HCA Data Explorer

Vento-tormo: Single cell profiling of COVID-19 patients: an international data resource from multiple tissues

Updated March 16, 2023

In late 2019 and through 2020, the COVID-19 pandemic swept the world, presenting both scientific and medical challenges associated with understanding and treating a previously unknown disease. To help address the need for great understanding of COVID-19, the scientific community mobilized and banded together rapidly to characterize SARS-CoV-2 infection, pathogenesis and its distinct disease trajectories. The urgency of COVID-19 provided a pressing use-case for leveraging relatively new tools, technologies, and nascent collaborative networks. Single-cell biology is one such example that has emerged over the last decade as a powerful approach that provides unprecedented resolution to the cellular and molecular underpinnings of biological processes. Early foundational work within the single-cell community, including the Human Cell Atlas, utilized published and unpublished data to characterize the putative target cells of SARS-CoV-2 sampled from diverse organs based on expression of the viral receptor ACE2 and associated entry factors TMPRSS2 and CTSL (Muus et al., 2020; Sungnak et al., 2020; Ziegler et al., 2020). This initial characterization of reference data provided an important foundation for framing infection and pathology in the airway as well as other organs. However, initial community analysis was limited to samples derived from uninfected donors and other previously-sampled disease indications. This report provides an overview of a single-cell data resource derived from samples from COVID-19 patients along with initial observations and guidance on data reuse and exploration.

Roser Vento-TormoWellcome Sanger Genome Centerrv4@sanger.ac.uk
Chan Zuckerberg Initiative Single-Cell COVID-19 Consortia1
Esteban Ballestar2
Donna Farber3
Sarah Glover4
Bruce Horwitz5
Kerstin Meyer6
Marko Nikolić7
Jose Ordovas-Montanes5
Peter Sims8
Alex Shalek9
Niels Vandamme4
Linos Vandekerckhove10
Roser Vento-Tormo6
Alexandra Chloe Villani11
1not applicable
2Josep Carreras Research Institute (IJC)
3Columbia University
4Vlaams Instituut voor Biotechnologie
5Boston Children’s Hospital
6Wellcome Sanger Genome Center
7University College London
8Columbia University Medical Center
9Massachusetts Institute of Technology
10University of Ghent
11Massachusetts General Hospital
None

To reference this project, please use the following link:

https://explore.data.humancellatlas.org/projects/2d4d89f2-ebeb-467c-ae60-a3efc5e8d4ba
None
None

For information regarding data sharing and data use, please see our Data Access Policy.

Analysis Portals

CZ CELLxGENECZ CELLxGENE
UCSC Cell BrowserUCSC Cell Browser

Project Label

COVID19autoimmunityPBMCs

Species

Homo sapiens

Sample Type

specimens

Anatomical Entity

blood

Organ Part

Unspecified

Selected Cell Types

peripheral blood mononuclear cell

Disease Status (Specimen)

4 disease statuses

Disease Status (Donor)

4 disease statuses

Development Stage

human adult stage

Library Construction Method

CITE-seq

Nucleic Acid Source

single cell

Paired End

false

Analysis Protocol

analysis_protocol_1, analysis_protocol_2

File Format

2 file formats

Cell Count Estimate

97.5k

Donor Count

22
h5ad1 file(s)xlsx1 file(s)