Sequencing Coordination and Data Analysis Core

测序协调和数据分析核心

• 批准号: 10238138
• 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 2025-07-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10238138
• 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 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 对于理解血压(BP)的遗传控制来说，最重大的挑战之一是 人类中大多数与BP相关的单核苷酸多态(SNPs)位于非编码区域 DNA的区域。本PPG的主要目标是了解BP相关的功能相关性 利用表观基因组学和基因组编辑研究特定BP相关细胞类型中的非编码SNPs。一种关键的方法， 为了实现这一目标，本PPG采用的三个方案都是应用下一代 测序(NGS)技术。这些包括rna-seq(用于分析mna和lncRNA图谱)、Small 非编码RNA-seq(即，用于分析microRNA图谱的SncRNA-seq)、RRBS(用于测量DNA甲基化 模式)、ATAC-SEQ(确定染色质可及性)、Cut&Tag(检测DNA-蛋白质相互作用)和 HI-C(揭示染色质相互作用)。核心B的目标是提供高度专业化的专业知识 这些分析所需的。在五年的时间里，这个PPG的三个项目将分析725个RNA-Seq，20个SncRNA- SEQ、65个RRBS、20个Hi-C、155个Cut&Tag和65个ATAC-Seq文库。样品和文库的准备将是 由个别项目的工作人员进行。集群的生成和排序将由井- 以收费方式建立MCW测序服务中心。核心B的作用是协调 对活动进行排序以提高效率并执行绝大多数数据分析，包括 序列读出的处理和作图，转录本或CpG区域的鉴定和量化， DNA-蛋白质相互作用、染色质相互作用和可及性的呼叫峰，组学的综合分析 数据和下游分析(例如，基因本体论和生物途径)。因此，核心有两个 明确的目标。目标1是协调NGS文库的多路传输和提交以进行测序。目标2是 分析和管理所有三个项目的测序数据。CORE B董事P.Liu，联合调查员M.梁 和Y.Liu是梁博士在2010年发起的一个兴趣小组的创始成员，该小组有12人参与 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RRBS 以及MCW的其他NGS应用。由于这一努力而建立的湿实验室和干实验室管道 已在&gt；20种出版物中使用。重要的是，这个小组已经发表了一些关于信使核糖核酸的初步研究， 利用RNA-SEQ进行高血压研究中的lncRNA、miRNA、DNA甲基化和染色质构象， SncRNA-seq、RRBS和染色质构象捕获。因此，酷睿B拥有丰富的经验和高度的 确保这些组学数据分析成功的专业知识，这些数据分析是 三个项目。