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项目总结 了解血压（BP）遗传控制的最大挑战之一是， 人类中大多数BP相关的单核苷酸多态性（SNP）位于非编码区， DNA的区域。本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在特定BP相关细胞类型中的非编码SNP。一个关键的方法， 为了实现这一目标，PPG的所有三个项目都采用了下一代 测序（NGS）技术。这些包括RNA-seq（分析mRNA和lncRNA谱），小 非编码RNA-seq（即，sncRNA-seq，分析microRNA谱）、RRBS（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，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库。样品和文库制备将 由个别项目的工作人员执行。聚类生成和测序将由井进行- 建立MCW测序服务中心，实行有偿服务。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 序列读数的处理和作图，转录物或CpG区域的鉴定和定量， DNA-蛋白质相互作用、染色质相互作用和可接近性的调用峰，组学的综合分析 数据和下游分析（例如，基因本体论和生物学途径）。核心有两个 具体目标。目的1是协调NGS文库的多重化和提交以用于测序。目标二是 分析和管理所有三个项目的测序数据。核心B总监P. Liu，合作研究者M.梁 和Y.刘先生是梁博士于2010年发起的一个兴趣小组的创始成员， 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。作为这项工作的结果，建立了湿实验室和干实验室管道， 已在20多个出版物中使用。重要的是，这个小组已经发表了一些关于mRNA的第一批研究， 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，核心B具有丰富的经验和 专业知识，以确保这些组学数据分析的成功，这些数据分析是 三个项目。