Core B - Epigenomics Core

项目概要-核心B：表观基因组学 在染色质中发现的表观遗传修饰（DNA甲基化和蛋白质的翻译后修饰）， 组蛋白）参与发育和分化过程中的基因调控。核心B将产生 来自人类、小鼠和非洲爪蟾的大规模平行多组测序的表观基因组学数据 神经管发育该核心将鉴定基因调控元件和表观基因组变体， 可能导致或影响表型。项目PI和核心B总监一起工作 在过去广泛地取得了巨大的成功，产生了重要的小鼠神经管表观基因组数据。艾克医生 在基因组学和表观基因组学领域以及采用 用于从单细胞生成多种类型的NGS数据集的多模式"多组学"技术。数据 从核心B产生的以及从项目I、II和III进口的，将被输送到核心C， 这些结果将交付给每个项目进行进一步验证。这些目标将通过以下方式实现： 开发涉及数据生产和分析的核心B的关键管道：1]批量全基因组 亚硫酸氢盐测序（WGBS）管道。Ecker实验室发表了第一个人类甲基化组， 在数据生产工作流程方面的重要专业知识。我们的数据工作流程已经建立， ENCODE项目制定和采用的操作程序，并将利用这些程序 我们的工作组工作流程的特点，使其成功的努力。2]单细胞甲基化组 测序（snmC-seq）流水线。单细胞甲基化组数据的产生和分析方法 snmC-seq2和最近的snmC-seq3已经建立，并制定了标准操作规程，用于 NIH BRAIN倡议。3]多组学分析结合两个不同的NGS数据集， 细胞这些包括snMethyl-3C-seq、snPaired-seq和snMethyl-HiC。表观基因组学核心和 生物信息学核心将共同分析核心B产生的所有表观基因组数据， 与现有管道或根据需要建立新的管道，并将共享项目I，II和III的数据。我们 预计将产生25，000个单细胞甲基化组/年，沿着详细分析。数据处理 使用一种基于DNA序列的方法， 我们之前开发的叫做Methylpy的算法。用于细胞类型分类的snmC-seq2数据的聚类 将利用mCG和mCH模式来有效地分类神经元和非神经元细胞类型。 神经管发育这些分析将产生候选标志物特征（基因和 预测的监管要素），将提供给项目PI进行进一步检查和验证。

PROJECT SUMMARY – Core B: Epigenomics The epigenetic modifications found in chromatin (DNA methylation and post-translational modifications of histones) are involved in gene regulation during development and differentiation. Core B will generate epigenomics data from massive parallel, multi-omic sequencing from human and mouse and xenopus developing neural tube. The Core will identify gene regulatory elements and epigenomic variants having the potential to cause or influence phenotypes. The Program PI and Director of Core B have worked together extensively in the past with great success producing significant mouse neural tube epigenomic data. Dr. Ecker has worked broadly in the area of genomics and epigenomics and in the development methodologies employing multi-modal ‘multi-omics’ techniques for generation multiple types of NGS datasets from single cells. The data generated from Core B, as well as imported from Project I, II and III, will be delivered to Core C for extraction of results which will be delivered to each of the Projects for further validation. These goals will be accomplished by developing the key pipelines of Core B that involve data production, and analysis: 1] Bulk whole genome bisulfite sequencing (WGBS) Pipeline. The Ecker lab published the first human methylome and thus has significant expertise in the workflow for data production. Our data workflow was established, and standard operating procedures developed and adopted, by the ENCODE project and will take advantage of the same features of our WGBS workflow that has made it successful for that effort. 2] Single cell methylome sequencing (snmC-seq) pipeline. The methods for production and analysis of single cell methylome data snmC-seq2 and more recently snmC-seq3, were established and standard operating procedures develop for the NIH BRAIN initiative. 3] Multi-omics analysis combining two different NGS datasets measured from single cells. These include snMethyl-3C-seq, snPaired-seq and snMethyl-HiC. The Epigenomics Core and the Bioinformatics Core will work together to perform analysis of all epigenomic data produced by Core B, will work with existing pipelines or create new pipelines as need demands, and will share data the Projects I, II and III. We anticipate that 25,000 single cell methylomes/yr will be generated, along with detailed analyses. Data processing quantification of genome wide unmethylated and methylated cytosine base calls are generated using an algorithm that we previously developed called Methylpy. Clustering of snmC-seq2 data for cell type classification will utilize both mCG and mCH patterns to effectively classify both neuronal and non-neuronal cell types in the developing neural tube. These analyses will result in a prioritized list of candidate marker features (genes and predicted regulatory elements) that will be provided to the project PIs for further examination and validation.