Dataset of the Week — GSE152418

Malavika Srikanth
May 30, 2023

Our ‘Dataset of the Week’ series features publicly available omics datasets of scientific value, intending to promote data sharing and reuse.

This week’s dataset is RNA-sequencing data from the publication titled Systems biological assessment of immunity to mild versus severe COVID-19 infection in humans', published in Science (Sep 2020).

SARS-CoV-2 induces a plethora of symptoms in infected individuals. Immune response, combined with a host of other factors such as pre-existing comorbidities and age, significantly affects clinical phenotypes and patient outcomes. This paper uses multiple computational biology techniques to delve deeper into the immunological underpinnings of SARS-CoV-2 infections.

Key Findings of the Publication

  • SARS-CoV-2 infection severely impaired the normal functioning of dendritic cells and prevented them from mounting a robust immune response.
  • RNA-seq analysis of peripheral blood mononuclear cells (PBMCs) showed that the expression levels of human leukocyte antigen class DR (HLA-DR) and numerous proinflammatory cytokines were diminished in cells of myeloid origins.
  • On the other hand, molecules associated with disease severity such as EN-RAGE, TNFSF14 and oncostatin M, were significantly upregulated.
  • Single-cell RNA sequencing analysis of myeloid cells from COVID-19 patients revealed diminished expression of type I interferons, as is observed in the case of other zoonotic coronavirus diseases such as SARS and MERS.

Significance of the Dataset

This dataset contains gene expression data from the immune cells of COVID-19 patients and healthy controls and could serve as a valuable resource in understanding the key molecular players and immune mechanisms involved in modulating the host immune response.

Experimental Design

PBMCs were isolated from the plasma samples of COVID-19 patients and healthy subjects (17 samples per group) and bulk RNA-sequencing analysis was performed.

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