Core C: Proteogenomics Core

核心 C：蛋白质组学核心

基本信息

批准号：
10602487
负责人：
Andrew Laurence Routh
金额：
$ 34.21万
依托单位：
UNIVERSITY OF TEXAS MED BR GALVESTON
依托单位国家：
美国
项目类别：
财政年份：
2021
资助国家：
美国
起止时间：
2021-04-15 至 2026-03-31
项目状态：
未结题

来源：
https://reporter.nih.gov/project-details/10602487
关键词：
ATAC-seq Acetylation Address Alternative Splicing Antibodies Antigen-Antibody Complex Bioinformatics Cell Culture Techniques Cells ChIP-seq Chromatin Chromium Collaborations Column Chromatography Complex Computer Analysis DNA DNA Methylation Data Data Analyses Data Files Databases Dendritic Cells Deposition Disabled Persons Ebola virus Epigenetic Process Event Evolution Experimental Designs Filovirus Flavivirus Infections Fractionation Gene Expression Genetic Transcription Goals Histone Acetylation Human Immune Immune response Infection Infrastructure Interferons Libraries Mass Spectrum Analysis Massive Parallel Sequencing Medical Messenger RNA Methodology Modeling Modification Molecular Molecular Biology Molecular Conformation Monitor Output Pathology Phosphorylation Poly A Polyadenylation Population Post-Translational Protein Processing Procedures Protein Isoforms Proteins Proteome Proteomics Publications Quality Control RNA RNA Viruses RNA chemical synthesis RNA metabolism Reaction Records Research Research Project Grants Research Support Resolution Role Sampling Schedule Signal Transduction Technology Texas Tissue-Specific Gene Expression Transcript Translations Ubiquitin Ubiquitination Universities Viral Virus Diseases bisulfite sequencing cell type conformational alteration dynamic system experience experimental study frontier high throughput technology histone methylation innovation instrument member mutant nanopore next generation sequencing nonhuman primate novel novel sequencing technology phenome posttranscriptional protein expression proteogenomics public database response ribosome profiling single-cell RNA sequencing transcriptome transcriptome sequencing transcriptomics

项目摘要

PROTEOGENOMICS CORE (Core C): PROJECT SUMMARY/ABSTRACT Ebola virus (EBOV) and other filoviruses cause devastating pathology, resulting in large part from a dysregulated immune response. At present, our characterization of immune cell-specific responses to EBOV is limited. To address this complex issue, the research projects of this proposal will employ a wide range of OMICS and high- throughput technologies focused at each stage of the “central dogma”; from RNA synthesis, through RNA metabolism, to protein translation and modification. The role of the Proteogenomics Core (Core C) will be to apply cutting-edge massively parallel sequencing and proteomics approaches in support of Research Projects 1, 2, and 3, and to develop novel procedures and technologies to tackle the uniquely complex immune response to EBOV. We will use a combination of short-read (Illumina) and long-read (Nanopore) approaches to characterize epigenetic, transcriptional, and posttranscriptional responses to EBOV infection. Output from sequencing and proteomic analysis will be integrated with the Bioinformatics and Modeling Core (Core D) and deposited in public databases. Finally, these results will be interpreted together with the original main Projects. The Proteogenomics Core comprises a group of experts with experience in the implementation of the wide range of approaches in molecular biology, experimental design, and downstream computational analyses. Core C has a well established track record of innovating novel and cutting-edge methodologies in both next-generation sequencing and mass spectrometry, and can therefore develop and provide state-of-the-art technical support to advance the proposed research to new frontiers. The core will be directed by Dr. Routh, an expert in applying novel sequencing technologies to study RNA virus evolution, transcriptomics, and bioinformatics. Drs. Russell and Widen (Associate Core Leads) are directors of the mass spectrometry and next-generation sequencing facilities, respectively, at the University of Texas Medical Branch. The overarching goal of the Proteogenomics Core is to provide a comprehensive and unprecedented characterization of the “phenome” of cells infected by EBOV, both in cell culture and NHP models. By comparing changes in the epigenetic landscape to observed perturbations in the transcriptome, we will first determine how these events are coordinated and subsequently manifest as changes in the host proteome.

蛋白质组学核心（核心 C）：项目摘要/摘要埃博拉病毒 (EBOV) 和其他丝状病毒会引起毁灭性的病理，这在很大程度上是由于失调引起的。目前，我们对 EBOV 免疫细胞特异性反应的描述还很有限。为了解决这个复杂的问题，本提案的研究项目将采用广泛的组学和高通量技术专注于“中心法则”的每个阶段；从 RNA 合成到 RNA 蛋白质基因组学核心（核心 C）的作用是：应用尖端的大规模并行测序和蛋白质组学方法来支持研究项目 1、2 和 3，并开发新的程序和技术来应对独特的复杂免疫反应我们将结合使用短读长 (Illumina) 和长读长 (Nanopore) 方法。表征对 EBOV 感染输出的表观遗传、转录和转录后反应。测序和蛋白质组分析将与生物信息学和建模核心（核心 D）集成最后，这些结果将与原始主要结果一起进行解释。项目。蛋白质基因组学核心由一组在广泛实施蛋白质组学方面具有丰富经验的专家组成。分子生物学、实验设计和下游计算分析的一系列方法。 C 在下一代创新和尖端方法方面拥有良好的记录测序和质谱分析，因此可以开发并提供最先进的技术支持将拟议的研究推进到新的领域。该核心将由应用专家劳斯博士指导。 Russell 博士研究 RNA 病毒进化、转录组学和生物信息学的新颖测序技术。和 Widen（副核心领导）是质谱和下一代测序的主管设施分别位于德克萨斯大学医学分部。蛋白质组学核心的总体目标是提供全面且前所未有的研究通过比较细胞培养物和 NHP 模型中 EBOV 感染细胞的“表型”特征。表观遗传景观的变化与观察到的转录组扰动的变化，我们将首先确定如何这些事件经过协调并随后表现为宿主蛋白质组的变化。