Module 3: Gene Expression/Proteomics

基因表达和蛋白质组学模块将为研究人员提供设计和 进行与视觉系统疾病相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，已经开发了许多高通量平台来研究 全球基因表达模式这些技术包括点样cDNA或寡核苷酸阵列、Affyssin 基因芯片微阵列，Illumina BeadChip微阵列，以及最近的下一代测序 这些技术包括RNA测序（RNA-Seq）和单细胞RNA测序（scRNA-seq）。这一核心 将使用RNA-Seq和scRNA-seq进行基因表达研究。同样，Liquid的发展- 在过去的十年中，色谱-质谱联用（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，即使是小体积的样品。一个最新的 这项技术的突破是Orbitrap Fusion Tribrid质谱仪，它使研究人员能够 扩展了蛋白质组学分析的范围，包括翻译后修饰。我们有这种仪器， 奥古斯塔大学和最近，我们已经成功地建立了一个协议，用于分析水 幽默蛋白质组学。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，可能会吓到研究人员，他们的科学专长在其他地方。的 新技术也提出了与高通量数据分析和解释相关的挑战。到 绕过这些障碍，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、适当技术的精心选择和生物信息学 支持测序和蛋白质组学分析。此外，该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。的目标 该模块将指导视觉研究人员进行高通量基因表达分析（使用测序） 和眼组织的蛋白质组学分析（使用质谱法）。本模块提供的服务反映了 敏锐地意识到与专门的眼组织实验相关的细微差别， 实现了两个目标。目标1：为核心研究者提供专家咨询，专门针对 可视化系统，对实验设计、样品制备和基因选择技术进行研究 眼组织的表达研究和/或蛋白质组分析。目标2：为核心研究者提供出色的 生物信息学支持分析高通量基因表达后产生的大数据集， 表达或蛋白质组学分析。

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.