Genomics and Computational Core

项目摘要/摘要-基因组学和计算核心（克劳斯- PI） 最先进的基因组技术结合尖端的计算工具， 极大地推进了我们对各种生物学中信号调节基因转录的理解， 系统.下一代基于测序的分析，如RNA测序（RNA-seq），全局运行 测序（GRO-seq）和染色质免疫沉淀测序（ChIP-seq），已经揭示了新的 关于稳态RNA水平调节的信息，以及 活跃地转录RNA聚合酶、转录因子和跨基因组的组蛋白修饰。的 由这些测定生成的全局视图提供了通过以下方式无法实现的独特信息视角： 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 虽然该组织已将基因组工具纳入其所有曲目，但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）， 所有四个研究项目的需求，所有这些项目都提出使用基因组方法作为发现工具， 分析以探测分子机制。GCC将消除每个实验室建立这些 或者使用通常只提供第一遍数据的按服务收费的替代方法 分析，并没有看到实验通过从开始到结束。在这方面，海合会将提供 全面的服务，包括实验设计，基因组文库制备，数据分析和数据 存档。此外，海湾合作委员会将采取行动，促进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 已经存在于绿色生殖生物科学中心。 具体而言，GCC将（1）在规划期间向PI及其实验室提供咨询 并设计所有基因组实验的阶段，（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）进行质量控制分析 对基因组文库和所得数据进行分析，以及（4）分析PI生成的基因组数据， 他们的实验室。我们预计GCC将大大提高（1）进行基因组测序的容易性， 实验，（2）所获得的数据和进行的分析的质量，以及（3）做的效率 基因组实验和随之而来的废物减少。最重要的是，海湾合作委员会将大大提高 PI及其实验室在从基因组中获得有意义的生物信息方面的努力 实验

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.