Single cell profiling of COVID-19 patients: an international data resource from multiple tissues
Chan Zuckerberg Initiative Single-Cell COVID-19 Consortia, Esteban Ballestar, Donna L. Farber, Sarah Glover, Bruce Horwitz, Kerstin Meyer, Marko Nikolić, Jose Ordovas-Montanes, Peter Sims, Alex Shalek, Niels Vandamme, Linos Vandekerckhove, Roser Vento-Tormo, Alexandra Chloe Villani
Abstract
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 Early foundational work within the single-cell community, including the Human Cell Atlas, utilized published and unpublished data to characterize the putative target cells of SARS-CoV-2 sampled from diverse organs based on expression of the viral receptor ACE2 and associated entry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.
Datasets
1. PBMC
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Source data
https://cellxgene.cziscience.com/collections/0434a9d4-85fd-4554-b8e3-cf6c582bb2fa
Alias names
Acute COVID-19 cohort across a range of WHO categories seen at the Department of Emergency Medicine at MGH
Cite this study
Chan Zuckerberg Initiative Single-Cell COVID-19 Consortia, Ballestar, E., Farber, D.L., Glover, S., Horwitz, B., Meyer, K., Nikolić, M., Ordovas-Montanes, J., Sims, P., Shalek, A. and Vandamme, N., 2020. Single cell profiling of COVID-19 patients: an international data resource from multiple tissues. MedRxiv, pp.2020-11. https://doi.org/10.1101/2020.11.20.20227355