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ScRNA-seq of PBMC and whole blood samples reveals a dysregulated myeloid cell compartment in severe COVID-19

In a dual-center, two-cohort study, we performed single-cell RNA-sequencing of whole blood and peripheral blood mononuclear cells to determine changes in immune cell composition and activation in mild vs. severe COVID-19 over time. This study provides detailed insights into the systemic immune response to SARS-CoV-2 infection and reveals profound alterations in the myeloid cell compartment associated with severe COVID-19.

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
EGAD00001006550 Illumina NovaSeq 6000 141
Publications Citations
Severe COVID-19 Is Marked by a Dysregulated Myeloid Cell Compartment.
Cell 182: 2020 1419-1440.e23
Optimized workflow for single-cell transcriptomics on infectious diseases including COVID-19.
STAR Protoc 1: 2020 100233
Convalescent COVID-19 patients are susceptible to endothelial dysfunction due to persistent immune activation.
Elife 10: 2021 e64909
Longitudinal proteomic analysis of severe COVID-19 reveals survival-associated signatures, tissue-specific cell death, and cell-cell interactions.
Cell Rep Med 2: 2021 100287
Transcriptional Changes in CD16+ Monocytes May Contribute to the Pathogenesis of COVID-19.
Front Immunol 12: 2021 665773
Dissecting the common and compartment-specific features of COVID-19 severity in the lung and periphery with single-cell resolution.
iScience 24: 2021 102738
An interactive single cell web portal identifies gene and cell networks in COVID-19 host responses.
iScience 24: 2021 103115
Early IFN-α signatures and persistent dysfunction are distinguishing features of NK cells in severe COVID-19.
Immunity 54: 2021 2650-2669.e14
Immune Response in Severe and Non-Severe Coronavirus Disease 2019 (COVID-19) Infection: A Mechanistic Landscape.
Front Immunol 12: 2021 738073
Differential Co-Expression Network Analysis Reveals Key Hub-High Traffic Genes as Potential Therapeutic Targets for COVID-19 Pandemic.
Front Immunol 12: 2021 789317
A human pluripotent stem cell-based model of SARS-CoV-2 infection reveals an ACE2-independent inflammatory activation of vascular endothelial cells through TLR4.
Stem Cell Reports 17: 2022 538-555
Severe COVID-19 Shares a Common Neutrophil Activation Signature with Other Acute Inflammatory States.
Cells 11: 2022 847
Single-cell transcriptomics reveal a unique memory-like NK cell subset that accumulates with ageing and correlates with disease severity in COVID-19.
Genome Med 14: 2022 46
The Genetic Risk for COVID-19 Severity Is Associated With Defective Immune Responses.
Front Immunol 13: 2022 859387
A systems biology approach identifies candidate drugs to reduce mortality in severely ill patients with COVID-19.
Sci Adv 8: 2022 eabm2510
Identification of COVID-19-Associated DNA Methylation Variations by Integrating Methylation Array and scRNA-Seq Data at Cell-Type Resolution.
Genes (Basel) 13: 2022 1109
Whole blood DNA methylation analysis reveals respiratory environmental traits involved in COVID-19 severity following SARS-CoV-2 infection.
Nat Commun 13: 2022 4597
scFeatures: multi-view representations of single-cell and spatial data for disease outcome prediction.
Bioinformatics 38: 2022 4745-4753
Longitudinal characterization of circulating neutrophils uncovers phenotypes associated with severity in hospitalized COVID-19 patients.
Cell Rep Med 3: 2022 100779
Neutrophil profiles of pediatric COVID-19 and multisystem inflammatory syndrome in children.
Cell Rep Med 3: 2022 100848
Protocol for bulk RNA sequencing of enriched human neutrophils from whole blood and estimation of sample purity.
STAR Protoc 4: 2023 102125
Benchmarking of analytical combinations for COVID-19 outcome prediction using single-cell RNA sequencing data.
Brief Bioinform 24: 2023 bbad159