DualSeqDB: the host-pathogen dual RNA sequencing database for infection processes

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  • dc.contributor.author Macho Rendón, Javier
  • dc.contributor.author Lang, Benjamin
  • dc.contributor.author Ramos Llorens, Marc
  • dc.contributor.author Tartaglia, Gian Gaetano
  • dc.contributor.author Torrent Burgas, Marc
  • dc.date.accessioned 2020-11-24T07:07:04Z
  • dc.date.available 2020-11-24T07:07:04Z
  • dc.date.issued 2020
  • dc.description.abstract Despite antibiotic resistance being a matter of growing concern worldwide, the bacterial mechanisms of pathogenesis remain underexplored, restraining our ability to develop new antimicrobials. The rise of high-throughput sequencing technology has made available a massive amount of transcriptomic data that could help elucidate the mechanisms underlying bacterial infection. Here, we introduce the DualSeqDB database, a resource that helps the identification of gene transcriptional changes in both pathogenic bacteria and their natural hosts upon infection. DualSeqDB comprises nearly 300 000 entries from eight different studies, with information on bacterial and host differential gene expression under in vivo and in vitro conditions. Expression data values were calculated entirely from raw data and analyzed through a standardized pipeline to ensure consistency between different studies. It includes information on seven different strains of pathogenic bacteria and a variety of cell types and tissues in Homo sapiens, Mus musculus and Macaca fascicularis at different time points. We envisage that DualSeqDB can help the research community in the systematic characterization of genes involved in host infection and help the development and tailoring of new molecules against infectious diseases. DualSeqDB is freely available at http://www.tartaglialab.com/dualseq.
  • dc.description.sponsorship Ministerio de Ciencia, Innovación y Universidades [SAF2015-72518-EXP, SAF2017-82158-R, BFU2017-86970-P and RYC-2012-09999]; European Research Council [RIBOMYLOME 309545]; Horizon 2020—Research and Innovation Framework Programme [727658, 793135 to B.L.]; Ministry of Economy and Competitiveness [BFU2017-86970-P]; Centro de Excelencia Severo Ochoa 2013–2017; Generalitat de Catalunya; European Society of Clinical Microbiology and Infectious Diseases Research Grant 2016. Funding for open access charge: Ministerio de Ciencia, Innovación y Universidades [BFU2017-86970-P].
  • dc.format.mimetype application/pdf
  • dc.identifier.citation Macho Rendón J, Lang B, Ramos Llorens M, Gaetano Tartaglia G, Torrent Burgas M. DualSeqDB: the host-pathogen dual RNA sequencing database for infection processes. Nucleic Acids Res. 2020 Oct 21;49(D1):D687-93. DOI: 10.1093/nar/gkaa890
  • dc.identifier.doi http://dx.doi.org/10.1093/nar/gkaa890
  • dc.identifier.issn 0305-1048
  • dc.identifier.uri http://hdl.handle.net/10230/45877
  • dc.language.iso eng
  • dc.publisher Oxford University Press
  • dc.relation.ispartof Nucleic Acids Research. 2020 Oct 21;49(D1):D687-93
  • dc.relation.projectID info:eu-repo/grantAgreement/EC/FP7/309545
  • dc.relation.projectID info:eu-repo/grantAgreement/ES/1PE/SAF2015-72518-EXP
  • dc.relation.projectID info:eu-repo/grantAgreement/ES/2PE/SAF2017-82158-R
  • dc.relation.projectID info:eu-repo/grantAgreement/ES/2PE/BFU2017-86970-P
  • dc.relation.projectID info:eu-repo/grantAgreement/EC/H2020/727658
  • dc.relation.projectID info:eu-repo/grantAgreement/EC/H2020/793135
  • dc.rights © The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
  • dc.rights.accessRights info:eu-repo/semantics/openAccess
  • dc.rights.uri http://creativecommons.org/licenses/by-nc/4.0/
  • dc.title DualSeqDB: the host-pathogen dual RNA sequencing database for infection processes
  • dc.type info:eu-repo/semantics/article
  • dc.type.version info:eu-repo/semantics/publishedVersion

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