Genomic Technology Core

基因组技术核心

• 批准号: 10685564
• 负责人: Chun Jimmie Ye
• 金额: $ 16.53万
• 依托单位: UNIVERSITY OF CALIFORNIA, SAN FRANCISCO
• 依托单位国家: 美国
• 财政年份: 2016
• 资助国家: 美国
• 起止时间: 2016-09-21 至 2026-08-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10685564
• 关键词: ATAC-seq; Address; Autoimmune Diseases; Bioinformatics; Biological Assay; Biological Specimen Banks; Biology; Cell physiology; Cell surface; Cells; Cellular Indexing of Transcriptomes and Epitopes by Sequencing; Censuses; Circulation; Clinical; Clinical Data; Clinical Informatics; Collaborations; Collection; Complex; Consultations; Data; Data Analyses; Data Management Resources; Data Set; Development; Disease; Dissection; Ensure; Experimental Designs; Generations; Genetic; Genetic Transcription; Genetic Variation; Genomic approach; Genomics; Goals; Human; Immune; Immunophenotyping; Individual; Informatics; Infrastructure; Investigation; Investments; Leadership; Metadata; Methodology; Methods; Molecular; Monitor; Pathogenesis; Pathway interactions; Patients; Preparation; Process; Proteome; Proteomics; Quality Control; RNA; Reproducibility; Research; Research Design; Research Personnel; Resolution; Resources; Rheumatism; Rheumatology; Sampling; Secure; Service delivery model; Services; Spatial Distribution; Specimen; Standardization; Surface; Symptoms; System; Systemic Lupus Erythematosus; Technical Degree; Technology; Tissues; Work; XCL1 gene; autoimmune rheumatologic disease; career; clinical phenotype; cost; data integrity; data sharing; data streams; direct application; disorder subtype; electronic data; empowerment; epigenome; experimental study; genome resource; genomic data; high dimensionality; immune function; improved; innovation; multimodality; novel; precision medicine; programs; single cell sequencing; single-cell RNA sequencing; skills; tool; transcriptome sequencing; transcriptomic profiling; transcriptomics; translational scientist; treatment response

PROJECT SUMMARY/ABSTRACT – Genomic Technology Core The latest, cutting-edge genomic technologies including bulk and single-cell profiling of the transcriptome (e.g. RNA-seq), epigenome (e.g. ATAC-seq) and proteome (e.g. CITE-seq), represent powerful new tools for the advancement of precision medicine research, particularly when used to analyze biospecimens from well clinically-phenotyped individuals. These rapidly evolving technologies, with their requirements for specialized sample preparation and storage, genomic expertise and informatics skills, present a challenge for many clinical and translational researchers in rheumatology, a field where the need for better molecular characterization and improved delineation of disease subtypes is also a tremendous need. The goal of the Genomic Technology (GT) Core is to provide autoimmune rheumatic disease investigators turn-key solutions to cutting-edge genomic assays. To achieve this goal, we propose the following Aims: 1) Develop novel genomic assays and tailor them for direct application to the investigation of rheumatic disease patients. The GT Core will leverage the innovative expertise of the Ye Lab to develop multimodal, single-cell sequencing assays, high-throughput single cell proteomic assays, and spatial single-cell transcriptomic approaches. 2) Provide genomic consultation services and at-scale services for bulk and single-cell sequencing assays. The GT Core will draw on the collaborative genomic resource lab, the Genomics CoLab (Led by co-director Dr. Eckalbar), to develop workflows and analytic pathways geared toward the study of autoimmune disease that can be used by rheumatic disease investigators following consultation on genomic assay choice and study design, enabling them to implement cutting-edge genomic technologies for their projects. 3) Integrate and oversee the centralized biospecimen collection, storage and project tracking systems that are available, to ensure optimal use of patient samples and the integration and sharing of data between projects. The GT Core will continue to monitor the rigor and reproducibility of complex experimental pathways to also ensure the quality of the experimental data. The GT Core will closely collaborate with the Clinical Data Informatics (CDI) cores, to develop project specific sample tracking and metdata storage systems through Research Electronic Data Capture (REDCap) to ensure appropriate linkage of clinical data with biospecimen results. The GT Core will work closely with the IB Core to ensure that genomic data streams can be easily integrated into analysis workflows. The GT Core provides a robust framework for the application of novel, cutting-edge genomic technologies and will enable rheumatology investigators to maximally utilize all the tools available for the advancement of precision medicine research in rheumatology.

项目摘要/摘要-基因组技术核心 最新的尖端基因组技术，包括转录组的批量和单细胞图谱(例如 RNA-seq)、表观基因组(例如atac-seq)和蛋白质组(例如cite-seq)是用于 精准医学研究进展，特别是用于井中生物检疫分析的研究进展 临床表型的个体。这些快速发展的技术及其对专门化的要求 样本的准备和存储、基因组专业知识和信息学技能，对许多临床医生提出了挑战 风湿学的翻译研究人员，这个领域需要更好的分子表征和 改进疾病亚型的划分也是一项巨大的需求。基因组技术的目标(GT) 核心是为自身免疫性风湿病研究人员提供尖端基因组的交钥匙解决方案 化验。为了实现这一目标，我们提出了以下目标：1)开发新的基因组分析方法并进行定制 直接应用于风湿病患者的调查。GT Core将利用创新的 Ye实验室开发多模式、单细胞测序分析、高通量单细胞分析的专业知识 蛋白质组学分析和空间单细胞转录组方法。2)提供基因组咨询服务 以及批量和单细胞测序分析的大规模服务。GT Core将利用协作 基因组资源实验室，基因组学CoLab(由联席主任埃卡尔巴博士领导)，以开发工作流程和分析 风湿病研究人员可利用的面向自身免疫性疾病研究的途径 在基因组分析选择和研究设计方面提供咨询，使他们能够实施尖端技术 为他们的项目提供基因组技术。3)整合和监督集中的生物菌种收集、储存 和可用的项目跟踪系统，以确保最佳使用患者样本并整合和 在项目之间共享数据。GT Core将继续监测Complex的严密性和可重复性 实验路径也要保证实验数据的质量。GT Core将密切合作 使用临床数据信息学(CDI)核心，开发特定于项目的样本跟踪和元数据存储 通过研究电子数据捕获(RedCap)系统确保临床数据与 生物菌素试验结果。GT核心将与IB核心密切合作，以确保基因组数据流可以 轻松集成到分析工作流中。GT Core为应用程序提供了一个强大的框架 新颖、尖端的基因组技术，将使风湿病研究人员能够最大限度地利用所有 可用于推进风湿病精准医学研究的工具。