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: 10676790
• 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/10676790
• 关键词: 3-Dimensional; ATAC-seq; Acceleration; Address; Affect; Alternative Splicing; Anatomy; Animal Model; Area; Base Sequence; Binding Sites; Biological; Biology; Cells; Cellular Indexing of Transcriptomes and Epitopes by Sequencing; Center Core Grants; ChIP-seq; Chromatin; Chromosomes; Collaborations; Communities; Consultations; Coupled; DNA; DNA Sequence; DNA sequencing; Data; Data Analyses; Development; Disease; Disparate; 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; Institution; Intake; 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; biological systems; cell type; cost; dashboard; data management; design; disease classification; epigenome; epigenomics; exome; exome sequencing; gene network; genetic analysis; genome sequencing; genome wide association study; genome-wide; histone modification; improved; 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研究社区的调查结果表明， 优先考虑的是获得基因组学、转录组学和表观遗传学的最先进的综合方法 分析正常稳态和疾病中的皮肤。核心C将提供最先进的开始到结束 这些尖端技术。核心将利用现有的校园资源，如 仪器和广泛的专业知识，在教师和研究人员的水平，提供技术和 为SBDRC研究社区提供智力支持。核心人员将嵌入皮肤研究 实验室，他们将熟悉皮肤作为一个生物系统和被问到的问题;这 将有助于确保他们能够最有效地向实验室人员提供实验设计和服务方面的建议， 解决生物学问题;相反，实验室人员将更加熟悉技术 他们可用的方法。具体而言，核心C将为SBDRC调查人员提供咨询， 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接收。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 在健康和患病皮肤中使用的RNA测序技术（bulk RNA-seq、poly（A）RNA-seq、small RNA-seq）。获得长期- 读取单分子测序（SMRT/PacBio）将有助于分析DNA中的结构变化， 由于剪接改变而精确鉴定RNA异构体。目标2中的服务将侧重于 利用表观基因组研究来鉴定在皮肤中起作用的调控元件（ATAC-seq、ChIP-seq、CUT&RUN）。 将通过Hi-C鉴定调控元件（增强子和启动子）之间的相互作用。集成 转录组学的发现将确认靶基因，并确定在皮肤稳态中起作用的改变的网络 和疾病目标3将集中在细胞异质性，提供单细胞技术的转录 在单细胞中进行scRNA-seq和表观遗传（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，从而确定所有基因的位置。 单个组织切片中的mRNA。随着新的“组学”技术的发展， 生物学研究，他们将被纳入这个核心的活动。数据将被分发到核心D， 计算生物学家将进行严格的分析，可视化和数据管理。总的来说，核心C是 中心的一个重要组成部分，旨在促进皮肤科学发现 通过为皮肤研究人员提供尖端的多组学研究，为生物学和皮肤疾病领域提供支持。