CITESeq v1 data release from the COMBAT consortium.

For further information please see the publication https://www.medrxiv.org/content/10.1101/2021.05.11.21256877v1 or visit the consortium website: https://www.combat.ox.ac.uk. The raw data, clinical metadata and additional datasets are avaliable via the EGA and Zenodo (10.5281/zenodo.5139561). For further details and EGA accession numbers please see the STAR methods section of the publication. For more information please contact stephen.sansom@kennedy.ox.ac.uk.

Here two versions of the CITESeq dataset are shared:

(1) COMBAT-CITESeq-DATA.h5ad

This anndata object contains the raw and normalised gene expression and ADT data (symbols prefixed with "AB_"), cluster annotations, summary repertoire information and detailed metadata as reported and analysed in the COMBAT consortium paper "A blood atlas of COVID-19 defines hallmarks of disease severity and specificity" (https://www.medrxiv.org/content/10.1101/2021.05.11.21256877v1).


(2) COMBAT-CITESeq-EXPRESSION-ATLAS.h5ad

This anndata object contains the raw and normalised gene expression data from an alternative mapping to a transcriptome index that additionally included genes belonging to the "lncRNA" biotype. It also includes the ADT data, cluster annotations and a subset of the clinical metadata from (1). It is designed to be suitable for visualization with cellxgene.