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

Macho Rendón, Javier; Lang, Benjamin; Ramos Llorens, Marc; Tartaglia, Gian Gaetano; Torrent Burgas, Marc

doi:http://dx.doi.org/10.1093/nar/gkaa890

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

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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

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.