Sequencing Coordination and Data Analysis Core

测序协调和数据分析核心

• 批准号: 10460344
• 负责人: Pengyuan Liu
• 金额: $ 41.22万
• 依托单位: MEDICAL COLLEGE OF WISCONSIN
• 依托单位国家: 美国
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-08-15 至 2023-06-09
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10460344
• 关键词: ATAC-seq; Adopted; Biological; Blood Pressure; Cells; Charge; Chromatin; DNA; DNA Methylation; DNA-Protein Interaction; Data; Data Analyses; Deposition; Ensure; Epigenetic Process; Fee-for-Service Plans; Generations; Genes; Genetic; Goals; Hi-C; Human; Hypertension; Individual; Interest Group; Laboratories; Libraries; Logistics; Measurement; Measures; Messenger RNA; MicroRNAs; Molecular Conformation; Ontology; Pathway interactions; Preparation; Process; Publications; Publishing; RNA; Research; Research Personnel; Role; Sampling; Sequence Read Archive; Services; Single Nucleotide Polymorphism; Technology; Tissues; Transcript; Untranslated RNA; Work; bioinformatics pipeline; blood pressure control; blood pressure regulation; cell type; chromosome conformation capture; cost; epigenome; epigenomics; experience; genome editing; genome-wide; improved; member; methylation pattern; next generation sequencing; payment; repository; success; transcriptome; transcriptome sequencing

CORE B PROJECT SUMMARY One of the most significant challenges for understanding genetic control of blood pressure (BP) is that the vast majority of BP-associated single nucleotide polymorphisms (SNPs) in humans are located in noncoding regions of DNA. The major objective of this PPG is to understand the functional relevance of BP-associated noncoding SNPs in specific BP relevant cell types using epigenomics and genome editing. A key approach that all three projects of this PPG have adopted to accomplish this objective is the application of next-generation sequencing (NGS) technologies. These include RNA-seq (to analyze mRNA and lncRNA profiles), small noncoding RNA-seq (i.e., sncRNA-seq, to analyze microRNA profiles), RRBS (to measure DNA methylation patterns), ATAC-seq (to determine chromatin accessibility), CUT&Tag (to detect DNA-protein interactions) and Hi-C (to uncover chromatin interactions). The goal of Core B is to provide the highly specialized expertise required for these analyses. Over five years, three projects of this PPG will analyze 725 RNA-seq, 20 sncRNA- seq, 65 RRBS, 20 Hi-C, 155 CUT&Tag and 65 ATAC-seq libraries. Sample and library preparation will be carried out by the staff of individual projects. Cluster generation and sequencing will be performed by the well- established MCW Sequencing Service Center via fee-for-service. The role of Core B is coordinating sequencing activities to improve efficiencies and performing the vast majority of the data analysis including the processing and mapping of the sequence reads, identification and quantification of transcripts or CpG regions, calling peaks of DNA-protein interaction, chromatin interaction and accessibility, integrative analysis of omics data and downstream analysis (e.g., gene ontology and biological pathways). The Core therefore has two specific aims. Aim 1 is to coordinate the multiplexing and submission of NGS libraries for sequencing. Aim 2 is to analyze and manage sequencing data for all three projects. Core B Director P. Liu, Co-Investigator M. Liang and Y. Liu were founding members of an interest group initiated by Dr. Liang in 2010 and involving 12 laboratories from seven departments at MCW that adopted NGS technologies to analyze RNA and later RRBS and other NGS applications at MCW. The wet lab and dry lab pipeline established as a result of this effort has been used in > 20 publications. Importantly, this group has published some of the first studies of mRNA, lncRNA, miRNA, DNA methylation and chromatin conformation in hypertension research that utilized RNA-seq, sncRNA-seq, RRBS and chromatin conformation capture. Therefore, Core B has the experience and the highly specialized expertise to ensure the success of these omics data analyses that are critical components of the three projects.

核心B项目摘要 理解血压遗传控制（BP）的最重要的挑战之一是 人类中大多数与BP相关的单核苷酸多态性（SNP）位于非编码中 DNA区域。该PPG的主要目的是了解BP相关的功能相关性 使用表观基因组学和基因组编辑中的特定BP相关细胞类型中的非编码SNP。一个关键方法 该PPG的所有三个项目都采用了实现这一目标的实现 测序（NGS）技术。其中包括RNA-Seq（分析mRNA和LNCRNA曲线），小 非编码RNA-seq（即SncRNA-Seq，分析microRNA轮廓），RRB（测量DNA甲基化 模式），ATAC-SEQ（确定染色质访问性），剪切和TAG（检测DNA-蛋白质相互作用）和 HI-C（以发现染色质相互作用）。核心B的目标是提供高度专业的专业知识 这些分析所需。在五年的时间里，该PPG的三个项目将分析725个RNA-Seq，20个Sncrna- SEQ，65 RRB，20 HI-C，155剪切和标签和65个ATAC-SEQ库。样本和图书馆的准备将是 由单个项目的工作人员进行。聚类的产生和测序将由良好进行 通过服务费用建立了MCW测序服务中心。核心B的作用正在协调 测序活动以提高效率并执行绝大多数数据分析，包括 序列读取，识别和定量转录本或CpG区域的处理和映射， 调用DNA-蛋白相互作用，染色质相互作用和可访问性的峰值，OMICS的综合分析 数据和下游分析（例如，基因本体论和生物学途径）。因此核心有两个 具体目标。 AIM 1是协调NGS库的多路复用和提交以进行测序。 AIM 2是 分析和管理所有三个项目的测序数据。 Core B主任P. Liu，共同投资者M. Liang 刘Y.是Liang博士于2010年发起的兴趣组的创始成员，涉及12 来自MCW七个部门的实验室，采用了NGS技术来分析RNA和后来的RRB 以及MCW的其他NGS申请。由于这项工作而建立的湿实验室和干燥的实验室管道 在> 20个出版物中使用。重要的是，该小组发表了一些mRNA的第一批研究， LNCRNA，miRNA，DNA甲基化和染色质构象在使用RNA-Seq的高血压研究中 SncRNA-SEQ，RRB和染色质构象捕获。因此，核心B具有经验和高度 专业知识以确保这些OMIC数据分析的成功，这些数据分析是关键组成部分 三个项目。