Core C - Functional Genomics and Computational Biology Core

核心摘要 这个PPG应用程序的总体目标是比较和对比抑制 受体PD1和LAG3在耐受和自身免疫、癌症和慢性疾病的背景下作用于T细胞 感染。在整个研究中使用的一个主要方法是在全基因组范围内应用 转录特征分析。功能基因组学和计算生物学核心(核心C)的目的是 为本计划的所有三个项目提供必要和集中的基于测序的基因组学服务。 此外，这个核心将提供逆转录病毒(RV)强制表达和敲除的服务 可以直接在体内测试通过计算分析确定的单个基因和途径的平台。因此， Core C将提供集成的生物信息和计算分析平台以及数据集成服务 与下游RV强制表达和敲除以及体内CRISPR/Cas9-Focus结合 基因筛查。目标是： 目标1：提供初始数据托管、标准化、预处理和分析以及执行 面向批量和单元格的跨项目数据集成与计算网络建模 转录和表观遗传学数据集。核心C将(I)提供原始数据质量控制、数据清理、预处理、 以及生成用于下游分析的文件，以及操作用于用户探索的网络门户界面 数据；(Ii)执行初级和次级基因组数据分析；以及(Iii)执行网络和集成 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(如上一个周期中的scRNA-seq)。 目的2：实现体内CRISPR/Cas9的筛选，并提供RV增强的表达和 PD-1调控基因和通路下游在体询问的已知敲除平台 和/或LAG3。Core C将协助设计体内CRISPR筛选平台的CRISPR筛选文库 通过对项目以及下游数据的分析。Core C还将提供体内逆转录病毒平台，以 强制高优先级GOI的表达或shRNA敲除。 从本质上讲，Core C与此PPG的其他组件具有高度的互动性。来自项目1、2和 3将进入Core C，它将根据项目的输入分析样本，并将结果整合到 三个项目。核心C将与核心A、B和D进行大量交互，以获得管理支持和识别基因 新的小鼠品系的目标和免疫染色分析。

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.