Core B - Epigenetics and Bioinformatics Core

核心 B - 表观遗传学和生物信息学核心

• 批准号: 9151369
• 负责人: JEREMY M. BOSS
• 金额: $ 35.13万
• 依托单位: EMORY UNIVERSITY
• 依托单位国家: 美国
• 资助国家: 美国
• 起止时间: 至
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/9151369
• 关键词: ATAC-seq; Autoimmunity; Base Sequence; Binding; Bioinformatics; Biological; Biological Assay; Cells; ChIP-seq; Chromatin; Computer Analysis; Cost Savings; DNA Methylation; DNA Sequence; Data; Data Analyses; Data Set; Data Storage and Retrieval; Disease; Ensure; Epigenetic Process; Equipment; Genomics; Health; Histones; Lead; Libraries; Maintenance; Maps; Mediation; Metabolism; Mining; Molecular; Molecular Biology; Plasma; Plasma Cells; Post-Translational Protein Processing; Preparation; Process; Protocols documentation; Quality Control; Research Personnel; Resources; Running; Sampling; Services; Staging; System; Techniques; Technology; Transcript; Transposase; base; bisulfite sequencing; cell type; computerized data processing; cost; data integration; data sharing; deep sequencing; epigenomics; histone modification; member; methylation pattern; plasma cell development; programs; reference genome; success; transcription factor; transcriptome; transcriptome sequencing; web site

Each of the projects within this PPG proposes aims that will determine the transcriptional and epigenetic programs of plasma cell development and maintenance. To provide expertise, ensure standardized protocols, integration of results and their subsequent analyses, and the sharing of data, the creation of an Epigenomics, Sequencing and Bioinformatics Core (Core B) within this PPG is proposed. Core B will provide state-of-the-art technologies, molecular biology expertise, and bioinformatic services that assess DNA methylation, chromatin state and accessibility, and transcript expression through deep sequencing. Core B will be an independent division within the Emory Integrated Genomics Core (EIGC), which is a full service genomics and computational facility. This relationship will allow Core B to take advantage of the EIGC's computational expertise, equipment, negotiated sequencing costs, and data storage. To serve the projects, four tasks are proposed. Task 1: Provide uniform and quality sequence library sample preparation. Core B will create high-quality sequencing libraries based on four technologies to derive an epigenetic program. RNA-seq will be used to determine the transcriptome. Reduced Representation Bisulfite Sequencing (RRBS) will be used to assess DNA methylation. The Assay for Transposase Accessible Chromatin (ATAC-seq) will determine chromatin accessibility. Chromatin Immunoprecipitation-sequencing (ChIP-seq) will be used to determine histone posttranslational modifications or transcription factor binding. Task 2: Determine library quality and complexity and coordinate sequence runs. This task will identify library quality, determine the final sequencing depth for each sample, and provide significant cost savings to the PPG by coordinating DNA sequencing across projects. Task 3: Provide initial DNA sequence mapping, quality analysis, and data storage and sharing. Core B will use an established pipeline for mapping of sequences to the respective reference genome, provide long-term data storage, and facilitate sharing of processed datasets. Task 4: Provide iterative bioinformatic computational analysis of datasets. A question driven, iterative bioinformatics analysis will be used to derive epigenetic maps, features, metabolic processes, and transcriptional circuitry associated with plasma differentiation and maintenance in each of the experimental systems of the PPG. The iterative process will allow similar datasets (e.g., RRBS vs. RRBS) to be compared and then integrated across technologies (e.g., RNA-seq and ATAC-seq). By combining all four technologies, we will develop a multi-dimensional view of the epigenetic programming of plasma cells. Accordingly, Core B will allow seamless integration of data across projects, allow systems comparisons between species, as well as determine differences between healthy vs disease states to take place. Thus, Core B will provide a common resource and analytical platform that will serve to facilitate the success of each of the projects.

该PPG中的每个项目提出的目的将决定转录和表观遗传 等离子体细胞开发和维护的程序。为了提供专业知识，请确保标准化协议， 结果的整合及其后续分析以及数据共享，创建表观基因组学， 提出了该PPG中的测序和生物信息学核心（核心B）。核心B将提供最新的 评估DNA甲基化，染色质的技术，分子生物学专业知识和生物信息学服务 状态和可访问性，以及通过深度测序的转录本表达。核心将是一个独立的 Emory综合基因组核心（EIGC）内的分裂，这是一种全面的服务基因组学和 计算设施。这种关系将使Core B可以利用EIGC的计算 专业知识，设备，协商测序成本和数据存储。为了服务项目，四个任务是 建议的。任务1：提供统一和质量的序列库样本准备。核心将创建 基于四种技术来得出表观遗传程序的高质量测序库。 RNA-seq将是 用于确定转录组。减少表示的亚硫酸盐测序（RRB）将用于 评估DNA甲基化。转座酶可访问的染色质（ATAC-SEQ）的测定将确定 染色质可及性。染色质免疫沉淀 - 将用于确定 组蛋白翻译后修饰或转录因子结合。任务2：确定图书馆质量和 复杂性和坐标序列运行。此任务将确定库质量，确定最终 每个样品的测序深度，并通过协调DNA为PPG节省大量成本 跨项目进行排序。任务3：提供初始DNA序列映射，质量分析和数据 存储和共享。核心B将使用已建立的管道将序列映射到相应 参考基因组，提供长期数据存储，并促进处理的数据集共享。任务4： 提供数据集的迭代生物信息学计算分析。一个问题驱动，迭代 生物信息学分析将用于得出表观遗传图，特征，代谢过程和 每个实验中与血浆分化和维护相关的转录电路 PPG的系统。迭代过程将允许比较类似的数据集（例如，RRB与RRB） 然后跨越技术（例如RNA-Seq和atac-seq）集成。通过结合所有四种技术， 我们将开发浆细胞表观遗传编程的多维视图。因此，核心b 将允许跨项目无缝集成数据，也可以进行系统比较 因为确定健康与疾病状态之间发生的差异。因此，核心B将提供 公共资源和分析平台将有助于每个项目的成功。