A compendium of multi-omics data illuminating host responses to lethal human virus infections

Journal Article · 01 April 2024 · Scientific Data

DOI: https://doi.org/10.1038/s41597-024-03124-3 · OSTI ID:2335704

Eisfeld-Fenney, Amie J. ^[1]; Anderson, Lindsey N.  ^[2]; Fan, Shufang ^[1]; Walters, Kevin B. ^[1]; Halfmann, Peter J. ^[1]; Westhoff-Smith, Danielle ^[1]; Thackray, Larissa B. ^[3]; Tan, Qing ^[3]; Sims, Amy C. ^[4]; Menachery, Vineet D. ^[4]; Schafer, Alexandra  ^[4]; Sheahan, Timothy P. ^[4]; Cockrell, Adam S. ^[4]; Stratton, Kelly G.  ^[2]; Webb-Robertson, Bobbie-Jo M.  ^[2]; Kyle, Jennifer E.  ^[2]; Burnum-Johnson, Kristin E.  ^[2]; Kim, Young-Mo  ^[2]; Nicora, Carrie D.  ^[2]; Peralta, Zuleyma ^[5] ; N'jai, Alhaji U. ^[6]; Sahr, Foday ^[7]; van Bakel, Harm  ^[5]; Diamond, Michael S. ^[3]; Baric, Ralph S.  ^[4]; Metz, Thomas O.  ^[2]; Smith, Richard D.  ^[2]; Kawaoka, Yoshihiro  ^[8]; Waters, Katrina M.  ^[2]

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1. University of Wisconsin, Madison, WI (United States)
2. Pacific Northwest National Laboratory (PNNL), Richland, WA (United States). Earth and Biological Sciences Directorate
3. Washington University, St. Louis, MO (United States)
4. University of North Carolina, Chapel Hill, NC (United States)
5. Icahn School of Medicine at Mount Sinai, New York, NY (United States)
6. University of Wisconsin, Madison, WI (United States); Fourah Bay College, Freetown (Sierra Leone); California University of Science and Medicine, Colton, CA (United States)
7. University of Sierra Leone, Freetown (Sierra Leone)
8. University of Wisconsin, Madison, WI (United States); University of Tokyo (Japan); National Center for Global Health and Medicine Research Institute, Tokyo (Japan)

Human infections caused by viral pathogens trigger a complex gamut of host responses that limit disease, resolve infection, generate immunity, and contribute to severe disease or death. Here, we present experimental methods and multi-omics data capture approaches representing the global host response to infection generated from 45 individual experiments involving human viruses from the Orthomyxoviridae, Filoviridae, Flaviviridae, and Coronaviridae families. Analogous experimental designs were implemented across human or mouse host model systems, longitudinal samples were collected over defined time courses, and global multi-omics data (transcriptomics, proteomics, metabolomics, and lipidomics) were acquired by microarray, RNA sequencing, or mass spectrometry analyses. For comparison, we have included transcriptomics datasets from cells treated with type I and type II human interferon. Raw multi-omics data and metadata were deposited in public repositories, and we provide a central location linking the raw data with experimental metadata and ready-to-use, quality-controlled, statistically processed multi-omics datasets not previously available in any public repository. This compendium of infection-induced host response data for reuse will be useful for those endeavouring to understand viral disease pathophysiology and network biology.

• Research Organization: Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)
• Sponsoring Organization: USDOE; National Institutes of Health (NIH)
• Grant/Contract Number: AC05-76RL01830
• OSTI ID: 2335704
• Report Number(s): PNNL-SA--189528; {"","Journal ID: ISSN 2052-4463"}
• Journal Information: Scientific Data, Journal Name: Scientific Data Journal Issue: 1 Vol. 11; ISSN 2052-4463
• Publisher: Nature Publishing GroupCopyright Statement
• Country of Publication: United States
• Language: English