Chromatin and Gene Analysis Core

染色质和基因分析核心

• 批准号: 9279584
• 负责人: Li Shen
• 金额: $ 36.61万
• 依托单位: ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI
• 依托单位国家: 美国
• 财政年份: 2012
• 资助国家: 美国
• 起止时间: 2012-05-01 至 2022-02-28
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9279584
• 关键词: ATAC-seq; Animal Model; Animals; Antidepressive Agents; Autopsy; Bioinformatics; Biological Assay; Brain; Brain region; Cells; ChIP-on-chip; ChIP-seq; Chromatin; Chromatin Structure; Collaborations; Collection; Communities; Complex; DNA Methylation; Data; Data Set; Development; Ensure; Epigenetic Process; Faculty; Foundations; Gene Expression; Gene Expression Regulation; Genes; Goals; Human; In Situ; Individual; Laboratories; Lead; Measures; Mental Depression; Methods; Molecular; Mus; Play; Predisposition; Publications; Regulation; Research Infrastructure; Research Personnel; Role; Running; Sex Characteristics; Technology; Work; analytical tool; bisulfite sequencing; brain cell; brain tissue; cell type; chromatin modification; data sharing; depression model; dissemination research; genome-wide; genome-wide analysis; improved; in vivo; next generation sequencing; novel; research data dissemination; tool; transcriptome sequencing; whole genome

PROJECT SUMMARY – CHROMATIN AND GENE ANALYSIS CORE The Chromatin and Gene Analysis Core provides the technical and bioinformatics infrastructure to optimally mine the large amount of genome-wide gene expression and chromatin data that are generated from the Center's work. Center investigators lead the field in several aspects of genome-wide chromatin analyses, including pioneering these approaches in brain, which offers several technical challenges. We have optimized methods for several next generation sequencing approaches, including RNA-seq, ChIP-seq, ATAC-seq, in situ HiC, and whole genome bisulfite sequencing, among others, for mouse and human brain, the latter offering an additional set of unique technical challenges. These approaches are being used increasingly to study individual cell types within a given limbic brain region, in both mouse and human. The Core has established expertise in analyzing the highly complex datasets obtained, and will continue work on further improving the tools available. All of the genome-wide data generated by our Center are analyzed by this Core. In parallel, the Core runs routine genome-wide assays on defined animal models, with the Animal Models Core, and thereby provides a foundation for the more specific and sophisticated measures in the individual Projects. Indeed, each Project focuses on genes that are among the most robustly regulated across mouse depression models and human depression. As well, the Core pilots novel experimental technologies; an example is our ability to target single chromatin modifications to a single gene within a single brain region and cell type in vivo, thus providing an unparalleled level of proof to establish epigenetic mechanisms of depression. By consolidating the analytical work and routine genome-wide analyses within a centralized Core, we ensure rigorous control over the data and facilitate comparisons of experimental findings across the four individual Projects. This consolidation also makes financial sense, since we concentrate and maximize efficient use of our expertise. Finally, the Core is responsible, with the Administrative Core, in maintaining a platform for sharing our genome-wide datasets and analytical tools across the Center's laboratories as well as with the scientific community and lay public at large.

项目摘要 – 染色质和基因分析核心 染色质和基因分析核心提供技术和生物信息学基础设施，以优化 挖掘从基因组生成的大量基因表达和染色质数据 中心的工作。中心研究人员在全基因组染色质分析的多个方面处于领先地位， 包括在大脑中开创这些方法，这带来了一些技术挑战。我们已经优化了 用于多种下一代测序方法的方法，包括 RNA-seq、ChIP-seq、ATAC-seq、原位测序 HiC 和全基因组亚硫酸氢盐测序等，用于小鼠和人脑，后者提供了 额外的一系列独特的技术挑战。这些方法越来越多地用于研究个体 小鼠和人类特定边缘脑区域内的细胞类型。核心已在以下方面建立了专业知识 分析获得的高度复杂的数据集，并将继续努力进一步改进可用的工具。 我们中心生成的所有全基因组数据均由该核心进行分析。同时，Core 运行 使用动物模型核心对定义的动物模型进行常规全基因组检测，从而提供 为各个项目中更具体和更复杂的措施奠定基础。确实，每个项目 重点关注小鼠抑郁症模型和人类抑郁症模型中受到最严格调控的基因 沮丧。此外，核心还试验了新颖的实验技术；一个例子是我们针对单一目标的能力 在体内对单个大脑区域和细胞类型内的单个基因进行染色质修饰，从而提供 建立抑郁症表观遗传机制的证据水平无与伦比。通过巩固分析 在集中核心内进行工作和常规全基因组分析，我们确保对数据的严格控制 并促进四个单独项目的实验结果的比较。此次整合还 具有财务意义，因为我们集中精力并最大限度地有效利用我们的专业知识。最后，核心是 负责与管理核心一起维护一个共享我们的全基因组数据集的平台， 中心实验室以及科学界和广大公众的分析工具。