Core C - Functional Genomics and Computational Biology Core

核心 C - 功能基因组学和计算生物学核心

• 批准号: 10239108
• 负责人: E. John Wherry
• 金额: $ 21.07万
• 依托单位: UNIVERSITY OF PITTSBURGH AT PITTSBURGH
• 依托单位国家: 美国
• 财政年份: 2015
• 资助国家: 美国
• 起止时间: 2015-05-15 至 2025-07-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10239108
• 关键词: Affect; Antiviral Agents; Autoimmune; Autoimmunity; Bioinformatics; Biological; Biology; CD4 Positive T Lymphocytes; CD8B1 gene; CRISPR screen; CRISPR/Cas technology; Cells; Chronic; Cluster Analysis; Computational Biology; Computer Analysis; Consultations; Coupled; Data; Data Analyses; Data Files; Data Set; Defect; Disease model; Emerging Technologies; Epigenetic Process; Functional disorder; Gene Expression; Gene Expression Profiling; Gene Targeting; Generations; Genes; Genetic; Genetic Screening; Genetic Transcription; Genomics; Goals; HIV; Hepatitis B Virus; Hepatitis C virus; Immunity; Immunologics; Individual; Infection; Informatics; Libraries; Lymphocytic choriomeningitis virus; Malignant Neoplasms; Modeling; Morbidity - disease rate; Mouse Strains; Mus; Nature; Output; Pathway Analysis; Pathway interactions; Quality Control; Reporter; Research Personnel; Role; Sampling; Services; Signal Transduction; System; T cell response; T-Lymphocyte; Technology; Tissue-Specific Gene Expression; Tumor Immunity; Validation; Variant; Vertebral column; Viral; Virus; analytical tool; antiviral immunity; archive data; archived data; base; bioinformatics tool; chronic infection; computational network modeling; computational suite; data cleaning; data exploration; data hosting; data integration; data mining; data quality; data visualization; design; exhaustion; flexibility; functional genomics; genome-wide; genomic data; immunoregulation; improved; in vivo; in vivo evaluation; insight; interest; knock-down; mortality; mouse model; novel; programmed cell death protein 1; programs; receptor; single-cell RNA sequencing; small hairpin RNA; synergism; transcription factor; transcriptomics; tumor; web portal

CORE SUMMARY The overall goal of this PPG application is to compare and contrast the mechanisms by which the inhibitory receptors PD1 and LAG3 operate on T cells in the context of tolerance and autoimmunity, cancer, and chronic infection. One major approach to be used throughout the studies is the application of genome-wide transcriptional profiling. The purpose of the Functional Genomics and Computational Biology Core (Core C) is to provide essential and centralized sequencing-based genomics services for all three Projects in this Program. In addition, this Core will operate provide the service of a retroviral (RV)-enforced expression and knockdown platform that can directly test in vivo individual genes and pathways identified from computational analyses. Thus, Core C will provide integrated bioinformatic and computational analytical platforms and data integration services coupled to downstream RV-enforced expression and knockdown as well as in vivo CRISPR/Cas9-focused genetic screening. The Aims are: AIM 1: To provide initial data hosting, normalization, preprocessing, and analysis as well as perform cross-Project data integration and computational network modeling for bulk and single-cell transcriptomic and epigenetic datasets. Core C will (i) provide raw data QC, data cleaning, pre-processing, and generation of files for downstream analyses as well as operate a web portal interface for user exploration of the data; (ii) perform primary and secondary genomics data analyses; and (iii) perform network and integrated analyses including. The Core also will support and/or develop new analytical tools as technologies become available (as for scRNA-seq in the last cycle). AIM 2: To enable in vivo CRISPR/Cas9 screening and provide an RV-enforced expression and knowckdown platform for downstream in vivo interrogation of genes and pathways regulated by PD-1 and/or LAG3. Core C will aid in design of CRISPR screening libraries for in vivo CRISPR screening platforms by the Projects as well as downstream data analysis. Core C will also provide an in vivo retroviral platform to enforce expression or shRNA knock-down of high-priority GOIs. By its nature, Core C is highly interactive with other components of this PPG. Samples from Projects 1, 2, and 3 will enter Core C, which will analyze samples with input from the Projects and integrate results among the three Projects. Core C will interact heavily with Cores A, B, and D for administrative support and to identify gene targets for novel mouse strains and immunostaining analysis.

核心摘要 本PPG应用程序的总体目标是比较和对比抑制性药物的作用机制。 受体PD 1和LAG 3在耐受性和自身免疫、癌症和慢性炎症的背景下对T细胞起作用。 感染在整个研究中使用的一个主要方法是应用全基因组 转录谱分析功能基因组学和计算生物学核心（核心C）的目的是 为该计划中的所有三个项目提供必要的和集中的基于测序的基因组服务。 此外，该核心将提供逆转录病毒（RV）强制表达和敲低的服务。 该平台可以直接测试从计算分析中识别的体内个体基因和途径。因此，在本发明中， 核心C将提供集成的生物信息学和计算分析平台以及数据集成服务 与下游RV-强制表达和敲低以及体内CRISPR/Cas9-聚焦结合， 基因筛选目标是： 目标1：提供初始数据托管、规范化、预处理和分析，并执行 跨项目数据集成和计算网络建模，适用于批量和单电池 转录组和表观遗传数据集。核心C将（i）提供原始数据QC、数据清理、预处理， 和生成用于下游分析的文件，以及操作用于用户探索 数据;（ii）进行初级和二级基因组学数据分析;以及（iii）进行网络和集成 分析包括。随着技术的发展，核心还将支持和/或开发新的分析工具。 可用（与上一个循环中的scRNA-seq相同）。 目的2：为了能够进行体内CRISPR/Cas9筛选并提供RV-强制表达， 用于PD-1调控的基因和途径的下游体内询问的knockdown平台 和/或LAG 3。核心C将帮助设计用于体内CRISPR筛选平台的CRISPR筛选文库 以及下游数据分析。Core C还将提供一个体内逆转录病毒平台， 实施高优先级GOI的表达或shRNA敲低。 就其本质而言，核心C与PPG的其他组件高度互动。项目1、2和 3将进入核心C，它将分析样本与项目的输入，并整合结果之间的 三个项目。核心C将与核心A、B和D进行大量交互，以提供管理支持并识别基因 新的小鼠品系和免疫染色分析的目标。