Single-cell RNA-seq data from Smart-seq2 sequencing of FACS sorted cells (v2)

Gene-count tables for FACS sorted cells sequenced with Smart-Seq2 from 20 organs of 7 mice. Cells are grouped by tissue of origin.

Includes data for 53,760 cells, 44,879 of which passed a QC cutoff of at least 500 genes and 50,000 reads.

Cell annotations using the Cell Ontology [1] controlled vocabulary are in a separate csv.

This differs from v1 by renaming "Brain_Neurons" --> "Brain_Non-microglia" to be consistent with the manuscript.

Update 2018-09-20: Updated annotations to latest manuscript version

Update 2018-02-16: Separated Diaphragm cells from Muscle cells, and Aorta cells from Heart cells.

Update 2018-02-20: Aorta and Heart erroneously contained Diaphragm and Muscle data, and have now been corrected.

Update 2018-03-09: Renamed tissues for nomenclature standards:
  • "Colon" --> "Large_Intestine"
  • "Muscle" --> "Limb_Muscle"
  • "Mammary" --> "Mammary_Gland"
  • "Brain_Microglia" --> "Brain_Myeloid"
  • "Brain_Non-microglia" --> "Brain_Non-Myeloid"
Update 2018-03-22: Renamed subtissues:

- tissue: Heart, subtissue: ? --> tissue: Heart, subtissue: Unknown
- tissue: Skin, subtissue: NA --> tissue: Skin, subtissue: Telogen

Update 2018-03-23: Removed row numbers in first column of metadata_FACS.csv

Update 2018-03-27: Added tissue tSNEs and cluster ids


[1] http://purl.obolibrary.org/obo/cl.owl