Resource Core C - Skin Genomics, Transcriptomics, and Epigenetics Core

资源核心 C - 皮肤基因组学、转录组学和表观遗传学核心

• 批准号: 10463724
• 负责人: Anne Mary Bowcock
• 金额: $ 16.19万
• 依托单位: ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI
• 依托单位国家: 美国
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-09-01 至 2026-08-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10463724
• 关键词: 3-Dimensional; ATAC-seq; Address; Affect; Alternative Splicing; Anatomy; Animal Model; Area; Base Sequence; Binding Sites; Biological; Biology; Cancer Grant Supplements (P30); Cells; Cellular Indexing of Transcriptomes and Epitopes by Sequencing; ChIP-seq; Chromatin; Chromosomes; Collaborations; Communities; Consultations; Coupled; DNA; DNA Sequence; DNA sequencing; Data; Data Analyses; Development; Disease; Distant; Elements; Enhancers; Ensure; Epigenetic Process; Epitopes; Experimental Designs; Faculty; Follow-Up Studies; Fostering; Funding; Gene Expression; Gene Expression Profiling; Genes; Genetic Transcription; Genome; Genomics; Goals; Heterogeneity; Hi-C; Histones; Homeostasis; Human Resources; Individual; Link; Location; Measurement; Medicine; Messenger RNA; Methods; Molecular Profiling; Nucleic Acid Regulatory Sequences; Pathogenesis; Poly(A)+ RNA; Process; Protein Isoforms; RNA; RNA Splicing; Reagent; Regulatory Element; Research; Research Personnel; Research Project Grants; Resolution; Resources; Scholarship; Service provision; Services; Skin; Small RNA; Specimen; Standardization; Structure; Surveys; Technology; Therapeutic Intervention; Tissues; Training; Transcript; Validation; Variant; Visualization; base; biological systems; cell type; cost; dashboard; data management; design; epigenome; epigenomics; exome; exome sequencing; gene network; genetic analysis; genome sequencing; genome wide association study; genome-wide; histone modification; insight; instrumentation; member; multiple omics; novel; promoter; risk variant; single cell analysis; single cell sequencing; single cell technology; single molecule; single-cell RNA sequencing; skin disorder; skin organogenesis; targeted sequencing; tool; transcription factor; transcriptome; transcriptome sequencing; transcriptomics; whole genome

Summary – Resource Core C The results of surveying the Research Community of the SBDRC at Mount Sinai indicated that a top strategic priority is access to state-of-the-art and integrated methods for genomics, transcriptomics, and epigenetic analysis of the skin in normal homeostasis and in disease. Core C will provide state-of-the-art start-to-finish technologies for these cutting-edge approaches. The Core will leverage existing campus resources, such as instrumentation and extensive expertise at both faculty and researcher levels, to provide technical and intellectual support to the SBDRC Research Community. Core personnel will be embedded in skin research labs where they will become familiarized with skin as a biological system and the questions being asked; this will help to ensure that they can most effectively advise lab personnel on experimental design and services to address the biological questions; conversely lab personnel will become more familiar with the technological approaches available to them. Specifically, Core C will provide SBDRC investigators with consultation and services centered on NexGen technologies. A robust organizational hub (the Smartsheet dashboard) will be utilized for specimen and project in-take, both internally and externally. As part of Aim 1, Core C will facilitate access to genomics (exome sequencing, whole genome sequencing and targeted capture) and transcriptomic technologies (bulk RNA-seq, poly(A) RNA-seq, small RNA-seq) in healthy and diseased skin. Access to long- read single molecule sequencing (SMRT/PacBio) will facilitate the analysis of structural changes in DNA and the precise identification of RNA isoforms due to altered splicing. Services in Aim 2 will focus on state-of-the art epigenomic studies to identify regulatory elements operating in the skin (ATAC-seq, ChIP-seq, CUT&RUN). Interactions across regulatory elements (enhancers and promoters) will be identified by Hi-C. Integration with transcriptomic findings will confirm target genes and identify altered networks operating in skin homeostasis and disease. Aim 3 will focus on cellular heterogeneity, providing single cell technologies for transcript (scRNA-seq) and epigenetic (scATAC-seq) analyses in single cells. CITE-Seq will provide simultaneous epitope and transcriptome measurements of single cells. Services from Aim 3 will also include spatial transcriptomics technology permitting the spatial resolution of RNA-seq data, and thereby the locations of all mRNAs in individual tissue sections. As novel “omics” technologies are developed that would enhance skin biology research, they will be incorporated into this Core’s activities. Data will be distributed to Core D where computational biologists will perform rigorous analysis, visualization and data management. Overall, Core C is an essential and integral component of the Center with the goal of facilitating scientific discoveries in skin biology and skin disease areas by providing cutting-edge multi-omics studies to skin researchers.

摘要 – 资源核心 C 对西奈山 SBDRC 研究界的调查结果表明，顶级战略 优先考虑的是获得最先进的基因组学、转录组学和表观遗传学综合方法 分析正常稳态和疾病状态下的皮肤。 Core C 将提供最先进的从头到尾 这些尖端方法的技术。核心将利用现有的校园资源，例如 仪器和教师和研究人员层面的广泛专业知识，以提供技术和 为 SBDRC 研究团体提供智力支持。核心人员将植入皮肤研究 他们将熟悉皮肤作为一个生物系统以及所提出的问题；这 将有助于确保他们能够最有效地为实验室人员提供有关实验设计和服务的建议 解决生物学问题；相反，实验室人员将更加熟悉技术 他们可以采用的方法。具体而言，核心 C 将为 SBDRC 调查人员提供咨询和 以 NexGen 技术为中心的服务。一个强大的组织中心（Smartsheet 仪表板）将 用于内部和外部的样本和项目采集。作为目标 1 的一部分，核心 C 将促进 获得基因组学（外显子组测序、全基因组测序和靶向捕获）和转录组学 健康和患病皮肤中的技术（bulk RNA-seq、poly(A) RNA-seq、small RNA-seq）。访问长- 读取单分子测序（SMRT/PacBio）将有助于分析 DNA 的结构变化和 由于剪接改变而精确鉴定 RNA 亚型。目标 2 中的服务将侧重于最先进的 艺术表观基因组研究，以确定在皮肤中起作用的调控元件（ATAC-seq、ChIP-seq、CUT&RUN）。 Hi-C 将识别调控元件（增强子和启动子）之间的相互作用。与集成 转录组研究结果将确认目标基因并识别在皮肤稳态中运作的改变网络 和疾病。目标3将重点关注细胞异质性，为转录提供单细胞技术 单细胞中的 (scRNA-seq) 和表观遗传学 (scATAC-seq) 分析。 CITE-Seq 将同时提供 单细胞的表位和转录组测量。 Aim 3 的服务还将包括空间 转录组学技术允许 RNA-seq 数据的空间分辨率，从而确定所有 单个组织切片中的 mRNA。随着新颖的“组学”技术的开发，可以增强皮肤 生物学研究，它们将被纳入该核心的活动中。数据将分发到 Core D，其中 计算生物学家将进行严格的分析、可视化和数据管理。总体而言，Core C 是 该中心的重要组成部分，其目标是促进皮肤科学发现 通过为皮肤研究人员提供尖端的多组学研究，在生物学和皮肤病领域开展研究。