A comprehensive collection of systems biology data characterizing the host response to viral infection

The Systems Biology for Infectious Diseases Research program was established by the U.S. National Institute of Allergy and Infectious Diseases to investigate host-pathogen interactions at a systems level. This program generated 47 transcriptomic and proteomic datasets from 30 studies that investigat...

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Published in:	Scientific data Vol. 1; no. 1; p. 140033
Main Authors:	Aevermann, Brian D., Pickett, Brett E., Kumar, Sanjeev, Klem, Edward B., Agnihothram, Sudhakar, Askovich, Peter S., Bankhead, Armand, Bolles, Meagen, Carter, Victoria, Chang, Jean, Clauss, Therese R.W., Dash, Pradyot, Diercks, Alan H., Eisfeld, Amie J., Ellis, Amy, Fan, Shufang, Ferris, Martin T., Gralinski, Lisa E., Green, Richard R., Gritsenko, Marina A., Hatta, Masato, Heegel, Robert A., Jacobs, Jon M., Jeng, Sophia, Josset, Laurence, Kaiser, Shari M., Kelly, Sara, Law, G. Lynn, Li, Chengjun, Li, Jiangning, Long, Casey, Luna, Maria L., Matzke, Melissa, McDermott, Jason, Menachery, Vineet, Metz, Thomas O., Mitchell, Hugh, Monroe, Matthew E., Navarro, Garnet, Neumann, Gabriele, Podyminogin, Rebecca L., Purvine, Samuel O., Rosenberger, Carrie M., Sanders, Catherine J., Schepmoes, Athena A., Shukla, Anil K., Sims, Amy, Sova, Pavel, Tam, Vincent C., Tchitchek, Nicolas, Thomas, Paul G., Tilton, Susan C., Totura, Allison, Wang, Jing, Webb-Robertson, Bobbie-Jo, Wen, Ji, Weiss, Jeffrey M., Yang, Feng, Yount, Boyd, Zhang, Qibin, McWeeney, Shannon, Smith, Richard D., Waters, Katrina M., Kawaoka, Yoshihiro, Baric, Ralph, Aderem, Alan, Katze, Michael G., Scheuermann, Richard H.
Format:	Journal Article
Language:	English
Published:	London Nature Publishing Group UK 14-10-2014 Nature Publishing Group
Subjects:	631/114/129 631/114/2164 631/326/596/2553 631/553/1833 Animals BASIC BIOLOGICAL SCIENCES Coronaviridae Coronavirus Data Collection Data Descriptor data mining Databases, Factual Host-Pathogen Interactions Humanities and Social Sciences Humans Influenza A virus - pathogenicity Influenza A virus - physiology Influenza, Human - physiopathology Influenza, Human - virology Mice multidisciplinary Orthomyxoviridae Orthomyxoviridae Infections - physiopathology Orthomyxoviridae Infections - virology proteomics SARS coronavirus Science systems analysis Systems Biology transcriptomics viral host response
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Summary:	The Systems Biology for Infectious Diseases Research program was established by the U.S. National Institute of Allergy and Infectious Diseases to investigate host-pathogen interactions at a systems level. This program generated 47 transcriptomic and proteomic datasets from 30 studies that investigate in vivo and in vitro host responses to viral infections. Human pathogens in the Orthomyxoviridae and Coronaviridae families, especially pandemic H1N1 and avian H5N1 influenza A viruses and severe acute respiratory syndrome coronavirus (SARS-CoV), were investigated. Study validation was demonstrated via experimental quality control measures and meta-analysis of independent experiments performed under similar conditions. Primary assay results are archived at the GEO and PeptideAtlas public repositories, while processed statistical results together with standardized metadata are publically available at the Influenza Research Database ( www.fludb.org ) and the Virus Pathogen Resource ( www.viprbrc.org ). By comparing data from mutant versus wild-type virus and host strains, RNA versus protein differential expression, and infection with genetically similar strains, these data can be used to further investigate genetic and physiological determinants of host responses to viral infection. Design Type(s) time series design • dose response design • strain comparison design • species comparison design • genetic modification design Measurement Type(s) protein expression profiling • transcription profiling assay Technology Type(s) mass spectrometry assay • DNA microarray Factor Type(s) Genotype • Pathogen • Dose • Timepoint • Replicate Sample Characteristic(s) Homo sapiens • Mus musculus • lung adenocarcinoma cell line • lung • Calu-3 cell • Calu3 cell (2B4 clonal line) • Human Airway Epithelial (HAE) cell Machine-accessible metadata file describing the reported data (ISA-Tab format)
Bibliography:	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 AC05-76RL01830 PNNL-SA-101269 USDOE Office of Science (SC), Biological and Environmental Research (BER) Present address: Kineta, Inc. 219 Terry Ave N Suite 300, Seattle, WA, USA Present address: Diagnostic Discovery, Genentech, Inc., South San Francisco, CA, USA Brian D. Aevermann prepared manuscript materials and curated data for loading into IRD/ViPR. Brett E. Pickett prepared manuscript materials and performed data analysis. Sanjeev Kumar responsible for databasing data in IRD/ViPR. Edward B. Klem provided input on manuscript. Sudhakar Agnihothram performed SARS-CoV mouse and cell experiments. Peter S. Askovich contributed to experiment design, data analysis, and methods development. Armand Bankhead III contributed to conception and experimental design, data analysis, and computational modelling. Meagen Bolles performed SARS-CoV mouse and cell experiments. Victoria Carter processed samples for microarray analysis and performed microarray assays. Jean Chang processed samples for microarray analysis and performed microarray assays. Therese R.W. Clauss operated LC-MS instrumentation for quantitative phosphoproteomics analyses. Pradyot Dash contributed to experiment design, mouse infections, tissue collection. Alan H. Diercks contributed to experiment design, data analysis, and methods development. Amie J. Eisfel contributed to experimental design, data analysis, and sample processing; edited manuscript. Amy Ellis performed A/California/04/2009 pandemic influenza virus cell experiments. Shufang Fan performed A/Viet Nam/1203/2004 avian influenza virus cell experiments. Martin T. Ferris titered A/California/04/2009 samples. Lisa E. Gralinski performed mouse infections using A/California/04/2009 virus, contributed to experimental design. Richard R. Green data dissemination and data submissions to ViPR/IRD. Marina A. Gritsenko prepared cell samples for quantitative phosphoproteomics analyses. Masato Hatta generated mutant influenza viruses and characterized viruses in cell culture and animal models. Robert A Heegel operated LC-MS instrumentation for quantitative proteomics analyses. Jon M. Jacobs participated in design of proteomics experiments. Sophia Jeng contributed to data analysis. Laurence Josset contributed to data QC and analysis. Shari M. Kaiser contributed to experiment design, sample preparation. Sara Kelly processed samples for microarray analysis and performed microarray assays. G. Lynn Law designed experiments, monitored data quality, data analysis, data dissemination and data submissions to ViPR/IRD. Chengjun Li performed A/Viet Nam/1203/2004 avian influenza virus cell and mouse experiments. Jianing Li performed data analysis. Casey Long performed viral infections, performed plaque assays, and prepared samples. Maria L. Luna prepared cell and lung samples for quantitative proteomics analyses. Melissa Matzke performed initial proteomic data analysis. Jason McDermott contributed to conception and experimental design and performed computational analysis. Vineet Menachery performed SARS-CoV mouse and cell experiments. Thomas O. Metz managed the Center for Systems Virology’s Proteomics and Metabolomics Core, designed proteomics experiments, monitored data quality, and processed quantitative proteomics data. Hugh Mitchell performed the computational analysis. Matthew E. Monroe constructed cell and lung accurate mass and time tag databases, monitored automated processing of quantitative proteomics data, and transferred proteomics raw data files to public repositories. Garnet Navarro performed sample preparation, methods development. Gabriele Neumann contributed to conception and experimental design. Rebecca L. Podyminogin performed sample preparation. Samuel O. Purvine maintained protein reference data files. Carrie M Rosenberger participated in experiment design. Catherine. J Sanders participated in experiment design, mouse infections. Athena A. Schepmoes prepared cell and lung samples for quantitative proteomics analyses. Anil K. Shukla operated LC-MS instrumentation for quantitative proteomics analyses. Amy Sims contributed to conception and experimental design, performed SARS-CoV cell and HAE experiments. Pavel Sova performed qPCR assays. Vincent C. Tam participated experiment design, sample preparation, methods development. Nicolas Tchitchek performed computational analysis, Paul G. Thomas participated experiment design, tissue collection. Susan C. Tilton performed initial proteomic data analysis. Allison Totura performed mouse infections. Jing Wang performed initial proteomic data analysis. Bobbie-Jo Webb-Robertson performed initial proteomic data analysis. Ji Wen performed initial proteomic data analysis. Jeffrey M. Weiss performed qPCR assays, data dissemination and data submissions to ViPR/IRD. Feng Yang participated in design of phosphoproteomics and monitored data quality. Boyd Yount maintained viral stocks; safety test materials for inactivation of the SARS-CoV. Qibin Zhang participated in design of proteomics experiments. Shannon McWeeney contributed to conception, experimental design, manuscript editing and approval. Richard D. Smith contributed to conception, experimental design, manuscript editing and approval. Katrina M. Waters contributed to conception, experimental design and proteomic measurement capabilities, manuscript editing and approval. Yoshihiro Kawaoka contributed to conception, experimental design, manuscript editing and approval. Ralph Baric contributed to conception, experimental design, manuscript editing and approval. Alan Aderem contributed to conception, participated in experiment design. Michael G. Katze contributed to conception, experimental design, manuscript editing and approval. Richard H. Scheuermann prepared manuscript materials, designed the validation and usage examples, interpreted results.
ISSN:	2052-4463 2052-4463
DOI:	10.1038/sdata.2014.33