Tabula Muris contains about 100,000 cells from 20 organs and tissues in mouse. The study is sex-balanced, with four male and four female mice. The organs included are skin, fat, mammary gland, heart, bladder, brain, thymus, spleen, kidney, limb muscle, tongue, marrow, trachea, pancreas, lung, large intestine, and liver. Many of these organs were processed using two methods: SMART-seq2 on FACS-sorted cells and microfluidic droplets from 10X Genomics.
Preprint here.
Below are instructions for getting four files: metadata (including annotations) and count data for each dataset.
Version-controlled metadata are available on github.
You can download complete count files as sparse matrices in .rds format for easy loading into R. Unzip TabulaMuris.zip. Load:
library(tidyverse)
tm.droplet.matrix = readRDS("TM_droplet_mat.rds")
tm.droplet.metadata = read_csv("TM_droplet_metadata.csv")You can download complete count files as sparse matrices in AnnData-formatted h5ad files for use in Python here. You can load them using the Scanpy library:
import pandas
import scanpy
tm_facs_metadata = pd.read_csv('data/TM_facs_metadata.csv')
tm_facs_data = scanpy.anndata.read_h5ad('data/TM_facs_mat.h5ad').transpose()The original data release is on FigShare.