Study

A blood atlas of COVID-19 defines hallmarks of disease severity and specificity

Study ID Alternative Stable ID Type
EGAS00001005493 Other

Study Description

Treatment of severe COVID-19 is currently limited by clinical heterogeneity and incomplete understanding of potentially druggable immune mediators of disease. To advance this, we present a comprehensive multi-omic blood atlas in patients with varying COVID-19 severity and compare with influenza, sepsis and healthy volunteers. We identify immune signatures and correlates of host response. Hallmarks of disease severity revealed cells, their inflammatory mediators and networks as potential therapeutic targets, including progenitor cells and specific myeloid and lymphocyte subsets, features of the immune repertoire, acute phase response, metabolism and coagulation. Persisting immune activation involving AP-1/p38MAPK was a specific feature of COVID-19. The plasma proteome enabled sub-phenotyping into patient clusters, predictive of severity and outcome. Tensor and matrix decomposition of the overall dataset revealed feature groupings linked with disease severity and specificity. Our systems-based integrative approach and blood atlas will inform future drug development, clinical trial ... (Show More)

Study Datasets 13 datasets.

Click on a Dataset ID in the table below to learn more, and to find out who to contact about access to these data

Dataset ID Description Technology Samples
EGAD00001007931
Anonymised patient metadata and associated data dictionary. For further information regarding this dataset, please contact Alexander Mentzer at contact@combat.ox.ac.uk.
611
EGAD00001007932
SmartSeq2 RNAseq data from 16 samples. For further information regarding this dataset, please contact Julian Knight and Alexander Mentzer at contact@combat.ox.ac.uk.
NextSeq 500 16
EGAD00001007957
Bulk RNAseq data from whole blood. For further information regarding this dataset, please contact Katie Burnham and Andew Kwok at contact@combat.ox.ac.uk.
Illumina NovaSeq 6000 144
EGAD00001007959
gVCF file per patient obtained from the bulk/mini-bulk RNAseq data. For further information regarding this dataset, please contact Stephen Sansom and Alexander Mentzer at contact@combat.ox.ac.uk.
228
EGAD00001007960
fastq and filtered fasta files for B-cell receptor sequencing. For further information regarding this dataset, please contact Rachael Bashford-Rogers at contact@combat.ox.ac.uk.
Illumina MiSeq 96
EGAD00001007961
fastq and filtered fasta files for T-cell receptor sequencing. For further information regarding this dataset, please contact Rachael Bashford-Rogers at contact@combat.ox.ac.uk.
Illumina MiSeq 91
EGAD00001007962
Raw Illumina sequencing data and CellRanger BAM output files. For further information regarding this dataset, please contact Stephen Sansom at contact@combat.ox.ac.uk.
Illumina NovaSeq 6000 10
EGAD00001007963
Raw Illumina sequencing data from single-cell ATACSeq experiments. For further information regarding this dataset, please contact Julian Knight and Tatjana Sauka-Spengler at contact@combat.ox.ac.uk.
Illumina NovaSeq 6000 1
EGAD00001007964
Raw Illumina sequencing data. For further information regarding this dataset, please contact Rachael Bashford-Rogers at contact@combat.ox.ac.uk.
Illumina NovaSeq 6000 10
EGAD00001007965
Raw Illumina sequencing data. For further information regarding this dataset, please contact Benjamin Fairfax and Rachael Bashford-Rogers at contact@combat.ox.ac.uk.
Illumina NovaSeq 6000 10
EGAD00001008007
Raw Illumina sequencing data and CellRanger BAM output files. For further information regarding this dataset, please contact Stephen Sansom at contact@combat.ox.ac.uk.
Illumina NovaSeq 6000 10
EGAD00001008008
Linker file for COMBAT CITEseq sequencing data. Links COMBAT sample IDs with sequencing pools and their associated raw sequence data. Sequence data can be found in the following datasets: ADT data: EGAD00001007962 GEX data: EGAD00001008007 VDJ (B-cell): EGAD00001007964 VDJ (T-cell): EGAD00001007965
140
EGAD00001008009
Other raw and processed phenotype data generated by the COMBAT consortium.
611

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