Project - Modelling Omics Lethal Human Viruses Project Profiling of the Host Response to Influenza A Virus Infection, Processed Experimental Dataset Catalog

Last updated on 2024-02-11T22:41:43+00:00 by LN Anderson

Omics-LHV Profiling of Host Response to Influenza A Virus Infection

Background

Influenza A virus (IAV) is a high risk biological agent belonging to the Orthomyxoviridae family is classified as a Category C priority pathogen by the National Institute of Allergy and Infectious Diseases (NIAID), and known to cause severe respiratory disease with high mortality rates in humans. Lethal host-pathogen invasion mechanisms and the cellular intricacies behind these fatal infections still remain unclear. The NIAID Modeling Host Responses to Understand Severe Human Virus Infections Research Program project (2013 - 2018) aimed to develop an improved comprehensive understanding of the host response to a suite of viruses causing lethal infections leveraging a systems biology approach. This project was comprised of a multidisciplinary team of researchers with expertise in virology, host genetics, advanced high-throughput technologies, computational modeling, and data management integration strategies for quantifying the host immune response to cellular trafficking activities identified in primary host tissues and cell lines.

Impact

Herein, PNNL sub-projects provide a never before released comprehensive infectious disease collection of primary and secondary transformation multi-Omics data profiling a series of priority pathogen primary experimental studies for enhanced open-access to viral Omics lifecycle datasets and project metadata. The knowledge gained from this work is expected to provide a strong foundation in facilitating a better understanding and treatment of Influenza A virus infections in humans for development of improved strategies for intervening with lethal virus disease, and unveiling mechanisms from highly collaborative state-of-the-art systems biology methodologies and unique data capture capabilities.

Viral Project Reference Citations

1. Anderson, Lindsey N, Eisfeld, Amie J, Waters, Katrina M, and Modeling Host Responses to Understand Severe Human Virus Infections Program Project. PNNL DataHub Project: Omics Lethal Human Viruses Project Profiling of the Host Response to Influenza A Virus Infection, Processed Experimental Dataset Catalog. United States. 2021. PNNL DataHub (Web). DOI: 10.25584/LHVFLU/1773428.
2. Eisfeld, A.J., Anderson, L.N., Fan, S. et al. A compendium of multi-omics data illuminating host responses to lethal human virus infections. Sci Data 11, 328 (2024). https://doi.org/10.1038/s41597-024-03124-3

Accessible Digital Data DOI Downloads

Secondary host-associated viral dataset downloads contain one or more statistically processed (normalization data transformation)  quantitative dataset collections resulting in qualitative expression analyses of primary host-pathogen experimental study designs. Leveraging unique high-resolution Omics capabilities for proteomics (P), metabolomics (M), lipidomics (L), and transcriptomics (T) dataset downloads each have a direct relationship to a primary sample submission corresponding to a specific Influenza A virus strain representing an H1N1, H5N1, H7N9 subtype experimental infection study.

• (P) Protein quantification by liquid chromatography mass spectrometry (LC-MS)
• (M) Metabolite quantification by gas chromatography mass spectrometry (GC-MS)
• (L) Lipid quantification by liquid chromatography mass spectrometry (LC-MS)
• (T) Expression profiling by array (mRNA) and/or Non-coding RNA profiling by array (miRNA)

Multi-omic Dataset Collections

Note: ICL105 and ICL106 provide primary metadata only and do not contain processed data downloads. DOIs represent metadata documentation archival and serve to support raw measurement data located at the primary data repository.

1. ICL102 DataHub DOI: 10.25584/LHVICL102/1661912 (PMLT)
2. ICL103 DataHub DOI: 10.25584/LHVICL103/1661913 (PMLT)
3. ICL104 DataHub DOI: 10.25584/LHVICL104/1661914 (PMLT)
4. ICL105 DataHub DOI: 10.25584/LHVICL105/1661915 (experimental metadata only)
5. ICL106 DataHub DOI: 10.25584/LHVICL105/1661916 (experimental metadata only)
6. IM101 DataHub DOI: 10.25584/LHVIM101/1661917 (T)
7. IM102 DataHub DOI: 10.25584/LHVIM102/1661918 (PMLT)
8. IM103 DataHub DOI: 10.25584/LHVIM103/1661919 (PMLT)

Host sample types include human lung adenocarcinoma cells (Calu-3) and mouse (strain C57BL/6J) whole lung tissue collections. 

Linked Primary Data Repository Standards

Sequencing Raw Measurement Data (T) 

Primary transcriptome experimental data collections and associated metadata are openly available from the Gene Expression Omnibus (GEO) data repository and have been linked to primary publication data accessions where possible. The GEO data repository is a public domain community data repository supported by the NIH, for promoting the free exchange of MIAME-compliant gene expression profile and array-based data for reuse and discovery.  

Mass Spectrometry Raw Measurement Data (PML)

Primary mass spectrometry proteome, metabolome, and lipidome experimental data and corresponding parameter files, including those used for accurate mass and time (AMT) tag database generation, are openly available for download at the Mass Spectrometry Interactive Virtual Environment (MassIVE). MassIVE is a public domain community data repository promoting the free exchange of mass spectrometry data for reuse and discovery. 

Acknowledgment of Federal Funding

The data described here was funded in whole or in part by the National Institute of Allergy and Infectious Diseases, of the National Institutes of Health under award number U19AI106772 and is a contribution of the "Modeling Host Responses to Understand Severe Human Virus Infections" Project at Pacific Northwest National Laboratory. Data generated by the Omics-LHV Core for proteomics, metabolomics, and lipidomics analyses for were performed at Pacific Northwest National Laboratory in the Environmental Molecular Sciences Laboratory, a national scientific user facility sponsored by the Department of Energy’s (DOE) Office, operating under the Battelle Memorial Institute for the DOE under contract number DE-AC05-76RLO1830. 

Citation Policy

In efforts to enable discovery, reproducibility, and reuse of NIH-funded project dataset citations, we ask that all reuse of project data and metadata download materials acknowledge all primary and secondary dataset citations where applicable and direct corresponding journal articles (Grant U19AI106772) where allowable in accordance with best practices outlined by the FORCE11 Joint Declaration of Data Citation Principles in alignment with NIH acknowledgement requirements.

Data Licensing

CC BY 4.0 (dataset DOI downloads), CC0 1.0 (PNNL DataHub policy default)