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| Status |
Public on May 18, 2020 |
| Title |
A single-cell atlas of the peripheral immune response to severe COVID-19 |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
There is an urgent need to better understand the pathophysiology of Coronavirus disease 2019 (COVID-19), the global pandemic caused by SARS-CoV-2 which has infected more than 3 million people worldwide. Approximately 20% of patients with COVID-19 develop severe disease and 5% require intensive care. Severe disease has been associated with changes in peripheral immune activity, including increased levels of pro-inflammatory cytokines that may be produced by a subset of inflammatory monocytes, lymphopenia, and T cell exhaustion. To elucidate pathways in peripheral immune cells that might lead to immunopathology or protective immunity in severe COVID-19, we applied single-cell RNA sequencing (scRNA-seq) to profile peripheral blood mononuclear cells (PBMCs) from 7 patients hospitalized for COVID-19 and 6 healthy controls. We identify reconfiguration of peripheral immune cell phenotype in COVID-19, including a heterogeneous interferon-stimulated gene (ISG) signature, HLA class II downregulation, and a developing neutrophil population that appears closely related to plasmablasts appearing in patients with acute respiratory failure requiring mechanical ventilation. Importantly, we found that peripheral monocytes and lymphocytes do not express substantial amounts of pro-inflammatory cytokines. Collectively, we provide a cell atlas of the peripheral immune response to severe COVID-19.
Sample IDs used in the manuscript were shortened for clarity. They relate to the titles of deposited files as follows:
covid_555_1: C1 A
covid_555_2: C1 B
covid_556: C2
covid_557: C3
covid_558: C4
covid_559: C5
covid_561: C7
HIP002: H1
HIP015: H2
HIP023: H3
HIP043: H4
HIP044: H5
HIP045: H6
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| Overall design |
Single-cell RNA sequencing of peripheral blood mononuclear cells (PBMCs) from 8 samples from COVID-19 patients and 6 healthy controls.
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| Contributor(s) |
Wilk AJ, Blish CA |
| Citation(s) |
32514174 |
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| Submission date |
May 17, 2020 |
| Last update date |
Jun 26, 2020 |
| Contact name |
Aaron James Wilk |
| E-mail(s) |
awilk@stanford.edu
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| Organization name |
Stanford University
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| Street address |
300 Pasteur Dr Bldg S131, Grant
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| City |
Stanford |
| State/province |
California |
| ZIP/Postal code |
94305 |
| Country |
USA |
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| Platforms (1) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
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| Samples (13)
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| Relations |
| BioProject |
PRJNA633393 |
| SRA |
SRP262058 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE150728_RAW.tar |
371.7 Mb |
(http)(custom) |
TAR (of RDS) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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