Omics, Bioinformatics, and Data Management Core

核心D项目总结 “组学，生物信息学和数据管理核心（核心D）通过提供高质量的 分辨率功能基因组学和生物信息学计算分析与统计集成。主要 核心的目标是定义基因表达特征及其功能输出， 68-1 RhCMV/SIV疫苗诱导恒河猴免疫应答 (RM)疫苗研究。核心将询问血液和组织中的单个CD 8 + T细胞，它们的特异性免疫应答的连接。 T细胞受体使用（以鉴定SIV特异性克隆型），血液和组织中的单个非CD 8 + T细胞，以及 全免疫组织，包括全血、淋巴结（LN）、脾、骨髓（BM）和肠相关的 淋巴组织（GALT），并将数据集与空间转录组学数据集联系起来，以定义基因表达 签名和网络，并将应用最先进的生物信息学方法来模拟其功能输出 并告知RhCMV/SIV疫苗接种程序免疫应答的作用机制， 针对SIV感染的复制抑制型保护。为了实现这些目标，核心D将解决以下问题 具体目的：1）使用10 X Genomics提供专门的CITE-seq和/或TCR序列鉴定 平台，2）进行全血和组织的Nanostring和批量RNAseq分析，3）提供生物信息学分析， 生物统计分析和计算机建模，以确定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）开发和管理一个全面的数据库， 对数据进行编程，以促进综合数据分析。核心D是由迈克尔盖尔博士，小，密切合作 Ben Bimber和Paul Edlefsen博士合作，提供一致的高质量功能基因组学数据生成， 集成数据分析、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。

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.