3 files

Single-cell RNA-seq data from microfluidic emulsion (v2)

posted on 20.09.2018 by Olga Botvinnik, James Webber, Joshua Batson, Angela Pisco
Gene-count files and metadata files for single cells from different organs of mice processed on the 10X Genomics Platform. The counts are given using the .mtx file output by the CellRanger program, with one folder per run.

Includes data for 422,803 droplets, 55,656 of which passed a QC cutoff of 500 genes and 1000 UMI.

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

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

Update 2018-09-20: Updated Annotations to latest version

Why it's different from the previous version (https://figshare.com/account/projects/27733/articles/5715025):
Renamed tissues for nomenclature standards:
  • "Colon" --> "Large_Intestine"
  • "Heart" --> "Heart_and_Aorta"
  • "Muscle" --> "Limb_Muscle"
  • "Mammary" --> "Mammary_Gland"
  • "Brain_Microglia" --> "Brain_Myeloid"
  • "Brain_Non-microglia" --> "Brain_Non-Myeloid"
Update 2018-03-28: Uploaded resubmitted annotations, with within-tissue (organ) tSNE coordinates


Chan Zuckerberg Biohub