1M-scBloodNL

Dataset

Gene expression data

Count matrices and metadata are available below. For more information on how to work with these, visit the GitHub page

Downloads

QC-ed raw gene expression counts (mtx format) of samples processed with 10x v2
QC-ed genes for raw gene expression counts of samples processed with 10x v2
QC-ed and SCT normalized counts (mtx format) of samples processed with 10x v2
QC-ed genes for SCT normalized counts of samples processed with 10x v2
QC-ed barcodes of samples processed with 10x v2

QC-ed raw gene expression counts (mtx format) of samples processed with 10x v3
QC-ed genes for raw gene expression counts of samples processed with 10x v3
QC-ed and SCT normalized counts (mtx format) of samples processed with 10x v3
QC-ed genes for SCT normalized counts of samples processed with 10x v3
QC-ed barcodes of samples processed with 10x v3

pre-QC raw gene expression counts (mtx format)
genes for pre-QC raw gene expression counts
barcodes for pre-QC raw gene expression counts

Cell type classification for every cell barcode
Sample assignment and condition for every cell barcode

Changelog


                        
                            2021-06-10: Initial data release
                            

                            2024-02-24: add features and barcodes as tsv files, separate the chemistries, add pre-QC counts

Raw data

Raw gene expression data is freely available and has been deposited at the European Genome-phenome Archive (EGA), which is hosted by the EBI and the CRG, under accession number EGAS00001005376. To gain access to the genotype data, please contact Lifelines Data Management