annotations_droplet.csv (7.41 MB)

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

Version 3 2018-09-20, 17:46
Version 2 2018-03-27, 19:57
Version 1 2018-03-09, 19:58
posted on 2018-09-20, 17:46 authored by Olga BotvinnikOlga Botvinnik, James WebberJames Webber, Joshua BatsonJoshua 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.


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

Why it's different from the previous version (
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