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. Genotype data can be made available via the UMCG HPC environment upon request. To gain access to the raw expression or genotype data, please fill in and sign the Data Sharing Agreement and the Data Access Request Form, then send these documents to M.G.P. van der Wijst.