Here we present a compendium of single-cell transcriptomic data from the model organism Mus musculus that comprises more than 100,000 cells from 20 organs and tissues. These data represent a new resource for cell biology, reveal gene expression in poorly characterized cell populations and enable the direct and controlled comparison of gene expression in cell types that are shared between tissues, such as T lymphocytes and endothelial cells from different anatomical locations. Two distinct technical approaches were used for most organs: one approach, microfluidic droplet-based 3′-end counting, enabled the survey of thousands of cells at relatively low coverage, whereas the other, full-length transcript analysis based on fluorescence-activated cell sorting, enabled the characterization of cell types with high sensitivity and coverage. The cumulative data provide the foundation for an atlas of transcriptomic cell biology.
Access optionsAccess options
Subscribe to Journal
Get full journal access for 1 year
only $3.90 per issue
All prices are NET prices.
VAT will be added later in the checkout.
Rent or Buy article
Get time limited or full article access on ReadCube.
All prices are NET prices.
All data, protocols and analysis scripts from the Tabula Muris are shared as a public resource (http://tabula-muris.ds.czbiohub.org/). Gene counts and metadata for FACS (https://doi.org/10.6084/m9.figshare.5829687.v7) and microfluidic droplets (https://doi.org/10.6084/m9.figshare.5968960.v2) from all single cells along with all produced R objects (https://doi.org/10.6084/m9.figshare.5821263.v1), as well as FACS Index data (https://doi.org/10.6084/m9.figshare.5975392) are accessible on Figshare (https://figshare.com/projects/Tabula_Muris_Transcriptomic_characterization_of_20_organs_and_tissues_from_Mus_musculus_at_single_cell_resolution/27733), and raw data are available from the Gene Expression Omnibus (GSE109774).
Publisher’s note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
We thank Sony Biotechnology for making an SH800S instrument available for this project. Some of the cell sorting/flow cytometry analysis for this project was performed using a Sony SH800S instrument in the Stanford Shared FACS Facility. Some FACS experiments used instruments in the VA Flow Cytometry Core, which is supported by the US Department of Veterans Affairs, Palo Alto Veterans Institute for Research and the National Institutes of Health. This work was supported by the Chan Zuckerberg Biohub, NIH Grant DP1 AG053015 and the NOMIS Foundation (T.W.-C.) as well as partly by the Stanford Islet Research Core in the Stanford Diabetes Research Center (P30 DK116074). We thank A. McGeever for contributions to the design of the Tabula Muris web portal.