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: 10670293
• 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/10670293
• 关键词: Core; Functional; Genomics; Computational; Biology

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 该PPG应用的总体目标是比较和对比抑制性的机制 受体PD1和LAG3在耐受性和自身免疫性，癌症和慢性的背景下在T细胞上运行 感染。在整个研究中要使用的一种主要方法是全基因组的应用 转录分析。功能基因组学和计算生物学核心（核心C）的目的是 为此计划中的所有三个项目提供基于基础测序的基本基因组学服务。 此外，该核心将运行，提供逆转录病毒（RV）强化表达和敲低的服务 可以直接在计算分析中直接测试体内个体基因和途径的平台。因此， 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 连接到下游RV强化的表达和敲低以及以CARSPR/CAS9为中心 基因筛查。目的是： 目标1：提供初始数据托管，归一化，预处理和分析以及执行 散装和单细胞的跨项目集成和计算网络建模 转录组和表观遗传数据集。 Core C将（i）提供原始数据QC，数据清洁，预处理， 以及用于下游分析的文件以及操作Web门户接口，以供用户探索 数据； （ii）进行主要和二级基因组学数据分析； （iii）执行网络并集成 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（与上一个周期中的scrna-seq一样）。 目标2：启用Vivo CRISPR/CAS9筛选并提供RV增强的表达和 Knowckdown平台，用于对PD-1调节的基因和途径的体内询问 和/或lag3。核心C将有助于设计CRISPR筛选图书馆，用于体内CRISPR筛选平台 通过项目以及下游数据分析。核心C还将为体内逆转录病毒平台提供 强制表达或shRNA敲低优先级的Gois。 从本质上讲，Core C与该PPG的其他组件高度互动。项目1、2和 3将输入Core C，该Core C将分析来自项目的输入的样本，并将结果整合在一起 三个项目。核心C将与核心A，B和D互动以获得管理支持并识别基因 新型小鼠菌株和免疫染色分析的靶标。