Module 3: Gene Expression/Proteomics

模块 3：基因表达/蛋白质组学

• 批准号: 10228014
• 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/10228014
• 关键词: Affect; Aqueous Humor; Awareness; Bioinformatics; Biological Markers; Center Core Grants; Consultations; Cornea; Custom; 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; System; Technology; Tissues; Trabecular meshwork structure; Transcript; Universities; Validation; Vision; Vision Disorders; Vision research; Visual; Visual system structure; 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; power analysis; 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设计专业知识 对与视觉疾病有关的全球基因表达谱和蛋白质组学改变的研究 系统。在过去的二十年中，已经开发了许多高吞吐量平台来调查 全球基因表达模式。这些技术包括斑点cDNA或寡核苷酸阵列，Affymetrix Genechip微阵列，Illumina Beadchip微阵列以及最近的下一代测序 包括RNA测序（RNA-SEQ）和单细胞RNA测序（SCRNA-SEQ）在内的技术。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 在过去的十年中，色谱质谱法（LC-MS/MS）彻底改变了蛋白质组学分析 通过其前所未有的深度，速度和准确性，即使使用少量样品。最新的 该技术的突破是Orbitrap融合三元质谱仪，它使研究人员能够 扩展蛋白质组学分析的限制，包括翻译后修饰。我们有这个乐器 奥古斯塔大学（Augusta University）和最近，我们成功建立了一项协议来分析水性 使用此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对研究人员的科学专业知识在其他地方进行。这 新技术还提出了与高吞吐量数据分析和解释相关的挑战。到 规避这些障碍，基因表达和蛋白质组学模块旨在指导研究人员 实验设计，样品准备，周到的适当技术和生物信息学 支持测序和蛋白质组学分析。此外，核心还将帮助研究人员 解释结果并设计进一步的实验，以确认/验证发现。目标 该模块是指导具有高吞吐量基因表达分析的视力研究人员（使用测序） 和蛋白质组学分析（使用质谱法）的眼组织。此模块中提供的服务反映 敏锐的对与专门的眼组织实验有关的细微差别的认识，将是 以两个目标完成。目标1：为核心调查人员提供专家咨询，量身定制为分析 视觉系统，实验设计，样品制备和进行基因的技术选择 眼组织的表达研究和/或蛋白质组学分析。目标2：为核心调查人员提供出色的 生物信息学支持在分析高吞吐量基因后生成的大数据集 眼组织的表达或蛋白质组学分析。