Systems Biology of Infection Lab, Department of Biochemistry and Molecular Biology, Biosciences Faculty, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain.
Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain.
Nucleic Acids Res. 2021 Jan 8;49(D1):D687-D693. doi: 10.1093/nar/gkaa890.
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.
尽管抗生素耐药性是一个日益引起全球关注的问题，但细菌发病机制仍未得到充分探索，这限制了我们开发新抗菌药物的能力。高通量测序技术的兴起提供了大量转录组数据，这些数据可以帮助阐明细菌感染的机制。在这里，我们介绍了 DualSeqDB 数据库，这是一个资源，可以帮助识别感染后病原菌及其天然宿主的基因转录变化。DualSeqDB 包含了来自八项不同研究的近 30 万条记录，其中包括在体内和体外条件下细菌和宿主差异基因表达的信息。表达数据值完全是从原始数据计算得出的，并通过标准化管道进行分析，以确保不同研究之间的一致性。它包含了来自七种不同病原菌菌株以及人类、小鼠和猕猴不同时间点的多种细胞类型和组织的信息。我们设想 DualSeqDB 可以帮助研究界系统地描述参与宿主感染的基因，并帮助开发和定制针对传染病的新分子。DualSeqDB 可在 http://www.tartaglialab.com/dualseq 免费获取。
