{"database":"MassIVE","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Other":["ftp://massive-ftp.ucsd.edu/v01/MSV000080026/"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":{"citationCount":0,"reanalysisCount":0,"viewCount":0,"searchCount":0},"additional":{"omics_type":["Proteomics"],"submitter":["Yoshihiro Kawaoka, Katrina Waters, Richard Smith and Thomas Metz"],"instrument_platform":["LTQ Orbitrap"],"species":["Influenza A Virus (a/wilson-smith/1933(h1n1)) (ncbitaxon:381518)","Homo Sapiens (ncbitaxon:9606)"],"full_dataset_link":["https://massive.ucsd.edu/ProteoSAFe/dataset.jsp?task=2246d50906e24b2e8e181acac5f4503d"],"sample_protocol":[""],"repository":["MassIVE"],"file_size":["129"],"ptm_modification":["UNIMOD:4 - \"Iodoacetamide derivative.\"","UNIMOD:35 - \"Oxidation or Hydroxylation.\""],"data_protocol":[""],"pubmed_abstract":["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."],"pubmed_title":["A compendium of multi-omics data illuminating host responses to lethal human virus infections."],"pubmed_authors":["Eisfeld Amie J AJ, Anderson Lindsey N LN, Fan Shufang S, Walters Kevin B KB, Halfmann Peter J PJ, Westhoff Smith Danielle D, Thackray Larissa B LB, Tan Qing Q, Sims Amy C AC, Menachery Vineet D VD, Schäfer Alexandra A, Sheahan Timothy P TP, Cockrell Adam S AS, Stratton Kelly G KG, Webb-Robertson Bobbie-Jo M BM, Kyle Jennifer E JE, Burnum-Johnson Kristin E KE, Kim Young-Mo YM, Nicora Carrie D CD, Peralta Zuleyma Z, N'jai Alhaji U AU, Sahr Foday F, van Bakel Harm H, Diamond Michael S MS, Baric Ralph S RS, Metz Thomas O TO, Smith Richard D RD, Kawaoka Yoshihiro Y, Waters Katrina M KM"],"description_synonyms":["MGC130048, gamma sarcoglycan, Culture Techniques, SGCG_HUMAN, DMDA1, 35 kDa dystrophin-associated glycoprotein, Peptidomics, SG-gamma, A4, gamma (35kDa dystrophin-associated glycoprotein), Cell, TYPE, Cell Culture Technique, SGCG, DAGA4, DMDA, 35kD dystrophin-associated glycoprotein, SCARMD2, 35DAG, Cell Cultures, gamma-sarcoglycan, sarcoglycan, LGMD2C., MAM, gamma-SG, Cell Culture, SCG3, Culture Technique"],"pubmed_abstract_synonyms":["Panomics, Experimental Designs, Networks, Viridae, MGC130048, host organism, deceased, Bru, Research Technique, Problem Formulations, Kinship, Adjustments, RNA Sequence Determination, Raw, Laboratory, Sequence Determination, Lipidomic, Mus domesticus, RNA Sequence, Design, Error Sources, Metabonomic, Infestations and Infections, A4, Virus Infection, Metabonomics, Cardiac Death, Technic, End-Of-Life, House Mouse, Virus Disease, Long Term, Transcript Expression Analysis, Techniques, Influenza Virus, diseases, Method, Virus, Gene Expression Monitorings, Virus Infections, Life Cycle, diseases and disorders, Analysis, Profilings, Effect, Family Life Cycle, Experimental Design, Mass Spectrum Analysis, Group, Svc, gamma sarcoglycan, Immune Processes, human disease, Immune Responses, Man (Taxonomy), Kinship Network, Viral Diseases, reference sample, Analyses, Determination, Matched Group, Torovirinae, Designs, Matched, End Of Life, Swiss Mice, Groups, procedures, Filovirus, Sequence Determinations, Gene Expression Analysis, Immune, Methodological Studies, Vira, Reporting, Research Techniques, gamma-sarcoglycan, Homo sapiens disease, Infections and Infestations, house mouse, Family Life Cycles, Long-Term Effects, Data Reporting, dysfunction., Flavivirus (arbovirus group B), Viral, Process, Research Technic, Research Methodology, statistics and numerical data, Modern, mouse, SG-gamma, Coronavirinae, Longterm Effect, Monitorings, Research Proposals, infections, Procedure, not genetically inherited, Spectrum Analysis, Research Proposal, Determinations, Spectroscopy, Gene Expression, Experimental, Influenza Viruses, Diseases, Metatags, numerical data, Near-Death Experience, sarcoglycan, Bafinivirus, Technics, Problem Formulation, Filiation, Problem, Orthomyxoviruses, White bream virus, Mus musculus, Multi Omics, Determination of Death, Bafiniviruses, Viral Infections, mice, Transcriptome Profilings, Viral Disease, Swiss Mouse, Integrative, Spectrometry, Infection and Infestation, Methodological, gamma (35kDa dystrophin-associated glycoprotein), Methodological Study, human, domesticus, Formulations, Life Cycles, disease, Lipidome, DMDA, Gene Expression Analyses, 35kD dystrophin-associated glycoprotein, microarray, Animal Viruses, Mouse, Expression Analysis, Interferon, Data Adjustments, humans, other disease, Orthomyxovirus, human being, Family Member, SGCG_HUMAN, Procedures, Effects, Peptidomics, Matched Groups, Myxovirus, Gene, Scoring Method, Network, Spectrum Analyses, TYPE, Human, Gene Expression Profilings, Multi-Omics, DAGA4, Adjustment, mRNA Differential Displays, Cardiac, Gene Expression Pattern Analysis, Homo sapiens, House, utilization, Scoring Methods, Sources, 35DAG, Studies, Mass, disease or disorder, Mus musculus domesticus, Del(8)44H, Animal, Metabolomic, MAM, gamma-SG, Mice, SCG3, Man, Technique, Mass Spectroscopy, Animal Virus, Methodology, Myxoviruses, Viruses, Scoring, Infections, Research, Longterm, Proposals, Swiss, Transcriptomics, Omics, Long-Term, Transcript Expression, Transcriptome Analysis, clinical infection, Sequencing, Monitoring, Research Strategy, non-neoplastic, Study, Infestation and Infection, Immune Response, RNA Sequence Analyses, Error Source, disorder, RNA Sequencing, Pan-Omics, Long-Term Effect, Kinship Networks, Strategies, Expression Analyses, Immune Process, Family, Metatag, Controlled, Sequence Analyses, Viral Infection, Profiling, RNA, Controlling, Disease, Integrative-Omics, use, Transcriptome, Family Research, 35 kDa dystrophin-associated glycoprotein, RNA Sequence Determinations, disorders, Lipidomes, Formulation, medical condition, Integrative Omics, Cell, SGCG, LGMD2C, Family Members, Research Strategies, viruses, Differential Display, Transcript Expression Analyses, MS, Mus, Long Term Effects, post-mortem, Infection, Multi-Omic, Pan Omics, condition, techniques, Zoophaginae, Death, mRNA Differential Display, Mass Spectrum Analyses, Proposal, Methods, Mass Spectrum, Gene Expression Monitoring, death, Col4a-1, Transcriptome Profiling, DMDA1, mRNA, Source, Research Designs, House Mice, Research Technics, Differential Displays, pathophysiology, Transcriptome Analyses, Longterm Effects, Laboratory Mice, Data Adjustment, Error, Data, White bream viruses, Families, Modern Man, RNA Sequence Analysis, SCARMD2, Response, Filoviruses, Strategy, Relatives, Laboratory Mouse, Severe, methodology"],"pubmed_title_synonyms":["Panomics, Multi Omics, host organism, Disease, Integrative-Omics, human being, Viral, Man (Taxonomy), Viral Diseases, Infections, Viral Infection., Viral Infections, Modern, Viral Disease, Integrative, Virus Infection, Omics, Integrative Omics, Virus Disease, human, Human, Multi-Omics, Homo sapiens, Modern Man, Diseases, Multi-Omic, Infection, Virus, Pan Omics, Virus Infections, Pan-Omics, Man, humans"],"name_synonyms":["Viridae, viruses, Animal Virus, Viruses, Vira, Virus, Calu-3, total expressed protein, Animal Viruses, Animal, Animal., Zoophaginae, Proteomes"],"citation_count":["0"],"additional_accession":[]},"is_claimable":true,"name":"Calu-3 cell proteome response to H1N1 virus","description":"Proteomics data from cell culture; Treated with wild-type H1N1 and mockulum; 5 biological replicates","dates":{"publication":"Thu Aug 04 14:46:00 BST 2016"},"accession":"MSV000080026","cross_references":{"pubmed":["38565538"]}}