SA_bone_marrow

scRNA-seq analysis for Radhouani et al. paper, Science Immunology, 2025.

The running order of the scripts is as follows:

1. Reading the data in R using:

   • R/1_read_in_pilot.Rmd
   • R/2_read_in_final.Rmd

2. Performing single-cell integration using scVI, initial annotation using scNym, and leiden clustering of mature and hematopoietic stem cells (HSC).

   • python/1_scvi_integration.ipynb
   • python/2_scnym_annotation.ipynb
   • python/3_clustering_for_manual_annotation.ipynb

3. Marker detection of the clusters.

   • R/3_hvg_DEGs_HSC_scnym_annotation.Rmd
   • R/4_hvg_DEGs_mature_scnym_annotation.Rmd

These markers have been used for manual annotation of the clusters.

4. Transfer and plotting of the data with manually annotated clusters. This script relies on python/4_dynamo_cell_cycle.ipynb for cell cycle annotation.

   • python/5_transfering_manual_annotation.ipynb

5. Differential expression between SA- and PBS-treated mice across cell types.

   • R/5_DEGs_HSC_scnym_annotation_manual_annotation.Rmd
   • R/6_DEGs_mature_scnym_annotation_manual_annotation.Rmd