Cell Reports
Volume 36, Issue 7, 17 August 2021, 109527
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The COVIDome Explorer researcher portal

https://doi.org/10.1016/j.celrep.2021.109527Get rights and content
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Highlights

  • Matched multi-omics datasets are generated for COVID-19 patients and controls

  • Transcriptome, proteome, metabolome, immune cell maps, and clinical data are linked

  • An online researcher portal enabling data access and analysis is created

  • Utility is illustrated by study of biosignatures associated with the biomarker CRP

Summary

COVID-19 pathology involves dysregulation of diverse molecular, cellular, and physiological processes. To expedite integrated and collaborative COVID-19 research, we completed multi-omics analysis of hospitalized COVID-19 patients, including matched analysis of the whole-blood transcriptome, plasma proteomics with two complementary platforms, cytokine profiling, plasma and red blood cell metabolomics, deep immune cell phenotyping by mass cytometry, and clinical data annotation. We refer to this multidimensional dataset as the COVIDome. We then created the COVIDome Explorer, an online researcher portal where the data can be analyzed and visualized in real time. We illustrate herein the use of the COVIDome dataset through a multi-omics analysis of biosignatures associated with C-reactive protein (CRP), an established marker of poor prognosis in COVID-19, revealing associations between CRP levels and damage-associated molecular patterns, depletion of protective serpins, and mitochondrial metabolism dysregulation. We expect that the COVIDome Explorer will rapidly accelerate data sharing, hypothesis testing, and discoveries worldwide.

Keywords

COVID-19
SARS
multi-omics
data portal
CRP
inflammation
infection
serpins
metabolism
immune system

Data and code availability

All data generated for this manuscript is made available through the online researcher gateway of the COVIDome Project, known as the COVIDome Explorer, which can be accessed at covidome.org. The RNaseq data have been deposited in NCBI Gene Expression Omnibus, with series accession number GSE167000. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository (Perez-Riverol et al., 2019) with the dataset identifier ProteomeXchange: PXD022817. The mass cytometry data has been deposited in Flow Repository: FR-FCM-Z367. The metabolomics data have been deposited in the Metabolomics Workbench: PR001110. All code required to run the COVIDome Explorer applications can be found at https://github.com/cusom/CUSOM.COVIDome.Shiny-Apps (Zenodo https://doi.org/10.5281/zenodo.5081091) and https://github.com/cusom/CUSOM.ShinyHelpers (Zenodo https://doi.org/10.5281/zenodo.5081093). Any additional information required to reanalyze the data reported in this paper is available from the lead contact upon request.

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Lead contact