A Comprehensive Resource for Escherichia coli Genomic Data and Tools

大肠杆菌基因组数据和工具的综合资源

• 批准号: 9765504
• 负责人: Julio Collado-Vides
• 金额: $ 38.97万
• 依托单位: BOSTON UNIVERSITY (CHARLES RIVER CAMPUS)
• 依托单位国家: 美国
• 财政年份: 2019
• 资助国家: 美国
• 起止时间: 2019-06-01 至 2023-02-28
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9765504
• 关键词: Animal Model; Bacteria; Benchmarking; Binding Sites; Biological; Biology; Biotechnology; Cell physiology; Cells; ChIP-seq; Characteristics; Clinical; Communities; DNA Binding; Data; Data Analyses; Data Set; Databases; Enterobacteriaceae; Escherichia coli; Eukaryota; Evolution; Family; Gene Expression Regulation; Generations; Genome; Genomics; Imagery; Klebsiella pneumonia bacterium; Knowledge; Literature; Manuals; Maps; Microbe; Molecular; Network-based; Operon; Paper; Prokaryotic Cells; Protocols documentation; Publishing; Regulation; Regulator Genes; Regulon; Resources; Salmonella enterica; Structure; Techniques; Testing; Transcriptional Regulation; Visualization software; Yersinia pestis; base; comparative; comparative genomics; design; genome annotation; genome browser; genomic data; genomic tools; insight; pathogen; reference genome; skills; tool; transcription factor; transcriptome; transcriptome sequencing

ABSTRACT Escherichia coli is the single most utilized cell in biology. It is the cornerstone of the biotechnology revolution, and the principal model organism for our understanding of bacterial molecular and cellular physiology. Despite its central importance, there is no single resource providing access to the growing body of E. coli genomics data. RegulonDB is already the primary portal for curated knowledge of E. coli gene regulation. We propose to expand RegulonDB to be a critically needed portal for E. coli genomic data in three key ways: (1) We will curate all available E. coli highthroughput genomic data sets, analyze these data sets in a consistent fashion, and integrate the data into RegulonDB with tools for access, query, visualization, and analysis. The datasets will include the first comprehensive map of the E. coli regulatory network based on ChIP-Seq and RNA-seq currently being generated by two of the PIs. (2) We will extend RegulonDB with comparative genomic data spanning the Enterobacteriaceae. This will include genomic data for representatives of all major Enterobacteriaceae genera. It will also include deep manual curation of the literature and genomic data sets for three key pathogens related to E. coli: Salmonella enterica, Klebsiella pneumoniae, and Yersinia pestis. In addition, we will perform the first comparative ChIP-Seq mapping in a set of conserved TFs in these three species and E. coli. This will provide the first broad view of the evolution of regulation between E. coli and these pathogens based on the comprehensive mapping of binding sites in conserved TFs. It will also provide a framework for generating complete regulatory maps in these and other Enterobacteriaceae species. (3) We will provide an online server for bacterial ChIP-Seq analysis. The server will be specifically tailored to the unique characteristics and pitfalls of ChIP-Seq in bacteria. The server will enable a new generation of microbiologists access to the power of ChIPSeq for the comprehensive mapping of transcription factor-DNA binding.

抽象的 大肠杆菌是生物学中最受使用的单元。它是生物技术革命的基石， 以及主要模型生物体，用于我们对细菌分子和细胞生理学的理解。尽管 它的核心重要性，没有一个资源可以访问对大肠杆菌基因组学的不断增长的体系 数据。 RegulondB已经是大肠杆菌基因调控知识的主要门户。我们建议 将RegulondB扩展为大肠杆菌基因组数据的迫切需要的门户：（1）我们将 策划所有可用的大肠杆菌高通量基因组数据集，以一致的方式分析这些数据集， 并将数据与访问，查询，可视化和分析的工具集成到RegulondB中。数据集 将包括基于CHIP-SEQ和RNA-SEQ的大肠杆菌调节网络的第一张综合图 目前是由两个PI生成的。 （2）我们将使用比较基因组数据扩展RegulondB 跨越肠杆菌科。这将包括所有主要主要代表的基因组数据 肠杆菌科属。它还将包括文献的深度手动策划和用于基因组数据集 三种与大肠杆菌有关的关键病原体：肠沙门氏菌，肺炎克雷伯氏菌和耶尔森氏菌。在 此外，我们将在这三个中的一组保守的TF中执行第一个比较芯片序列映射 物种和大肠杆菌。这将为大肠杆菌和大肠杆菌之间的监管演变提供首要的视野 这些病原体基于保守TF中结合位点的全面映射。它也将提供 在这些和其他肠杆菌科中生成完整的调节图的框架。 （3）我们会的 提供一个在线服务器进行细菌芯片分析。该服务器将专门针对唯一的 细菌中chip-seq的特征和陷阱。该服务器将启用新一代的微生物学家 访问Chipseq在转录因子-DNA结合的综合映射方面的功能。