A compendium of multi-omics data illuminating host responses to lethal human virus infections.
Amie J Eisfeld, Lindsey N Anderson, Shufang Fan, Kevin B Walters, Peter J Halfmann, Danielle Westhoff Smith, Larissa B Thackray, Qing Tan, Amy C Sims, Vineet D Menachery, Alexandra Schäfer, Timothy P Sheahan, Adam S Cockrell, Kelly G Stratton, Bobbie-Jo M Webb-Robertson, Jennifer E Kyle, Kristin E Burnum-Johnson, Young-Mo Kim, Carrie D Nicora, Zuleyma Peralta, Alhaji U N'jai, Foday Sahr, Harm van Bakel, Michael S Diamond, Ralph S Baric, Thomas O Metz, Richard D Smith, Yoshihiro Kawaoka, Katrina M Waters
Author Information
Amie J Eisfeld: Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, 53706, USA. amie.eisfeld@wisc.edu.
Lindsey N Anderson: Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA. ORCID
Shufang Fan: Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, 53706, USA.
Kevin B Walters: Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, 53706, USA.
Peter J Halfmann: Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, 53706, USA.
Danielle Westhoff Smith: Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, 53706, USA.
Larissa B Thackray: Department of Medicine, Washington University School of Medicine, Saint Louis, MO, 63110, USA.
Qing Tan: Department of Medicine, Washington University School of Medicine, Saint Louis, MO, 63110, USA.
Amy C Sims: Department of Epidemiology, University of North Carolina at Chapel Hill, North Carolina, 27599, USA.
Vineet D Menachery: Department of Epidemiology, University of North Carolina at Chapel Hill, North Carolina, 27599, USA.
Alexandra Schäfer: Department of Epidemiology, University of North Carolina at Chapel Hill, North Carolina, 27599, USA. ORCID
Timothy P Sheahan: Department of Epidemiology, University of North Carolina at Chapel Hill, North Carolina, 27599, USA.
Adam S Cockrell: Department of Epidemiology, University of North Carolina at Chapel Hill, North Carolina, 27599, USA.
Kelly G Stratton: Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA. ORCID
Bobbie-Jo M Webb-Robertson: Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA. ORCID
Jennifer E Kyle: Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA. ORCID
Kristin E Burnum-Johnson: Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
Young-Mo Kim: Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA. ORCID
Carrie D Nicora: Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA. ORCID
Zuleyma Peralta: Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York City, NY, 10029, USA.
Alhaji U N'jai: Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, 53706, USA.
Foday Sahr: Department of Microbiology, College of Medicine and Health Sciences, University of Sierra Leone, Freetown, Sierra Leone.
Harm van Bakel: Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York City, NY, 10029, USA. ORCID
Michael S Diamond: Department of Medicine, Washington University School of Medicine, Saint Louis, MO, 63110, USA.
Ralph S Baric: Department of Epidemiology, University of North Carolina at Chapel Hill, North Carolina, 27599, USA. ORCID
Thomas O Metz: Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA. ORCID
Richard D Smith: Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA. ORCID
Yoshihiro Kawaoka: Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, 53706, USA. ORCID
Katrina M Waters: Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA. katrina.waters@pnnl.gov. ORCID
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.
