Last updated on 2023-01-30T00:09:57+00:00 by LN Anderson
Omics-LHV Profiling of Host Response to West Nile Virus Infection
West Nile virus (WNV) is classified as a Category B priority pathogen (mosquito-borne Flaviviridae) by the National Institute of Allergy and Infectious Diseases (NIAID), and are known to cause severe infections in humans where lethal host-associated mechanisms are not clearly defined. 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.
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 West Nile 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.
Anderson, Lindsey N, Eisfeld, Amie J, Waters, Katrina M, and Modeling Host Responses to Understand Severe Human Virus Infections Program Project. PNNL DataHub Omics-LHV Project Profiling of the Host Response to West Nile Virus Infection, a Processed Dataset DOI Catalog Experimental Collection. United States. 2021. PNNL DataHub (Web). DOI: https://doi.org/10.25584/LHVWNV/1784305
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 West Nile virus [NCBITAXON:11082] (WNV-NY99 382) 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)
Processed Omics Dataset Collections
- WCB001 DataHub DOI: 10.25584/LHVWCB001/1661948 (PMLT)
- WCN002 DataHub DOI: 10.25584/LHVWCN002/1661950 (T)
- WCN003 DataHub DOI: 10.25584/LHVWCN003/1661952 (T)
- WCT001 DataHub DOI: 10.25584/LHVWCT001/1661954 (PMLT)
- WDC010 DataHub DOI: 10.25584/LHVWDC010/1661955 (PT)
- WDC011 DataHub DOI: 10.25584/LHVWDC011/1661956 (T)
- WGCN002 DataHub DOI: 10.25584/LHVWGCN002/1661957 (T)
- WGCN003 DataHub DOI: 10.25584/LHVWGCN003/1661958 (T)
- WLN002 DataHub DOI: 10.25584/LHVWLN002/1661960 (T)
- WLN003 DataHub DOI: 10.25584/LHVWLN003/1661961 (PML)
- WSE001 DataHub DOI: 10.25584/LHVWSE001/1661962 (PM)
Host sample types include cerebellum ["CB", BTO:0000232], cortical neurons ["CN", BTO:0004102], cortex ["CT", BTO:0000233], dendritic cells ["DC", BTO:0002042], granule cell neurons ["GCN", BTO:0003393], lymph node ["LN", BTO:0000784], and serum ["SE", BTO:0001239] from mouse tissue collections. BTO ontology identifiers assigned under release version: 2021-10-26.
Linked Primary Data Repository Standards
Sequencing Raw Measurement Data (T) - 10.25504/FAIRsharing.aqhv1y; 10.25504/FAIRsharing.5hc8vt
Primary transcriptome experimental data collections and associated metadata are openly available from the NCBI BioProject platform, and have been linked to primary publication data accessions where possible. Dataset series have been deposited at the Gene Expression Omnibus (GEO), 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) - 10.25504/FAIRsharing.LYsiMd
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 MassIVE data repository under the following accessions. The Mass Spectrometry Interactive Virtual Environment (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.
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.
CC BY-SA 4.0 (secondary dataset download DOIs), CC0 1.0 (project metadata and PNNL DataHub policy default)