EBAII n1 scRNAseq : 10X PBMC10K Cell Ranger v3 MEX matrices

Published November 4, 2024 | Version v6

Dataset Open

A public dataset created and provided by 10X Genomics, that consists in ~ 10,000 PBMC (peripheral bone marrow cells) from a human donor
The experiment was performed with the 3’ capture kit v3
The analysis was performed with Cell Ranger v3
Mapping was performed on the GRCh38-2020-A manufacturer reference
The structure of these Cell Ranger outputs are described here
The sparse matrix format corresponds to the Market Exchange Format (MEX)
For educational purpose (speed), the dataset columns were reduced to 1/5th (from 737,280 to 147,456 barcodes)

Notes (English)

matrix.mtx.gz : sparse count matrix (compressed with gzip), as MEX

barcodes.tsv.gz : table of droplet barcodes, as TSV

features.tsv.gz : Table of features (genes), as TSV

pbmc_10k_v3_summary.html : Cell Ranger 3 metrics summary report, as HTML

Name	Size	Download all
barcodes.tsv.gz md5:2d346d29b3a711fce04db4d3fcd5180c	707.1 kB	Download
features.tsv.gz md5:94de35b473b5275b8e18f49372b70a27	260.4 kB	Download
matrix.mtx.gz md5:394dc0272b33e711d711af8e40ce0b44	5.8 MB	Download
pbmc_10k_v3_summary.html md5:a3edf5d766bd31b25eb049e161f9ec0b	4.6 MB	Download