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A curated transcriptome dataset collection to investigate the blood transcriptional response to viral respiratory tract infection and vaccination
- Source :
- F1000Research
- Publication Year :
- 2019
-
Abstract
- The human immune defense mechanisms and factors associated with good versus poor health outcomes following viral respiratory tract infections (VRTI), as well as correlates of protection following vaccination against respiratory viruses, remain incompletely understood. To shed further light into these mechanisms, a number of systems-scale studies have been conducted to measure transcriptional changes in blood leukocytes of either naturally or experimentally infected individuals, or in individual’s post-vaccination. Here we are making available a public repository, for research investigators for interpretation, a collection of transcriptome datasets obtained from human whole blood and peripheral blood mononuclear cells (PBMC) to investigate the transcriptional responses following viral respiratory tract infection or vaccination against respiratory viruses. In total, Thirty one31 datasets, associated to viral respiratory tract infections and their related vaccination studies, were identified and retrieved from the NCBI Gene Expression Omnibus (GEO) and loaded in a custom web application designed for interactive query and visualization of integrated large-scale data. Quality control checks, using relevant biological markers, were performed. Multiple sample groupings and rank lists were created to facilitate dataset query and interpretation. Via this interface, users can generate web links to customized graphical views, which may be subsequently inserted into manuscripts to report novel findings. The GXB tool enables browsing of a single gene across projects, providing new perspectives on the role of a given molecule across biological systems in the diagnostic and prognostic following VRTI but also in identifying new correlates of protection. This dataset collection is available at: http://vri1.gxbsidra.org/dm3/geneBrowser/list.
- Subjects :
- 0301 basic medicine
Immune defense
Bioinformatics
Viral respiratory infection
PBMC
Computational biology
Biology
Health outcomes
Data Note
Peripheral blood mononuclear cell
General Biochemistry, Genetics and Molecular Biology
Transcriptome
03 medical and health sciences
0302 clinical medicine
Viral Respiratory Tract Infection
Databases, Genetic
Humans
Influenza viruses
030212 general & internal medicine
General Pharmacology, Toxicology and Pharmaceutics
Transcriptomics
Respiratory Tract Infections
Whole Blood
General Immunology and Microbiology
Respiratory tract infections
Vaccination
General Medicine
Articles
030104 developmental biology
Blood
Respiratory syncytial viruses (RSV)
Rhinoviruses
Viruses
Leukocytes, Mononuclear
Transcriptional response
Software
Subjects
Details
- ISSN :
- 20461402
- Volume :
- 8
- Database :
- OpenAIRE
- Journal :
- F1000Research
- Accession number :
- edsair.doi.dedup.....a89dffc6af3a114347517e43fe74b273