Genomics and Computational Core

基因组学和计算核心

• 批准号: 10063450
• 负责人: WILLIAM Lee KRAUS
• 金额: $ 20.42万
• 依托单位: UT SOUTHWESTERN MEDICAL CENTER
• 依托单位国家: 美国
• 财政年份: 2016
• 资助国家: 美国
• 起止时间: 2016-12-15 至 2023-11-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10063450
• 关键词: Biological; Biological Assay; Biology; Birth; Catalogs; Cervix Uteri; ChIP-seq; Clinical; Clinical Research; Collaborations; Consultations; Core Facility; DNA Sequencing Facility; DNA-Directed RNA Polymerase; Data; Data Analyses; Data Set; Experimental Designs; Fee-for-Service Plans; Genes; Genetic Transcription; Genome; Genomic Library; Genomic approach; Genomics; Goals; Guidelines; Human Resources; Infrastructure; Laboratories; Laboratory Scientists; Lead; Libraries; Methodology; Molecular; Molecular Biology; Molecular Probes; Nuclear; Pregnancy; Premature Birth; Preparation; Prolonged labor; Quality Control; RNA; Regulation; Reproductive Biology; Research Project Grants; Running; Sampling; Science; Scientist; Services; Signal Transduction; Site; Technology; Testing; Therapeutic Intervention; Time; Tissues; Work; archive data; archived data; base; biological systems; computerized tools; cost; cost effective; data archive; data standards; deep sequencing; design; experimental study; follow-up; genomic data; genomic tools; global run on sequencing; histone modification; meetings; myometrium; next generation sequencing; prevent; public repository; skills; tool; transcription factor; transcriptome sequencing; translational study; wasting

Project Summary/Abstract - Genomics and Computational Core (Kraus - PI) State-of-the-art genomic technologies combined with cutting-edge computational tools have dramatically advanced our understanding of signal-regulated gene transcription in a wide variety of biological systems. Next generation sequencing-based assays, such as RNA sequencing (RNA-seq), global run-on sequencing (GRO-seq), and chromatin immunoprecipitation sequencing (ChIP-seq), have revealed new information about the regulation of steady-state RNA levels, as well as the localization and regulation of actively transcribing RNA polymerase, transcription factors, and histone modifications across the genome. The global views generated by these assays provide a uniquely informative perspective that cannot be achieved by analyzing one or a few genes at a time. Although the field of reproductive biology has begun to incorporate genomic tools into its repertoire, it has yet to maximize the use of these unique discovery and analysis tools. The goal of this project is to establish a Genomics and Computational Core (GCC) that will serve the needs of all four research projects, all of which propose to use genomic approaches as discovery tools and as assays to probe molecular mechanisms. The GCC will eliminate the need for each lab to establish these methodologies on its own, or to use fee-for-service alternatives that typically only provide first pass data analysis and do not see the experiment through from start to finish. In this regard, the GCC will provide comprehensive service that includes experimental design, genomic library preparation, data analysis, and data archiving. In addition, the GCC will act to promote and facilitate collaborations between the personnel working in different labs. To save costs and increase efficiency, the GCC will leverage infrastructure and expertise already present in the Green Center for Reproductive Biology Sciences. Specifically, the GCC will (1) provide consultation to the PIs and their laboratories during the planning and design stages of all genomic experiments, (2) prepare high-quality genomic libraries from samples collected by the PIs and their laboratories for next generation sequencing, (3) perform quality control analyses on the genomic libraries and the resulting data, and (4) analyze the genomic data generated by the PIs and their laboratories. We anticipate that the GCC will greatly enhance (1) the ease of performing genomic experiments, (2) the quality of the data obtained and the analyses performed, and (3) the efficiency of doing genomic experiments and concomitant waste reduction. Most importantly, the GCC will greatly enhance the efforts of the PIs and their laboratories in obtaining meaningful biological information from genomic experiments.

项目摘要/摘要-基因组学和计算核心(Kraus-Pi) 最先进的基因组技术与尖端计算工具相结合 极大地提高了我们对信号调节的基因转录在各种生物中的理解 系统。基于下一代测序的分析，如RNA测序(RNA-seq)、全球运行 测序(GRO-SEQ)和染色质免疫沉淀测序(CHIP-SEQ)揭示了新的 关于稳态RNA水平的调节，以及本地化和调节 在基因组中主动转录RNA聚合酶、转录因子和组蛋白修饰。这个 这些分析生成的全局视图提供了一个独特的信息丰富的视角，这是通过以下方式无法实现的 一次分析一个或几个基因。尽管生殖生物学领域已经开始将 在将基因组工具纳入其全套功能之后，它尚未最大限度地利用这些独特的发现和分析工具。 该项目的目标是建立一个基因组学和计算核心(GCC)，将服务于 所有四个研究项目的需求，所有这些项目都建议使用基因组方法作为发现工具和 探索分子机制的分析方法。GCC将不再需要每个实验室建立这些 方法本身，或者使用通常只提供首次通过数据的收费服务替代方案 分析，不要把实验从头到尾看完。对此，GCC将提供 全面的服务，包括实验设计、基因组文库准备、数据分析和数据 存档。此外，GCC还将推动和便利工作人员之间的合作 在不同的实验室。为了节省成本和提高效率，GCC将利用基础设施和专业知识 已经在绿色生殖生物学科学中心工作。 具体来说，GCC将(1)在规划过程中向私人投资总监及其实验室提供咨询 和所有基因组实验的设计阶段，(2)从样品中制备高质量的基因组文库 由PI及其实验室收集用于下一代测序，(3)执行质量控制分析 基因组文库和结果数据，以及(4)分析由PI和 他们的实验室。我们预计，GCC将极大地提高(1)基因组操作的简便性 实验，(2)获得的数据和进行的分析的质量，以及(3)做实验的效率 基因组实验和随之而来的废物减少。最重要的是，GCC将极大地提升 PIs及其实验室在从基因组中获取有意义的生物信息方面的努力 实验。