Core C: Systems Biology Core

核心 C：系统生物学核心

• 批准号: 10723638
• 负责人: Michael Gale
• 金额: $ 43.01万
• 依托单位: UNIVERSITY OF WASHINGTON
• 依托单位国家: 美国
• 财政年份: 2023
• 资助国家: 美国
• 起止时间: 2023-08-01 至 2028-07-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10723638
• 关键词: Animals; Bioinformatics; Biological Assay; Biometry; Blood; Blood specimen; Bone Marrow; Cell Culture Techniques; Cells; Cellular Indexing of Transcriptomes and Epitopes by Sequencing; Collaborations; Communication; Data; Data Management Resources; Data Set; Databases; Deposition; Epitopes; Gene Expression; Generations; Gut associated lymphoid tissue; Human Resources; Immune; Immune response; Immunity; Intercept; Interleukin-15; Libraries; Link; Macaca mulatta; Mediating; Molecular; Molecular Profiling; Office of Administrative Management; Preparation; Process; Production; Program Research Project Grants; Publications; Quality Control; RNA; Research; SIV; SIV Vaccines; Sampling; Secure; Spleen; Standardization; Support System; Systems Biology; Tissues; Vaccination; Vaccines; Viral; Whole Blood; Work; big data management; cohort; cytokine; data exchange; data management; data resource; data sharing; differential expression; digital; functional genomics; gene network; genomic data; indexing; lymph nodes; multidimensional data; nano-string; next generation sequencing; operation; preclinical study; programs; public database; public repository; quality assurance; response; single-cell RNA sequencing; synergism; transcriptome; transcriptome sequencing; transcriptomics; vaccine efficacy; vaccine response; web-accessible

The Systems Biology Core C (SB Core C) serves this P01 Program to provide high-throughput pipelines from sample acquisition through quality control, library preparation, sequencing, and pre-processing of sequencing data sets. The main objective of the Core is to generate gene expression data sets for analyses to define the RHCMV/SIV vaccine response and programming by IL-15 for SIV vaccine protection in rhesus macaque (RM) vaccine cohorts of pre-clinical studies. Core C will conduct the following Specific Aims: 1) Perform next- generation sequencing assays of whole blood, tissue, and single cell samples received from Projects 1 and 2; 2) Conduct NanoString nCounter analyses on whole blood samples from Project 1 to assess baseline IL-15 expression and response, and to interrogate the whole blood predictive protective signature to inform study assignments; 3) Manage big datasets of next-gen sequencing data for quality assurance, analysis, public database disposition, publication, and Program access. The Core will prepare and/or sequence libraries generated from tissues for spatial transcriptomics, libraries generated from single cells in blood and tissues for single cell RNA-seq analysis, and whole immune tissues including whole blood, lymph node (LN), spleen, bone marrow (BM) and gut-associated lymphoid tissues (GALT) for bulk and single cell RNA-seq analysis, including CITEseq. The Core will provide consistent, high-quality functional genomics data that will be housed by a secure data management system. Data generated by the Core will undergo quality control, pre-processing, and normalized matrix generation prior to being delivered for bioinformatics analyses to support all aspects of the scientific program.

系统生物学核心 C (SB Core C) 服务于该 P01 计划，提供来自 通过质量控制、文库制备、测序和测序预处理进行样品采集 数据集。核心的主要目标是生成基因表达数据集进行分析，以定义 RHCMV/SIV 疫苗反应和 IL-15 编程用于恒河猴 (RM) 的 SIV 疫苗保护 临床前研究的疫苗队列。核心 C 将实现以下具体目标： 1) 执行下一步- 对从项目 1 和 2 收到的全血、组织和单细胞样本进行世代测序分析； 2) 对项目 1 的全血样本进行 NanoString nCounter 分析，以评估基线 IL-15 表达和反应，并询问全血预测保护特征，为研究提供信息 作业； 3) 管理下一代测序数据的大数据集，以进行质量保证、分析、公开 数据库处置、发布和程序访问。核心将准备和/或测序库 从组织中生成用于空间转录组学，从血液和组织中的单细胞生成文库用于 单细胞 RNA-seq 分析，以及整个免疫组织，包括全血、淋巴结 (LN)、脾脏、骨骼 用于批量和单细胞 RNA-seq 分析的骨髓 (BM) 和肠道相关淋巴组织 (GALT)，包括 CITE 序列。该核心将提供一致、高质量的功能基因组学数据，这些数据将由安全的 数据管理系统。核心生成的数据将经过质量控制、预处理和 在进行生物信息学分析之前生成标准化矩阵，以支持生物信息学的各个方面 科学计划。