Omics, Bioinformatics, and Data Management Core

组学、生物信息学和数据管理核心

基本信息

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
项目类别：
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

项目摘要

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 项目摘要 “组学、生物信息学和数据管理核心（核心 D）通过提供高分辨率功能基因组学和生物信息学计算分析与统计整合。主要核心的目标是定义基因表达特征及其功能输出，以编程 68-1 RhCMV/SIV 疫苗的免疫反应介导临床前恒河猴中 SIV 复制停滞（RM）疫苗研究。核心将询问血液和组织中的单个 CD8+ T 细胞，以及它们与特定细胞之间的联系。 T 细胞受体的使用（识别 SIV 特异性克隆型）、血液和组织中的单个非 CD8+ T 细胞，以及整个免疫组织，包括全血、淋巴结 (LN)、脾脏、骨髓 (BM) 和肠道相关淋巴组织（GALT），并将数据集与空间转录组数据集联系起来，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 疫苗接种计划免疫反应的作用机制针对 SIV 感染的复制停滞型保护。为了实现这些目标，Core D 将解决以下问题具体目标：1) 使用 10X Genomics 提供专门的 CITE-seq 和/或 TCR 序列鉴定平台，2) 对全血和组织进行 Nanostring 和批量 RNAseq 分析，3) 提供生物信息学和生物统计分析以及计算模型，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，4) 为所有人开发和管理一个综合数据库对数据进行编程以促进综合数据分析。 Core D 由 Michael Gale, Jr. 博士指导，密切合作与博士。 Ben Bimber 和 Paul Edlefsen，提供一致、高质量的功能基因组学数据生成，为所有人提供集成数据分析、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。