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

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

doi:10.1038/s41597-024-03124-3

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

Journal Article · Tue Apr 02 00:00:00 EDT 2024 · Scientific Data

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

Eisfeld-Fenney, Amie J. ^[1]; ^[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]; ^[4]; Sheahan, Timothy P. ^[4]; Cockrell, Adam S. ^[4]; ^[2]; ^[2]; ^[2]; ^[2]; ^[2]; ^[2]; Peralta, Zuleyma ^[5] more »

University of Wisconsin, Madison, WI (United States)
Pacific Northwest National Laboratory (PNNL), Richland, WA (United States). Earth and Biological Sciences Directorate
Washington University, St. Louis, MO (United States)
University of North Carolina, Chapel Hill, NC (United States)
Icahn School of Medicine at Mount Sinai, New York, NY (United States)
University of Wisconsin, Madison, WI (United States); Fourah Bay College, Freetown (Sierra Leone); California University of Science and Medicine, Colton, CA (United States)
University of Sierra Leone, Freetown (Sierra Leone)
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.

View Accepted Manuscript (DOE)

Research Organization:: Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)

Sponsoring Organization:: National Institutes of Health (NIH); USDOE

Grant/Contract Number:: AC05-76RL01830

OSTI ID:: 2335704

Report Number(s):: PNNL-SA--189528

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

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Eh001 Waters, Katrina; Anderson, Lindsey; McDermott, Jason Pacific Northwest National Laboratory 2; EMSL; PNNL https://doi.org/10.25584/LHVEH001/1661904	dataset	January 2020
Ehuh001 Waters, Katrina; Anderson, Lindsey; McDermott, Jason Pacific Northwest National Laboratory 2; EMSL; PNNL https://doi.org/10.25584/LHVEHUH001/1661905	dataset	January 2020
Ehuh002 Waters, Katrina; Anderson, Lindsey; McDermott, Jason Pacific Northwest National Laboratory 2; EMSL; PNNL https://doi.org/10.25584/LHVEHUH002/1661906	dataset	January 2020
Ehuh003 Waters, Katrina; Anderson, Lindsey; McDermott, Jason Pacific Northwest National Laboratory 2; EMSL; PNNL https://doi.org/10.25584/LHVEHUH003/1661907	dataset	January 2020
Ehuvec001 Waters, Katrina; Anderson, Lindsey; McDermott, Jason Pacific Northwest National Laboratory 2; EMSL; PNNL https://doi.org/10.25584/LHVEHUVEC001/1661908	dataset	January 2020
Eu937001 Waters, Katrina; Anderson, Lindsey; McDermott, Jason Pacific Northwest National Laboratory 2; EMSL; PNNL https://doi.org/10.25584/LHVEU937001/1661911	dataset	January 2020
PNNL DataHub Project Omics-LHV Profiling of Host Response to Influenza Infection Post-Processed Data Package DOIs Anderson, Lindsey; McDermott, Jason; Waters, Katrina Pacific Northwest National Laboratory 2; PNNL https://doi.org/10.25584/LHVFLU/1773428	dataset	January 2021
Icl102 Waters, Katrina; Anderson, Lindsey; McDermott, Jason Pacific Northwest National Laboratory 2; EMSL; PNNL https://doi.org/10.25584/LHVICL102/1661912	dataset	January 2020
Icl103 Waters, Katrina; Anderson, Lindsey; McDermott, Jason Pacific Northwest National Laboratory 2; EMSL; PNNL https://doi.org/10.25584/LHVICL103/1661913	dataset	January 2020
Icl104 Waters, Katrina; Anderson, Lindsey; McDermott, Jason Pacific Northwest National Laboratory 2; EMSL; PNNL https://doi.org/10.25584/LHVICL104/1661914	dataset	January 2020
Icl105 Waters, Katrina; Anderson, Lindsey; McDermott, Jason Pacific Northwest National Laboratory 2; EMSL; PNNL https://doi.org/10.25584/LHVICL105/1661915	dataset	January 2020
Icl106 Waters, Katrina; Anderson, Lindsey; McDermott, Jason Pacific Northwest National Laboratory 2; EMSL; PNNL https://doi.org/10.25584/LHVICL106/1661916	dataset	January 2020
PNNL DataHub Project: Omics Lethal Human Viruses Project Profiling of the Host Interferon-Stimulated Response to Virus Infection, Processed Experimental Dataset Catalog Anderson, Lindsey; McDermott, Jason; Waters, Katrina Pacific Northwest National Laboratory 2; PNNL https://doi.org/10.25584/LHVIFN/1786979	dataset	January 2021
Ifnfb001 Waters, Katrina; Anderson, Lindsey; McDermott, Jason Pacific Northwest National Laboratory 2; EMSL; PNNL https://doi.org/10.25584/LHVIFNFB001/1661927	dataset	January 2020
Ifnmve001 Waters, Katrina; Anderson, Lindsey; McDermott, Jason Pacific Northwest National Laboratory 2; EMSL; PNNL https://doi.org/10.25584/LHVIFNMVE001/1661928	dataset	January 2020
Omics-Lethal Human Viruses, Interferon-Stimulated Response Experiment IFNaCL001 Anderson, Lindsey N.; Eisfeld, Amie J.; Waters, Katrina M. https://doi.org/10.25584/LHVIFNaCL001/1661929	dataset	January 2021
IFNaIHH01 Waters, Katrina; Anderson, Lindsey; McDermott, Jason Pacific Northwest National Laboratory 2; EMSL; PNNL https://doi.org/10.25584/LHVIFNaIHH01/1661926	dataset	January 2020
IFNaaHUHH0011 Waters, Katrina; Anderson, Lindsey; McDermott, Jason Pacific Northwest National Laboratory 2; EMSL; PNNL https://doi.org/10.25584/LHVIFNaaHUHH0011/1661922	dataset	January 2020
Im101 Waters, Katrina; Anderson, Lindsey; McDermott, Jason Pacific Northwest National Laboratory 2; EMSL; PNNL https://doi.org/10.25584/LHVIM101/1661917	dataset	January 2020
Im102 Waters, Katrina; Anderson, Lindsey; McDermott, Jason Pacific Northwest National Laboratory 2; EMSL; PNNL https://doi.org/10.25584/LHVIM102/1661918	dataset	January 2020
Im103 Waters, Katrina; Anderson, Lindsey; McDermott, Jason Pacific Northwest National Laboratory 2; EMSL; PNNL https://doi.org/10.25584/LHVIM103/1661919	dataset	January 2020
Mcl001 Waters, Katrina; Anderson, Lindsey; McDermott, Jason Pacific Northwest National Laboratory 2; EMSL; PNNL https://doi.org/10.25584/LHVMCL001/1661931	dataset	January 2020
Mcl002 Waters, Katrina; Anderson, Lindsey; McDermott, Jason Pacific Northwest National Laboratory 2; EMSL; PNNL https://doi.org/10.25584/LHVMCL002/1661933	dataset	January 2020
Mcl003 Waters, Katrina; Anderson, Lindsey; McDermott, Jason Pacific Northwest National Laboratory 2; EMSL; PNNL https://doi.org/10.25584/LHVMCL003/1661945	dataset	January 2020
Mcl004 Waters, Katrina; Anderson, Lindsey; McDermott, Jason Pacific Northwest National Laboratory 2; EMSL; PNNL https://doi.org/10.25584/LHVMCL004/1661946	dataset	January 2020
Mcl005 Waters, Katrina; Anderson, Lindsey; McDermott, Jason Pacific Northwest National Laboratory 2; EMSL; PNNL https://doi.org/10.25584/LHVMCL005/1661947	dataset	January 2020
Omics Lethal Human Viruses Project Profiling of the Host Response to MERS-CoV Infection, Processed Experimental Dataset Catalog Anderson, Lindsey; McDermott, Jason; Waters, Katrina Pacific Northwest National Laboratory 2; PNNL https://doi.org/10.25584/LHVMERS/1813911	dataset	January 2021
Mfb001 Waters, Katrina; Anderson, Lindsey; McDermott, Jason Pacific Northwest National Laboratory 2; EMSL; PNNL https://doi.org/10.25584/LHVMFB001/1661935	dataset	January 2020
Mfb002 Waters, Katrina; Anderson, Lindsey; McDermott, Jason Pacific Northwest National Laboratory 2; EMSL; PNNL https://doi.org/10.25584/LHVMFB002/1661936	dataset	January 2020
Mfb003 Waters, Katrina; Anderson, Lindsey; McDermott, Jason Pacific Northwest National Laboratory 2; EMSL; PNNL https://doi.org/10.25584/LHVMFB003/1661937	dataset	January 2020
Mhae001 Waters, Katrina; Anderson, Lindsey; McDermott, Jason Pacific Northwest National Laboratory 2; EMSL; PNNL https://doi.org/10.25584/LHVMHAE001/1661938	dataset	January 2020
Mhae002 Waters, Katrina; Anderson, Lindsey; McDermott, Jason Pacific Northwest National Laboratory 2; EMSL; PNNL https://doi.org/10.25584/LHVMHAE002/1661939	dataset	January 2020
Mhae003 Waters, Katrina; Anderson, Lindsey; McDermott, Jason Pacific Northwest National Laboratory 2; EMSL; PNNL https://doi.org/10.25584/LHVMHAE003/1661940	dataset	January 2020
Mm001 Waters, Katrina; Anderson, Lindsey; McDermott, Jason Pacific Northwest National Laboratory 2; EMSL; PNNL https://doi.org/10.25584/LHVMM001/1661941	dataset	January 2020
Mmve001 Waters, Katrina; Anderson, Lindsey; McDermott, Jason Pacific Northwest National Laboratory 2; EMSL; PNNL https://doi.org/10.25584/LHVMMVE001/1661942	dataset	January 2020
Mmve002 Waters, Katrina; Anderson, Lindsey; McDermott, Jason Pacific Northwest National Laboratory 2; EMSL; PNNL https://doi.org/10.25584/LHVMMVE002/1661943	dataset	January 2020
Mmve003 Waters, Katrina; Anderson, Lindsey; McDermott, Jason Pacific Northwest National Laboratory 2; EMSL; PNNL https://doi.org/10.25584/LHVMMVE003/1661944	dataset	January 2020
Wcb001 Waters, Katrina; Anderson, Lindsey; McDermott, Jason Pacific Northwest National Laboratory 2; EMSL; PNNL https://doi.org/10.25584/LHVWCB001/1661948	dataset	January 2020
Wcn002 Waters, Katrina; Anderson, Lindsey; McDermott, Jason Pacific Northwest National Laboratory 2; EMSL; PNNL https://doi.org/10.25584/LHVWCN002/1661950	dataset	January 2020
Wcn003 Waters, Katrina; Anderson, Lindsey; McDermott, Jason Pacific Northwest National Laboratory 2; EMSL; PNNL https://doi.org/10.25584/LHVWCN003/1661952	dataset	January 2020
Wct001 Waters, Katrina; Anderson, Lindsey; McDermott, Jason Pacific Northwest National Laboratory 2; EMSL; PNNL https://doi.org/10.25584/LHVWCT001/1661954	dataset	January 2020
Wdc010 Waters, Katrina; Anderson, Lindsey; McDermott, Jason Pacific Northwest National Laboratory 2; EMSL; PNNL https://doi.org/10.25584/LHVWDC010/1661955	dataset	January 2020
Wdc011 Waters, Katrina; Anderson, Lindsey; McDermott, Jason Pacific Northwest National Laboratory 2; EMSL; PNNL https://doi.org/10.25584/LHVWDC011/1661956	dataset	January 2020
Wgcn002 Waters, Katrina; Anderson, Lindsey; McDermott, Jason Pacific Northwest National Laboratory 2; EMSL; PNNL https://doi.org/10.25584/LHVWGCN002/1661957	dataset	January 2020
Wgcn003 Waters, Katrina; Anderson, Lindsey; McDermott, Jason Pacific Northwest National Laboratory 2; EMSL; PNNL https://doi.org/10.25584/LHVWGCN003/1661958	dataset	January 2020
Wln002 Waters, Katrina; Anderson, Lindsey; McDermott, Jason Pacific Northwest National Laboratory 2; EMSL; PNNL https://doi.org/10.25584/LHVWLN002/1661960	dataset	January 2020
Wln003 Waters, Katrina; Anderson, Lindsey; McDermott, Jason Pacific Northwest National Laboratory 2; EMSL; PNNL https://doi.org/10.25584/LHVWLN003/1661961	dataset	January 2020
PNNL DataHub Omics Lethal Human Viruses Project, Modeling Host Responses to West Nile Infection Post-Processed Data Package DOIs Anderson, Lindsey; McDermott, Jason; Waters, Katrina Pacific Northwest National Laboratory 2; PNNL https://doi.org/10.25584/LHVWNV/1784305	dataset	January 2021
Wse001 Waters, Katrina; Anderson, Lindsey; McDermott, Jason Pacific Northwest National Laboratory 2; EMSL; PNNL https://doi.org/10.25584/LHVWSE001/1661962	dataset	January 2020
PNNL DataHub NIAID Program Project: Modeling Host Responses to Understand Severe Human Virus Infections, Multi-Omic Viral Dataset Catalog Collection Anderson, Lindsey; Eisfeld, Amie; Waters, Katrina Pacific Northwest National Laboratory (PNNL), Richland, WA (United States) https://doi.org/10.25584/PRJ.U19AI106772/1971764	dataset	January 2023
Immunopathogenesis of Different Emerging Viral Infections: Evasion, Fatal Mechanism, and Prevention Yang, Betsy; Yang, Kuender D. Frontiers in Immunology, Vol. 12 https://doi.org/10.3389/fimmu.2021.690976	journal	July 2021

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60 APPLIED LIFE SCIENCES
DataHub
Ebola virus
Interferon response
MERS-Coronavirus
Omics-LHV
West Nile virus
influenza A virus
mass spectrometry
microarray

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

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References (121)

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