Core B - Epigenomics Core

核心 B - 表观基因组学核心

• 批准号: 10300068
• 负责人: Joseph R Ecker
• 金额: $ 15.05万
• 依托单位: UNIVERSITY OF CALIFORNIA, SAN DIEGO
• 依托单位国家: 美国
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-12-01 至 2025-11-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10300068
• 关键词: 3-Dimensional; Adopted; Algorithms; Anatomy; Animals; Anterior; Area; BRAIN initiative; Bioinformatics; California; Candidate Disease Gene; Carbon; Cells; Chromatin; Classification; Code; Complex; Cytosine; DNA Methylation; DNA Sequence Alteration; DNA methylation profiling; Data; Data Set; Development; Dimensions; Dorsal; Epigenetic Process; Exposure to; Folic Acid; Funding; Gene Expression Regulation; Generations; Genes; Genetic; Genetic Transcription; Genome; Genomics; Global Change; Goals; Human; Individual; Informatics; Institutes; International; Lateral; Measures; Medial; Meningomyelocele; Methodology; Methods; Modification; Molecular Conformation; Mus; Mutate; Mutation; Neural tube; Neuroglia; Neurons; Pathway interactions; Patients; Pattern; Phenotype; Post-Translational Protein Processing; Procedures; Production; Productivity; Publishing; Recording of previous events; Regenerative Medicine; Regulator Genes; Regulatory Element; Risk; Techniques; Technology; Tissues; United States National Institutes of Health; Untranslated RNA; Ursidae Family; Validation; Variant; Work; Xenopus; base; bisulfite sequencing; candidate marker; cell type; computerized data processing; cost effective; data sharing; epigenetic profiling; epigenome; epigenomics; gene environment interaction; genetic variant; genome-wide; histone modification; innovation; knockout animal; methylome; multimodality; multiple omics; programs; relating to nervous system; single cell analysis; single cell sequencing; success; synergism; transcriptome; whole genome

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.

项目摘要-核心B：表观基因组学 染色质中的表观遗传修饰(DNA甲基化和翻译后修饰 组蛋白)参与发育和分化过程中的基因调控。核心B将生成 来自人、鼠和非洲爪鼠的大规模平行多基因组测序的表观基因组学数据 发育中的神经管。核心将确定基因调控元件和表观基因组变体具有 可能导致或影响表型。项目PI和Core B的主管曾合作过 在过去广泛地成功地产生了重要的小鼠神经管表观基因组数据。埃克尔博士 在基因组学和表观基因组学领域以及在开发方法论方面进行了广泛的工作 用于从单个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，将被交付到核心C进行提取 结果将提交给每个项目以供进一步验证。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 亚硫酸氢盐排序(WGBS)管道。埃克尔实验室发布了第一个人类甲基组，因此 在数据生产的工作流程方面具有丰富的专业知识。我们的数据工作流程已经建立，并且符合标准 由ENCODE项目制定和通过的操作程序，并将利用相同的 我们的WGBS工作流程的特点使其成功地完成了这项工作。2]单细胞甲基组 测序(SNMC-SEQ)管线。单细胞甲基组数据的产生和分析方法 制定了SNMC-SEQ2和最近的SNMC-SEQ3，并制定了标准操作程序 美国国立卫生研究院的大脑计划。3]结合两个不同的NGS数据集的多组学分析 细胞。这些化合物包括SnMethyl-3C-seq、SnPaired-seq和SnMethyl-hic。表观基因组学的核心和核心 生物信息学核心将共同努力，对核心B产生的所有表观基因组数据进行分析，将发挥作用 或根据需要新建管道，并将共享项目I、II和III的数据。我们 预计每年将产生25,000个单细胞甲基基因组，并进行详细的分析。数据处理 全基因组未甲基化和甲基化的胞嘧啶碱基调用的量化是使用 我们之前开发的一种名为甲基吡啶的算法。用于细胞类型分类的SNMC-SEQ2数据的聚类 将利用MCG和MCH模式来有效地对神经和非神经元细胞类型进行分类 发育中的神经管。这些分析将产生候选标记特征(基因和 预测的监管要素)，将提供给项目绩效指标以供进一步审查和验证。