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，最先进的基因组技术，包括转录组的批量和单细胞分析（例如， RNA-Seq），表观基因组（例如ATAC-SEQ）和蛋白质组（例如Cite-Seq）代表了强大的新工具 精确医学研究的进步，特别是在用于分析井中的生物测量时 临床上型的个体。这些迅速发展的技术，其对专业的要求 样本准备和存储，基因组专业知识和信息技能，对许多临床提出了挑战 并翻译了风湿病学研究人员，该领域需要更好地分子表征和 改善疾病亚型的描述也是巨大的需求。基因组技术（GT）的目标 核心是提供自身免疫性风湿病研究者的交钥匙解决方案 测定。为了实现这一目标，我们提出以下目的：1）开发新颖的基因组测定并量身定制 直接应用风湿病患者的投资。 GT核心将利用创新性 YE实验室的专业知识以开发多模式，单细胞测序测定法，高通量单细胞 蛋白质组学评估和空间单细胞转录组方法。 2）提供基因组咨询服务 以及用于散装和单细胞测序测定法的尺度服务。 GT核心将借鉴协作 基因组资源实验室，基因组学COLAB（由共同导演Eckalbar博士领导），以发展工作流程和分析 风湿病研究人员可以使用的自身免疫性疾病的途径 经过基因组评估选择和研究设计的咨询，使他们能够实施尖端 其项目的基因组技术。 3）集成和监督集中式生物测量系列，存储 以及可用的项目跟踪系统，以确保最佳使用患者样本和集成和 项目之间的数据共享。 GT核心将继续监视复杂的严格性和可重复性 实验途径也可以确保实验数据的质量。 GT核心将密切合作 使用临床数据信息学（CDI）核心，以开发项目特定的样本跟踪和METDATA存储 通过研究电子数据捕获（REDCAP）的系统，以确保临床数据与 生物测量结果。 GT核心将与IB核心紧密合作，以确保基因组数据流可以 轻松地集成到分析工作流程中。 GT核心为应用提供了强大的框架 新颖的，尖端的基因组技术，将使风湿病研究人员最大化利用所有 可用于进步风湿病研究的工具。