A curated transcriptome dataset collection to investigate the blood transcriptional response to viral respiratory tract infection and vaccination.
<p dir="ltr">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...
محفوظ في:
| المؤلف الرئيسي: | |
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| مؤلفون آخرون: | , , |
| منشور في: |
2019
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| الموضوعات: | |
| الوسوم: |
إضافة وسم
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| _version_ | 1864513511750631424 |
|---|---|
| author | Salim Bougarn (413372) |
| author2 | Sabri Boughorbel (846228) Damien Chaussabel (26369) Nico Marr (349853) |
| author2_role | author author author |
| author_facet | Salim Bougarn (413372) Sabri Boughorbel (846228) Damien Chaussabel (26369) Nico Marr (349853) |
| author_role | author |
| dc.creator.none.fl_str_mv | Salim Bougarn (413372) Sabri Boughorbel (846228) Damien Chaussabel (26369) Nico Marr (349853) |
| dc.date.none.fl_str_mv | 2019-03-13T06:00:00Z |
| dc.identifier.none.fl_str_mv | 10.12688/f1000research.18533.1 |
| dc.relation.none.fl_str_mv | https://figshare.com/articles/journal_contribution/A_curated_transcriptome_dataset_collection_to_investigate_the_blood_transcriptional_response_to_viral_respiratory_tract_infection_and_vaccination_/26020819 |
| dc.rights.none.fl_str_mv | CC BY 4.0 info:eu-repo/semantics/openAccess |
| dc.subject.none.fl_str_mv | Biological sciences Bioinformatics and computational biology Genetics Biomedical and clinical sciences Cardiovascular medicine and haematology Immunology Transcriptomics Bioinformatics Software Viral respiratory infection Influenza viruses Respiratory syncytial viruses (RSV) Rhinoviruses Whole Blood PBMC |
| dc.title.none.fl_str_mv | A curated transcriptome dataset collection to investigate the blood transcriptional response to viral respiratory tract infection and vaccination. |
| dc.type.none.fl_str_mv | Text Journal contribution info:eu-repo/semantics/publishedVersion text contribution to journal |
| description | <p dir="ltr">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. </p><h2>Other Information</h2><p dir="ltr">Published in: F1000Research<br>License: <a href="http://creativecommons.org/licenses/by/4.0/" target="_blank">http://creativecommons.org/licenses/by/4.0/</a><br>See article on publisher's website: <a href="https://dx.doi.org/10.12688/f1000research.18533.1" target="_blank">https://dx.doi.org/10.12688/f1000research.18533.1</a></p> |
| eu_rights_str_mv | openAccess |
| id | Manara2_02ed9c83e01a7dfdebb20365560d65d8 |
| identifier_str_mv | 10.12688/f1000research.18533.1 |
| network_acronym_str | Manara2 |
| network_name_str | Manara2 |
| oai_identifier_str | oai:figshare.com:article/26020819 |
| publishDate | 2019 |
| repository.mail.fl_str_mv | |
| repository.name.fl_str_mv | |
| repository_id_str | |
| rights_invalid_str_mv | CC BY 4.0 |
| spelling | A curated transcriptome dataset collection to investigate the blood transcriptional response to viral respiratory tract infection and vaccination.Salim Bougarn (413372)Sabri Boughorbel (846228)Damien Chaussabel (26369)Nico Marr (349853)Biological sciencesBioinformatics and computational biologyGeneticsBiomedical and clinical sciencesCardiovascular medicine and haematologyImmunologyTranscriptomicsBioinformaticsSoftwareViral respiratory infectionInfluenza virusesRespiratory syncytial viruses (RSV)RhinovirusesWhole BloodPBMC<p dir="ltr">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. </p><h2>Other Information</h2><p dir="ltr">Published in: F1000Research<br>License: <a href="http://creativecommons.org/licenses/by/4.0/" target="_blank">http://creativecommons.org/licenses/by/4.0/</a><br>See article on publisher's website: <a href="https://dx.doi.org/10.12688/f1000research.18533.1" target="_blank">https://dx.doi.org/10.12688/f1000research.18533.1</a></p>2019-03-13T06:00:00ZTextJournal contributioninfo:eu-repo/semantics/publishedVersiontextcontribution to journal10.12688/f1000research.18533.1https://figshare.com/articles/journal_contribution/A_curated_transcriptome_dataset_collection_to_investigate_the_blood_transcriptional_response_to_viral_respiratory_tract_infection_and_vaccination_/26020819CC BY 4.0info:eu-repo/semantics/openAccessoai:figshare.com:article/260208192019-03-13T06:00:00Z |
| spellingShingle | A curated transcriptome dataset collection to investigate the blood transcriptional response to viral respiratory tract infection and vaccination. Salim Bougarn (413372) Biological sciences Bioinformatics and computational biology Genetics Biomedical and clinical sciences Cardiovascular medicine and haematology Immunology Transcriptomics Bioinformatics Software Viral respiratory infection Influenza viruses Respiratory syncytial viruses (RSV) Rhinoviruses Whole Blood PBMC |
| status_str | publishedVersion |
| title | A curated transcriptome dataset collection to investigate the blood transcriptional response to viral respiratory tract infection and vaccination. |
| title_full | A curated transcriptome dataset collection to investigate the blood transcriptional response to viral respiratory tract infection and vaccination. |
| title_fullStr | A curated transcriptome dataset collection to investigate the blood transcriptional response to viral respiratory tract infection and vaccination. |
| title_full_unstemmed | A curated transcriptome dataset collection to investigate the blood transcriptional response to viral respiratory tract infection and vaccination. |
| title_short | A curated transcriptome dataset collection to investigate the blood transcriptional response to viral respiratory tract infection and vaccination. |
| title_sort | A curated transcriptome dataset collection to investigate the blood transcriptional response to viral respiratory tract infection and vaccination. |
| topic | Biological sciences Bioinformatics and computational biology Genetics Biomedical and clinical sciences Cardiovascular medicine and haematology Immunology Transcriptomics Bioinformatics Software Viral respiratory infection Influenza viruses Respiratory syncytial viruses (RSV) Rhinoviruses Whole Blood PBMC |