Multi-omic single-cell profiling of peripheral blood immune cells from COVID-19 patients and controls.

The COVID-19 pandemic, caused by SARS coronavirus 2 (SARS-CoV-2), has resulted in excess morbidity and mortality as well as economic decline. To characterise the systemic host immune response to SARS-CoV-2, we performed single-cell RNA-sequencing coupled with analysis of cell surface proteins, providing molecular profiling of over 800,000 peripheral blood mononuclear cells from a cohort of 130 patients with COVID-19. Our cohort, from three UK centres, spans the spectrum of clinical presentations and disease severities ranging from asymptomatic to critical. Three control groups were included: healthy volunteers, patients suffering from a non-COVID-19 severe respiratory illness and healthy individuals administered with intravenous lipopolysaccharide to model an acute inflammatory response. Full single cell transcriptomes are coupled with quantification of 188 cell surface proteins, and T and B lymphocyte antigen receptor repertoires.

Type: Other
Archiver: European Genome-Phenome Archive (EGA)

3 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
EGAD00001007865	Single-cell multi-omic profiling of COVID19 patients recruited from University College London. Data represent RNA-seq, surface protein measurements (CITE-seq) of 192 antibody targets, along with VDJ-seq profiling of single T cell and B cell receptors. Samples are pooled, with 4 donors per pool. Germ-line genotypes derived from previous single-cell RNA-sequencing are provided (VCF) to aid demultiplexing of single-cell and assignment to specific patient donor samples.	Illumina NovaSeq 6000	21
EGAD00001007866	Single-cell multi-omic profiling of healthy controls, asymptomatic and hosptial-admitted COVID19 patients recruited from Newcastle University hospitals. These data also include healthy control volunteers treated with IV-LPS as inflammatory controls. Data represent RNA-seq, surface protein measurements (CITE-seq) of 192 antibody targets, along with VDJ-seq profiling of single T cell and B cell receptors.	Illumina NovaSeq 6000	73
EGAD00001007867	Single-cell multi-omic profiling of healthy controls, asymptomatic and hosptial-admitted COVID19 patients recruited from Addenbrookes and Royal Papworth hospitals, in collaboration with the NIHR Cambridge Bioresource. Data represent RNA-seq, surface protein measurements (CITE-seq) of 192 antibody targets, along with VDJ-seq profiling of single T cell and B cell receptors. Samples are pooled, with 4 donors per pool. Germ-line genotypes are provided (VCF) to aid demultiplexing of single-cell and assignment to specific patient donor samples.	Illumina NovaSeq 6000	96