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

基本信息

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
项目类别：
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

项目摘要

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 在西奈山调查SBDRC研究界的结果表明，最高战略优先级是访问基因组学，转录组学和表观遗传学的最新和集成方法对正常稳态和疾病中皮肤的分析。核心C将提供最先进的开始到最新的这些尖端方法的技术。核心将利用现有的校园资源，例如教师和研究人员级别的仪器和广泛的专业知识，以提供技术和 SBDRC研究社区的智力支持。核心人员将嵌入皮肤研究中实验室将熟悉皮肤作为生物系统以及所提出的问题；这将有助于确保他们可以最有效地为实验设计和服务的实验室人员提供建议解决生物学问题；相反，实验室人员将变得更加熟悉技术他们可以使用的方法。具体而言，核心C将为SBDRC调查人员提供咨询，并以Nexgen Technologies为中心的服务。强大的组织中心（Smartsheet仪表板）将是用于内部和外部的标本和项目。作为目标1的一部分，核心C将有助于访问基因组学（外显子组测序，整个基因组测序和靶向捕获）和转录组学在健康和患病的皮肤中，技术（Bulk RNA-Seq，Poly（A）RNA-Seq，小RNA-Seq）。访问长期读取单分子测序（SMRT/PACBIO）将有助于分析DNA和由于剪接改变而导致的RNA同工型的精确鉴定。 AIM 2中的服务将重点介绍艺术表观基因组学研究以识别皮肤中运行的调节元素（ATAC-SEQ，CHIP-SEQ，CUT＆RUN）。跨监管元件（增强子和启动子）之间的相互作用将通过HI-C确定。与转录组发现将确认目标基因并识别皮肤稳态中运行的改变的网络和疾病。 AIM 3将重点放在细胞异质性上，为成绩单提供单细胞技术（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技术允许空间分辨率分辨率RNA-seq数据，从而使所有位置单个组织切片中的mRNA。随着新颖的“ OMICS”技术的发展，可以增强皮肤生物学研究，它们将纳入该核心的活动中。数据将分配给核心D 计算生物学家将执行严格的分析，可视化和数据管理。总体而言，核心C是中心的重要组成部分，目的是促进皮肤科学发现生物学和皮肤疾病区域通过为皮肤研究人员提供尖端的多词研究。