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Tabula Muris

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.



Count files for R

You can download complete count files as sparse matrices in .rds format for easy loading into R. Download TM_facs_mat.rds and TM_droplet_mat.rds. Load:


tm.droplet.matrix = readRDS("TM_droplet_mat.rds")
tm.droplet.metadata = read_csv("TM_droplet_metadata.csv")

Count files for Python

You can download complete count files as sparse matrices using anndata's h5ad file format for use in Python here and here. You can process the resulting AnnData object using, for instance, Scanpy.

import pandas as pd
from anndata import read_h5ad

tm_facs_metadata = pd.read_csv('data/TM_facs_metadata.csv')
tm_facs_data = read_h5ad('data/TM_facs_mat.h5ad')

CSV and MTX files

The original data release is on FigShare.