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A curated transcriptome dataset collection to investigate the blood transcriptional response to viral respiratory tract infection and vaccination.

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submitted on 2024-07-07, 11:44 and posted on 2024-07-07, 11:45 authored by Salim Bougarn, Sabri Boughorbel, Damien Chaussabel, Nico Marr

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.

Other Information

Published in: F1000Research
License: http://creativecommons.org/licenses/by/4.0/
See article on publisher's website: https://dx.doi.org/10.12688/f1000research.18533.1

Funding

Qatar National Research Fund (NPRP10-0205-170348), Establishing a Foundation for "Collective Data"-enabled Biomedical Research in Qatar.

History

Language

  • English

Publisher

F1000 Research

Publication Year

  • 2019

License statement

This Item is licensed under the Creative Commons Attribution 4.0 International License.

Institution affiliated with

  • Sidra Medicine

Related Datasets

Bougarn, S., Boughorbel, S., Chaussabel, D., & Marr, N. (2019). A curated transcriptome dataset collection to investigate the blood transcriptional response to viral respiratory tract infection and vaccination. F1000Research, 8, 284. https://doi.org/10.12688/f1000research.18533.1. SIDRA : GBX : Gene Expression Browser. http://vri1.gxbsidra.org/dm3/geneBrowser/list Bougarn, S., Boughorbel, S., Chaussabel, D., & Marr, N. (2019). A curated transcriptome dataset collection to investigate the blood transcriptional response to viral respiratory tract infection and vaccination. F1000Research, 8, 284. https://doi.org/10.12688/f1000research.18533.1. National Institutes of Health : National Center for Biotechnology Information : Genes & Expressions : Gene Expression Omnibus (GEO) Datasets : Accession number GSE17763. https://www.ncbi.nlm.nih.gov/gds/?term=GSE17763