Genomic/Genetic and Proteome

摘要： 基因组和蛋白质组核心（PPG核心B）将提供必要的，尖端的基因组学，蛋白质组学， 生物信息学专业知识，以促进这种高度整合的PPG的翻译影响。核心B将响应- 能够为研究人员提供：（i）对公开可用的DNA和RNA的专家询问 测序数据集和全基因组DNA甲基化数据集，以从这些平台生成可解释的数据， 形式;（ii）测试PPG靶基因DNA变异体与sus之间关联所需的遗传专业知识， （iii）人内皮细胞（EC）系和基因组编辑的细胞系的产生 具有选择的单核苷酸敲入或基于缺失的敲除突变的功能遗传模型 （iv）对免疫沉淀的PPG靶标进行传统的蛋白质组质谱分析 用于蛋白质翻译修饰（PTM）鉴定的蛋白质，包括磷酸化、硝化和ubiq- （v）计算机蛋白质结构建模，以确定功能性非同义词的影响， Mous编码变体对蛋白质结构和功能（蛋白质-蛋白质相互作用，催化活性，后反式- 离子修饰），其中蛋白质-蛋白质相互作用通过表面等离子体共振验证;以及，（vi）实验- 旨在监督在PTM或SNP位点发生突变的重组蛋白的生产。作为集中 Core B（位于亚利桑那州图森）将进行所有相关分析 所有四个项目的实验样品，因为每个PPG项目将需要提供服务， 核心B。

ABSTRACT: The Genome and Proteome Core (PPG Core B) will provide essential, cutting-edge genomics, proteomics, and bioinformatics expertise to facilitate the translational impact of this highly integrated PPG. Core B will be respon- sible for providing the research investigators with: (i) expert interrogation of publicly available DNA and RNA sequencing datasets and genome-wide DNA methylome datasets to generate interpretable data from these plat- forms; (ii) genetic expertise needed to test for associations between PPG target gene DNA variants and sus- ceptibility and severity of ARDS; (iii) generation of human endothelial cell (EC) lines and genome-edited cell line models with selected single nucleotide knock in or deletion-based knock out mutations for functional genetic analyses; (iv) execution of traditional proteomic mass spectrometry analysis of immunoprecipitated PPG target proteins for protein translational modification (PTM) identification, including phosphorylation, nitration, and ubiq- uitination; (v) in silico computational protein-structure modeling to identify the impact of functional non-synony- mous coding variants on protein structure and function (protein-protein interaction, catalytic activity, post-trans- lational modification), with protein-protein interactions validated by surface plasmon resonance; and, (vi) exper- tise to oversee production of recombinant proteins with mutations at sites of PTMs or SNPs. As a centralized core for all genome and proteome analyses, Core B (located in Tucson AZ) will perform all relevant analysis of experimental samples for all four projects as each PPG Project will require the services provided by Core B.