA
Alba 2022,"Leg, 2months, regenerated",NA,whole,limb,NA,NA,NA,NA,species not available from Ensembl,FALSE,TRUE,Parhyale hawaiensis,GSE206980,GSM6267528,3p_v3,fastq,SRR19859296;SRR19859297;SRR19859298;SRR19859299,NA,SRX15902838,NA,NA,SAMN29363671,NA,NA,NA,NA,NA,NA,NA,NA
Fly Cell Atlas 2021,body,NA,whole,body,NA,NA,NA,NA,NA,FALSE,TRUE,Drosophila melanogaster,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,"Fly Cell Atlas, bioRxiv, 2021",10.1101/2021.07.04.451050,NA,NA,NA,NA
Fly Cell Atlas 2021,leg,NA,whole,leg,NA,NA,NA,NA,NA,FALSE,TRUE,Drosophila melanogaster,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,"Fly Cell Atlas, bioRxiv, 2021",10.1101/2021.07.04.451050,NA,NA,NA,NA
Metikala 2021,Zf_30h_trunk,NA,whole,embryo,cell,NA,NA,NA,NA,TRUE,TRUE,Danio rerio,GSE152982,GSM4631066,3p_v2,fastq,SRR12067712;SRR12067711,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Walter 2023,Ger_D0_A,NA,muscle,tibialis anterior,cell,female,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE232106,GSM7312234,3p_v3,fastq,SRR24488973;SRR24488974;SRR24488975;SRR24488976;SRR24488977;SRR24488978;SRR24488979;SRR24488980,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Walter 2023,Ger_D0_B,NA,muscle,tibialis anterior,cell,female,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE232106,GSM7312235,3p_v3,fastq,SRR24488965;SRR24488966;SRR24488967;SRR24488968;SRR24488969;SRR24488970;SRR24488971;SRR24488972,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Walter 2023,Ger_D0_C,NA,muscle,tibialis anterior,cell,female,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE232106,GSM7312236,3p_v3,fastq,SRR24488957;SRR24488958;SRR24488959;SRR24488960;SRR24488961;SRR24488962;SRR24488963;SRR24488964,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Walter 2023,Ger_D0_D,NA,muscle,tibialis anterior,cell,female,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE232106,GSM7312237,3p_v3,fastq,SRR24488949;SRR24488950;SRR24488951;SRR24488952;SRR24488953;SRR24488954;SRR24488955;SRR24488956,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Walter 2023,Ger_D1_A,NA,muscle,tibialis anterior,cell,female,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE232106,GSM7312238,3p_v3,fastq,SRR24488941;SRR24488942;SRR24488943;SRR24488944;SRR24488945;SRR24488946;SRR24488947;SRR24488948,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Walter 2023,Ger_D1_B,NA,muscle,tibialis anterior,cell,female,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE232106,GSM7312239,3p_v3,fastq,SRR24488858;SRR24488859;SRR24488903;SRR24488904;SRR24488905;SRR24488906;SRR24488907;SRR24488908,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Walter 2023,Ger_D1_C,NA,muscle,tibialis anterior,cell,female,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE232106,GSM7312240,3p_v3,fastq,SRR24488887;SRR24488888;SRR24488889;SRR24488890;SRR24488891;SRR24488892;SRR24488893;SRR24488894,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Walter 2023,Ger_D1_D,NA,muscle,tibialis anterior,cell,female,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE232106,GSM7312241,3p_v3,fastq,SRR24488879;SRR24488880;SRR24488881;SRR24488882;SRR24488883;SRR24488884;SRR24488885;SRR24488886,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Walter 2023,Ger_D2_A,NA,muscle,tibialis anterior,cell,female,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE232106,GSM7312242,3p_v3,fastq,SRR24488871;SRR24488872;SRR24488873;SRR24488874;SRR24488875;SRR24488876;SRR24488877;SRR24488878,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Walter 2023,Ger_D2_B,NA,muscle,tibialis anterior,cell,female,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE232106,GSM7312243,3p_v3,fastq,SRR24488863;SRR24488864;SRR24488865;SRR24488866;SRR24488867;SRR24488868;SRR24488869;SRR24488870,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Walter 2023,Ger_D2_C,NA,muscle,tibialis anterior,cell,female,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE232106,GSM7312244,3p_v3,fastq,SRR24488853;SRR24488854;SRR24488855;SRR24488856;SRR24488857;SRR24488860;SRR24488861;SRR24488862,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Walter 2023,Ger_D2_D,NA,muscle,tibialis anterior,cell,female,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE232106,GSM7312245,3p_v3,fastq,SRR24488933;SRR24488934;SRR24488935;SRR24488936;SRR24488937;SRR24488938;SRR24488939;SRR24488940,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Walter 2023,Ger_D3.5_A,NA,muscle,tibialis anterior,cell,female,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE232106,GSM7312246,3p_v3,fastq,SRR24488925;SRR24488926;SRR24488927;SRR24488928;SRR24488929;SRR24488930;SRR24488931;SRR24488932,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Walter 2023,Ger_D3.5_B,NA,muscle,tibialis anterior,cell,female,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE232106,GSM7312247,3p_v3,fastq,SRR24488917;SRR24488918;SRR24488919;SRR24488920;SRR24488921;SRR24488922;SRR24488923;SRR24488924,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Walter 2023,Ger_D3.5_C,NA,muscle,tibialis anterior,cell,female,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE232106,GSM7312248,3p_v3,fastq,SRR24488909;SRR24488910;SRR24488911;SRR24488912;SRR24488913;SRR24488914;SRR24488915;SRR24488916,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Walter 2023,Ger_D3.5_D,NA,muscle,tibialis anterior,cell,female,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE232106,GSM7312249,3p_v3,fastq,SRR24488895;SRR24488896;SRR24488897;SRR24488898;SRR24488899;SRR24488900;SRR24488901;SRR24488902,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Walter 2023,Ger_D5_A,NA,muscle,tibialis anterior,cell,female,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE232106,GSM7312250,3p_v3,fastq,SRR24488845;SRR24488846;SRR24488847;SRR24488848;SRR24488849;SRR24488850;SRR24488851;SRR24488852,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Walter 2023,Ger_D5_B,NA,muscle,tibialis anterior,cell,female,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE232106,GSM7312251,3p_v3,fastq,SRR24488837;SRR24488838;SRR24488839;SRR24488840;SRR24488841;SRR24488842;SRR24488843;SRR24488844,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Walter 2023,Ger_D5_C,NA,muscle,tibialis anterior,cell,female,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE232106,GSM7312252,3p_v3,fastq,SRR24488829;SRR24488830;SRR24488831;SRR24488832;SRR24488833;SRR24488834;SRR24488835;SRR24488836,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Walter 2023,Ger_D5_D,NA,muscle,tibialis anterior,cell,female,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE232106,GSM7312253,3p_v3,fastq,SRR24488821;SRR24488822;SRR24488823;SRR24488824;SRR24488825;SRR24488826;SRR24488827;SRR24488828,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Walter 2023,Ger_D7_A,NA,muscle,tibialis anterior,cell,female,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE232106,GSM7312254,3p_v3,fastq,SRR24488813;SRR24488814;SRR24488815;SRR24488816;SRR24488817;SRR24488818;SRR24488819;SRR24488820,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Walter 2023,Ger_D7_B,NA,muscle,tibialis anterior,cell,female,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE232106,GSM7312255,3p_v3,fastq,SRR24488805;SRR24488806;SRR24488807;SRR24488808;SRR24488809;SRR24488810;SRR24488811;SRR24488812,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Walter 2023,Ger_D7_C,NA,muscle,tibialis anterior,cell,female,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE232106,GSM7312256,3p_v3,fastq,SRR24488797;SRR24488798;SRR24488799;SRR24488800;SRR24488801;SRR24488802;SRR24488803;SRR24488804,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Walter 2023,Ger_D7_D,NA,muscle,tibialis anterior,cell,female,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE232106,GSM7312257,3p_v3,fastq,SRR24488789;SRR24488790;SRR24488791;SRR24488792;SRR24488793;SRR24488794;SRR24488795;SRR24488796,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Walter 2023,Yng_D1_A,NA,muscle,tibialis anterior,cell,female,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE232106,GSM7328463,3p_v3,fastq,SRR24518407;SRR24518408;SRR24518409;SRR24518410;SRR24518411;SRR24518412;SRR24518413;SRR24518414,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Walter 2023,Yng_D1_B,NA,muscle,tibialis anterior,cell,female,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE232106,GSM7328464,3p_v3,fastq,SRR24518399;SRR24518400;SRR24518401;SRR24518402;SRR24518403;SRR24518404;SRR24518405;SRR24518406,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Walter 2023,Yng_D1_C,NA,muscle,tibialis anterior,cell,female,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE232106,GSM7328465,3p_v3,fastq,SRR24518391;SRR24518392;SRR24518393;SRR24518394;SRR24518395;SRR24518396;SRR24518397;SRR24518398,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Walter 2023,Yng_D1_D,NA,muscle,tibialis anterior,cell,female,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE232106,GSM7328466,3p_v3,fastq,SRR24518383;SRR24518384;SRR24518385;SRR24518386;SRR24518387;SRR24518388;SRR24518389;SRR24518390,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Walter 2023,Yng_D3.5_A,NA,muscle,tibialis anterior,cell,female,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE232106,GSM7328467,3p_v3,fastq,SRR24518375;SRR24518376;SRR24518377;SRR24518378;SRR24518379;SRR24518380;SRR24518381;SRR24518382,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Walter 2023,Yng_D3.5_B,NA,muscle,tibialis anterior,cell,female,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE232106,GSM7328468,3p_v3,fastq,SRR24518367;SRR24518368;SRR24518369;SRR24518370;SRR24518371;SRR24518372;SRR24518373;SRR24518374,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Walter 2023,Yng_D3.5_C,NA,muscle,tibialis anterior,cell,female,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE232106,GSM7328469,3p_v3,fastq,SRR24518359;SRR24518360;SRR24518361;SRR24518362;SRR24518363;SRR24518364;SRR24518365;SRR24518366,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Walter 2023,Yng_D3.5_D,NA,muscle,tibialis anterior,cell,female,NA,NA,NA,TRUE,TRUE,Mus musculus,GSE232106,GSM7328470,3p_v3,fastq,SRR24518351;SRR24518352;SRR24518353;SRR24518354;SRR24518355;SRR24518356;SRR24518357;SRR24518358,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Barruet 2023,Vastus Lateralis 20M,NA,muscle,vastus lateralis,cell,male,NA,NA,NA,TRUE,FALSE,Homo sapiens,GSE196554,GSM5889068,3p_v3,fastq,SRR17988614;SRR17988615,NA,NA,NA,NA,NA,NA,NA,NA,NA,https://pubmed.ncbi.nlm.nih.gov/37192223/,NA,NA,NA
Barruet 2023,Pectoralis Major 21F,NA,muscle,pectoralis major,cell,female,NA,NA,NA,TRUE,FALSE,Homo sapiens,GSE196554,GSM5889069,3p_v3,fastq,SRR17988620;SRR17988621;SRR17988622;SRR17988623,NA,NA,NA,NA,NA,NA,NA,NA,NA,https://pubmed.ncbi.nlm.nih.gov/37192223/,NA,NA,NA
Barruet 2023,Pectoralis Major 40F,NA,muscle,pectoralis major,cell,female,NA,NA,NA,TRUE,FALSE,Homo sapiens,GSE196554,GSM5889070,3p_v3,fastq,SRR17988616;SRR17988617;SRR17988618;SRR17988619,NA,NA,NA,NA,NA,NA,NA,NA,NA,https://pubmed.ncbi.nlm.nih.gov/37192223/,NA,NA,NA
Barruet 2023,Vastus Lateralis 52M,NA,muscle,vastus lateralis,cell,male,NA,NA,NA,TRUE,FALSE,Homo sapiens,GSE196554,GSM5889071,3p_v3,fastq,SRR17988612;SRR17988613,NA,NA,NA,NA,NA,NA,NA,NA,NA,https://pubmed.ncbi.nlm.nih.gov/37192223/,NA,NA,NA
Barruet 2023,Vastus Lateralis 55M,NA,muscle,vastus lateralis,cell,male,NA,NA,NA,TRUE,FALSE,Homo sapiens,GSE196554,GSM5889072,3p_v3,fastq,SRR17988606;SRR17988607,NA,NA,NA,NA,NA,NA,NA,NA,NA,https://pubmed.ncbi.nlm.nih.gov/37192223/,NA,NA,NA
Barruet 2023,Rectus Abdominis 56F,NA,muscle,rectus abdominis,cell,female,NA,NA,NA,TRUE,FALSE,Homo sapiens,GSE196554,GSM5889073,3p_v3,fastq,SRR17988608;SRR17988609;SRR17988610;SRR17988611,NA,NA,NA,NA,NA,NA,NA,NA,NA,https://pubmed.ncbi.nlm.nih.gov/37192223/,NA,NA,NA
Barruet 2023,Vastus Lateralis 57F,NA,muscle,vastus lateralis,cell,female,NA,NA,NA,TRUE,FALSE,Homo sapiens,GSE196554,GSM5889074,3p_v3,fastq,SRR17988604;SRR17988605,NA,NA,NA,NA,NA,NA,NA,NA,NA,https://pubmed.ncbi.nlm.nih.gov/37192223/,NA,NA,NA
Barruet 2023,Rectus Abdominis 59F,NA,muscle,rectus abdominis,cell,female,NA,NA,NA,TRUE,FALSE,Homo sapiens,GSE196554,GSM5889075,3p_v3,fastq,SRR17988600;SRR17988601;SRR17988602;SRR17988603,NA,NA,NA,NA,NA,NA,NA,NA,NA,https://pubmed.ncbi.nlm.nih.gov/37192223/,NA,NA,NA
Barruet 2023,Vastus Lateralis 66M,NA,muscle,vastus lateralis,cell,male,NA,NA,NA,TRUE,FALSE,Homo sapiens,GSE196554,GSM5889076,3p_v3,fastq,SRR17988598;SRR17988599,NA,NA,NA,NA,NA,NA,NA,NA,NA,https://pubmed.ncbi.nlm.nih.gov/37192223/,NA,NA,NA
Barruet 2023,Vastus Lateralis 73M,NA,muscle,vastus lateralis,cell,male,NA,NA,NA,TRUE,FALSE,Homo sapiens,GSE196554,GSM5889077,3p_v3,fastq,SRR17988596;SRR17988597,NA,NA,NA,NA,NA,NA,NA,NA,NA,https://pubmed.ncbi.nlm.nih.gov/37192223/,NA,NA,NA
Barruet 2023,Vastus Lateralis 83M,NA,muscle,vastus lateralis,cell,male,NA,NA,NA,TRUE,FALSE,Homo sapiens,GSE196554,GSM5889078,3p_v3,fastq,SRR17988590;SRR17988591,NA,NA,NA,NA,NA,NA,NA,NA,NA,https://pubmed.ncbi.nlm.nih.gov/37192223/,NA,NA,NA
Barruet 2023,Gastrocnemius 87F,NA,muscle,gastrocnemius,cell,female,NA,NA,NA,TRUE,FALSE,Homo sapiens,GSE196554,GSM5889079,3p_v3,fastq,SRR17988592;SRR17988593;SRR17988594;SRR17988595,NA,NA,NA,NA,NA,NA,NA,NA,NA,https://pubmed.ncbi.nlm.nih.gov/37192223/,NA,NA,NA