Omics, Bioinformatics, and Data Management Core

组学、生物信息学和数据管理核心

• 批准号: 10709011
• 负责人: Michael Gale
• 金额: $ 115.84万
• 依托单位: OREGON HEALTH & SCIENCE UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2022
• 资助国家: 美国
• 起止时间: 2022-09-22 至 2027-06-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10709011
• 关键词: Bar Codes; Big Data; Bioinformatics; Biological; Biological Assay; Biometry; Blood; Bone Marrow; CD8-Positive T-Lymphocytes; Cell physiology; Cells; Cellular Indexing of Transcriptomes and Epitopes by Sequencing; Computer Analysis; Computer Models; Data; Data Analyses; Data Management Resources; Data Set; Databases; Experimental Designs; Gene Expression; Gene Expression Profile; Generations; Genes; Goals; Gut associated lymphoid tissue; Immune; Immune Response Genes; Immune response; Immunization Programs; Immunologics; Infection; Laboratories; Link; Macaca mulatta; Measurement; Mediating; Membrane Proteins; Messenger RNA; Methods; Modeling; Monitor; Output; Peptides; Resolution; SIV; SIV Vaccines; Secure; Spleen; Study Subject; T cell differentiation; T cell response; T-Cell Receptor; T-cell receptor repertoire; Tissues; Vaccinated; Vaccination; Vaccines; Virus; Whole Blood; Work; antigen-specific T cells; big data management; cohort; data curation; data handling; data integration; data management; functional genomics; gene function; genomic data; genomic platform; lymph nodes; multidimensional data; multiple omics; nano-string; pre-clinical; preclinical study; predictive signature; programs; response; transcriptome sequencing; transcriptomics; vaccine efficacy; vaccine trial; web server; web-accessible

CORE D PROJECT SUMMARY The `Omics, Bioinformatics, and Data Management Core (Core D) serves this Program by providing high resolution functional genomics and bioinformatics computation analyses with statistical integration. The main objective of the Core is to define the gene expression signatures and their functional output that program the immune response for 68-1 RhCMV/SIV vaccine mediated SIV replication arrest in pre-clinical rhesus macaque (RM) vaccine studies. The Core will interrogate single CD8+ T cells in blood and tissues, their linkage of specific T cell receptor usage (to identify SIV-specific clonotypes), single non-CD8+ T cells in blood and tissues, and whole immune tissues including whole blood, lymph node (LN), spleen, bone marrow (BM) and gut-associated lymphoid tissues (GALT), and will link data sets with spatial transcriptomic data sets, to define gene expression signatures and networks, and will apply cutting edge bioinformatics approaches to model their functional output and inform the mechanisms of action by which RhCMV/SIV vaccination programs the immune response for replication arrest-type protection against SIV infection. To meet these goals, Core D will address the following Specific Aims: 1) provide specialized CITE-seq and/or TCR sequence identification using the 10X Genomics platform, 2) conduct Nanostring and bulk RNAseq analysis of whole blood and tissues, 3) provide bioinformatic and biostatistical analyses, and computational modeling, to define immune response gene expression signatures linked with vaccine actions and virus control, and 4) develop and manage a comprehensive database for all Program data to facilitate integrated data analysis. Core D is directed by Dr. Michael Gale, Jr., working closely with Drs. Ben Bimber and Paul Edlefsen, to provide consistent, high-quality functional genomics data generation, integrated data analysis, biostatistical analyses and computational modeling, with big data management, for all aspects of the scientific program.

核心D项目总结 `OMICS、生物信息学和数据管理核心(核心D)通过提供高质量的 解析功能基因组学和生物信息学计算分析与统计整合。主 核心的目标是定义基因表达签名及其功能输出，以编程 68-1RhCMV/SIV疫苗对临床前恒河猴SIV复制抑制的免疫应答 (RM)疫苗研究。核心将询问血液和组织中的单个CD8+T细胞，它们之间的特定联系 T细胞受体的使用(以识别SIV特异性克隆类型)，血液和组织中单个非CD8+T细胞，以及 全血、淋巴(LN)、脾、骨髓(BM)和肠道相关免疫组织 淋巴组织(GALT)，并将数据集与空间转录数据集链接，以定义基因表达 签名和网络，并将应用尖端生物信息学方法来模拟其功能输出 并告知RhCMV/SIV疫苗计划免疫反应的作用机制 针对SIV感染的复制阻止型保护。为了实现这些目标，核心D将解决以下问题 具体目标：1)使用10X基因组学提供专门的CITE-SEQ和/或TCR序列识别 平台，2)进行全血和组织的纳米串和批量RNAseq分析，3)提供生物信息学 以及生物统计分析和计算建模，以定义免疫反应基因表达特征 与疫苗行动和病毒控制相联系，以及4)为所有人开发和管理一个全面的数据库 对数据进行编程，以便于进行综合数据分析。核心D由小迈克尔·盖尔博士执导，密切合作 与Ben Bimber博士和Paul Edlefsen博士合作，提供一致的、高质量的功能基因组数据生成， 面向所有人的综合数据分析、生物统计分析和计算建模，以及大数据管理 科学计划的各个方面。