Module 3: Gene Expression/Proteomics

模块 3：基因表达/蛋白质组学

• 批准号: 10700862
• 负责人: Yutao Liu
• 金额: $ 7.04万
• 依托单位: AUGUSTA UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-09-01 至 2025-08-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10700862
• 关键词: Affect; Aqueous Humor; Awareness; Bioinformatics; Biological Markers; Center Core Grants; Consultations; Cornea; Data; Data Analyses; Development; Devices; Disease; Disease Progression; Experimental Designs; Expression Profiling; Funding; Future; Gene Chips; Gene Expression; Gene Expression Profile; Gene Expression Profiling; Gene Proteins; Genetic Transcription; Genomics; Goals; Mass Spectrum Analysis; Measurement; Oligonucleotide Microarrays; Onset of illness; Pathway Analysis; Pathway interactions; Post-Translational Protein Processing; Preparation; Proteome; Proteomics; Protocols documentation; RNA analysis; Research Personnel; Retina; Sampling; Scientist; Services; Speed; Spottings; System; Technology; Tissues; Trabecular meshwork structure; Transcript; Universities; Validation; Vision; Vision Disorders; Vision research; Visual; Visual System; bead chip; cDNA Arrays; design; experimental study; high throughput technology; insight; instrument; large datasets; lens; liquid chromatography mass spectrometry; mass spectrometer; new technology; next generation sequencing; novel; protein expression; single-cell RNA sequencing; transcriptome; transcriptome sequencing

The gene expression and proteomics module will provide investigators with expertise in designing and performing studies of global gene expression profiles and proteomic alterations related to diseases of the visual system. In the last two decades, a number of high throughput platforms have been developed to investigate global gene expression patterns. These technologies include spotted cDNA or oligonucleotide arrays, Affymetrix GeneChip microarrays, Illumina BeadChip microarrays, and most recently next-generation sequencing technologies including RNA sequencing (RNA-Seq) and Single-cell RNA sequencing (scRNA-seq). This Core will use RNA-Seq and scRNA-seq for gene expression studies. Similarly, the development of Liquid- Chromatography Mass Spectrometry (LC-MS/MS) over the last decade has revolutionized proteomic analyses through its unprecedented depth, speed and accuracy even with small volume samples. One of the latest breakthroughs in this technology is the Orbitrap Fusion Tribrid mass spectrometer, which allows researchers to extend the limits of proteomic analyses including post-translational modifications. We have this instrument at Augusta University and recently, we have successfully established a protocol for the analysis of the aqueous humor proteome using this device. These latest sequencing and mass-spec technologies, used to evaluate gene expression and protein levels, can be intimidating to researchers, whose scientific expertise lies elsewhere. The new technologies also present challenges associated with high throughput data analyses and interpretation. To circumvent these hurdles, the gene expression and proteomics module is intended to guide researchers in experimental design, sample preparation, thoughtful selection of appropriate technology, and bioinformatics support for sequencing and proteomic profiling. In addition, the core will also help researchers with the interpretation of results and designing further experiments for confirmation/validation of findings. The goal of this module is to guide vision researchers with high throughput gene expression analyses (using sequencing) and proteomic analyses (using mass-spectrometry) of ocular tissues. The services offered in this module reflect keen awareness of the nuances related to experimentation with specialized ocular tissues and will be accomplished in two aims. Aim 1: Provide core investigators with expert consultation, tailored to analysis of the visual system, on experimental design, sample preparation and selection of technology to conduct gene expression studies and/or proteomic analyses of ocular tissues. Aim 2: Provide core investigators with excellent bioinformatics support in analyzing the large data sets that are generated following high throughput gene expression or proteomic analyses of ocular tissues.

基因表达和蛋白质组学模块将为研究人员提供设计和蛋白质组学方面的专业知识。 进行与视觉疾病相关的整体基因表达谱和蛋白质组改变的研究 系统。在过去的二十年中，已经开发了许多高通量平台来研究 全局基因表达模式。这些技术包括斑点 cDNA 或寡核苷酸阵列、Affymetrix GeneChip 微阵列、Illumina BeadChip 微阵列和最新的新一代测序 技术包括RNA测序（RNA-Seq）和单细胞RNA测序（scRNA-seq）。这个核心 将使用 RNA-Seq 和 scRNA-seq 进行基因表达研究。同样，液体的发展 过去十年中，色谱质谱 (LC-MS/MS) 彻底改变了蛋白质组分析 即使对于小体积样品，也具有前所未有的深度、速度和准确性。最新的之一 这项技术的突破是 Orbitrap Fusion Tribrid 质谱仪，它使研究人员能够 扩展蛋白质组分析的局限性，包括翻译后修饰。我们有这个仪器在 奥古斯塔大学和最近，我们成功建立了水分析方案 使用该设备的幽默蛋白质组。这些最新的测序和质谱技术，用于评估基因 表达和蛋白质水平可能会让研究人员感到害怕，因为他们的科学专业知识在其他地方。这 新技术还带来了与高通量数据分析和解释相关的挑战。到 为了克服这些障碍，基因表达和蛋白质组学模块旨在指导研究人员 实验设计、样品制备、适当技术的深思熟虑和生物信息学 支持测序和蛋白质组分析。此外，该核心还将帮助研究人员 对结果的解释并设计进一步的实验以确认/验证结果。目标是 该模块旨在指导视觉研究人员进行高通量基因表达分析（使用测序） 以及眼组织的蛋白质组学分析（使用质谱法）。该模块提供的服务反映了 对与特殊眼组织实验相关的细微差别有敏锐的认识，并将 实现了两个目标。目标 1：为核心调查人员提供针对分析问题量身定制的专家咨询 视觉系统，关于实验设计、样品制备和基因技术选择 眼组织的表达研究和/或蛋白质组分析。目标2：为核心研究者提供优秀的 生物信息学支持分析高通量基因生成的大数据集 眼组织的表达或蛋白质组分析。