Reproducibility repository accompanying Wilk, Lee, Wei, Parks, et al. "Multi-omic profiling reveals widespread dysregulation of innate immunity and hematopoiesis in COVID-19" JExMed (2021).
Raw data (fastq) and processed data (.rds count matrices) are deposited under GEO accession GSE174072
Raw and processed data from our earlier study (https://www.nature.com/articles/s41591-020-0944-y) are deposited under an earlier accession (GSE150728)
Fully processed objects (Seurat .rds and AnnData .h5ad) are hosted at the COVID-19 cell atlas: https://www.covid19cellatlas.org/index.patient.html
This dataset will also be hosted for quick exploration on cellxgene shortly!
A processed Seurat .rds of granulocytes from a healthy donor (see Fig. S4) is hosted here: https://covid-scmultiome-public.s3.us-west-1.amazonaws.com/201130--neut_combined.seu.rds
Raw and processed data are deposited under GEO accession GSE174072
FCS files and associated metadata are available at ImmPort (https://www.immport.org) under study accession SDY1708
FCS files are also hosted here:
PBMCs: https://covid-scmultiome-public.s3.us-west-1.amazonaws.com/mass_cytometry_pbmc_fcs.zip
Isolated NK cells: https://covid-scmultiome-public.s3.us-west-1.amazonaws.com/mass_cytometry_nk_cells_fcs.zip