Core A: Bioinformatics Core

描述 这个核心的目的是提供转录、DNA-蛋白质相互作用和染色质构象捕获项目的生物信息学分析。下一代测序仪已经改变了基因组研究，但这些数据的分析仍然是一个瓶颈。我们的核心将提供基本的数据分析服务，使本计划项目的成员能够访问和解释这些数据。这一核心的PI和工作人员在基因组数据分析方面拥有丰富的经验，并熟悉相关项目的基本生物学。尽管加州大学洛杉矶分校有微阵列和测序核心，但没有 其中，将数据分析作为服务提供。因此，没有内部计算专业知识的典型生物群体往往只剩下数据，没有能力解释这些数据。我们在这里提议的核心将消除这一障碍，以便该计划项目中的所有小组不仅能够从他们的样本中收集测序数据，而且还可以获得经过处理和分析的数据，这些数据可以由研究人员直接解释，而不需要计算专业知识。这一功能将使本计划项目的所有成员更容易获得基因组学研究。我们还将与本计划每个实验室中具有计算经验的研究人员合作，改进分析工具。这一核心的目标是： 1.RNA-SEQ数据分析：我们将提供RNA-SEQ数据的量化和变异检测分析。 2.ChlP-seq数据的分析：我们将提供峰的位置、平均峰分布和模体。 3.4C数据分析：我们将提供与“诱饵”基因座相互作用的结构域的位置，并结合其他基因组数据分析它们的性质。 4.UCSC基因组浏览器上的数据显示：在所有情况下，该核心都会将全基因组数据加载到我们安装的UCSC基因组浏览器上，这样用户就可以在单一碱基分辨率下看到每个样本产生的数据。我们还将把数据和分析工具上传到维基网站进行交流。 5.数据质量指标：我们将为序列数据生成质量指标，以提供对样本质量的估计。

Description The purpose of this Core is to provide bioinformatic analysis of transcriptomic, DNA-protein interactions and Chromatin Conformation Capture projects. Next-generation sequencers have transformed genomic research, yet the analysis of these data remains a bottleneck. Our Core will provide the essential data analysis service to render these data accessible and interpretable to the members of this Program Project. The PI and staff of this Core have extensive experience in the analysis of genomic data, as well as familiarity with the underlying biology of the associated projects. Despite the fact that microarray and sequencing cores exist at UCLA, none of these provide data analysis as a service. Therefore the typical biology group that does not have internal computational expertise is often left with data and no ability to interpret it. The Core we are proposing here will remove this impediment so that all the groups within this Program Project will be able to not only collect sequencing data from their samples, but also obtain processed and analyzed data that can be directly interpreted by researchers without computational expertise. This functionality should render genomics research far more accessible to all members of this Program Project. We will also work with computationally experienced researchers in each lab of this Program to refine analysis tools. The Aims of this Core are: 1. Analysis of RNA-seq data: we will provide quantification and variant detection analyses of RNA-seq data. 2. Analysis of ChlP-seq data: we will provide the location of peaks, average peak distributions and motifs. 3. Analysis of 4C data: we will provide the locations of domains that interact with "bait" loci, and analyze their properties with other genomic data. 4. Data display on the UCSC genome browser: in all cases, this core will also load genome-wide data onto our installation of the UCSC genome browser so that users can see at single base resolution the data generated from each sample. We will also upload data and analysis tools to the Wiki site for exchange. 5. Data quality metrics: we will generate quality metrics for sequence data to provide an estimate of the quality of the sample.