La Jolla Interdisciplinary Neuroscience Center Cores - Gene Analysis Core BU

拉荷亚跨学科神经科学中心核心 - 基因分析核心事业部

• 批准号: 7925703
• 负责人: STUART A LIPTON
• 金额: $ 10.19万
• 依托单位: SANFORD BURNHAM PREBYS MEDICAL DISCOVERY INSTITUTE
• 依托单位国家: 美国
• 财政年份: 2009
• 资助国家: 美国
• 起止时间: 2009-09-01 至 2011-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7925703
• 关键词: Acceleration; Address; Affect; Agar Gel Electrophoresis; Agreement; Area; Bar Codes; Base Pairing; Bioinformatics; Biological; Biological Assay; Biotin; Blood capillaries; Breeding; Cancer Center; Capillary Electrophoresis; Cells; Chemicals; Collaborations; Color; Communities; Comparative Study; Complementary DNA; Computer software; Core Facility; Cultured Cells; Custom; DNA; DNA Sequence; Data; Data Analyses; Data Quality; Data Set; Databases; Deoxyribonucleases; Development; Electronics; Electrophoresis; Floor; Fostering; Freezing; Fresh Tissue; Funding; Gel; Gene Expression; Gene Expression Microarray Analysis; Gene Family; Gene Targeting; Genes; Genetic Transcription; Genome; Genotype; Harvest; Health Services Accessibility; Housekeeping; Human; Human Resources; Hybridization Array; Ice; Incubators; Informatics; Knowledge; Label; Laboratories; Lasers; Lead; Length; Location; Mediating; Methods; Microarray Analysis; Mission; Mus; Names; Neural Pathways; Neurosciences; One-Step dentin bonding system; Online Systems; Pathway Analysis; Pathway interactions; Patients; Phage Display; Plasmids; Preparation; Problem Solving; Procedures; Process; Productivity; Publications; Publishing; Quality Control; RNA; RNA Splicing; RNA amplification; RNA analysis; RNase protection assay; Reaction; Reading; Reagent; Reference Standards; Relative (related person); Reproducibility; Research; Research Personnel; Resolution; Resource Informatics; Resource Sharing; Resources; Reverse Transcription; Sampling; Scanning; Screening procedure; Sepharose; Sequence Analysis; Services; Signal Transduction; Site; Slide; Specificity; Spottings; Staining method; Stains; Stem cells; Stimulus; Streptavidin; System; Systems Biology; Tail; Techniques; Technology; Testing; Time; Tissue Sample; Tissues; Training; Transgenic Mice; Transgenic Mouse Facility; Tube; Validation; Vertebral column; Whole Genome PCR; Work; base; capillary; cost; data sharing; density; design; digital; enhancing factor; follow-up; instrument; instrumentation; interest; investigator training; meetings; melting; mouse model; oligo (dT); programs; promoter; reagent testing; research study; square foot; trizol; user-friendly

GENE ANALYSIS CORE 1. MAIN OBJECTIVES AND NEW DIRECTIONS The mission of the proposed Gene Analysis Resource is to provide routine services such as DNA sequencing and mouse genotyping, but the major focus is more cutting-edge analysis of gene expression through real-time quantitative PCR and whole genome microarray expression analysis. The BIMR core facility, directed by Craig Mauser, is currently a part of the Burnham NIH-funded Cancer Center, but the current capacity of Q-PCR and microarray analysis is just sufficient to serve the needs of the Cancer Center. Thus, the La Jolla neuroscierice community has very limited if any access to these services. The microarray and Q-PCR services provided by the core located at the BMIR will provide unique and valuable resources to the La Jolla neuroscience community. The BIMR core performs Microarray analysis using the Illumina BeadStation platform, which has been found to produce outstanding quality data for global gene expression analysis. This analysis is far more reproducible than spotted arrays, and can be performed at about half the total cost of the Affymetrix or Agilent-based core facilities in La Jolla, or through the Neuroscience Microarray Consortium sites. In addition to the array technology, an important component of the BIMR gene analysis core is its close integration with the Informatics core. This informatics resource provides assistance in array data analysis, not only for array data that has been generated in the core, but comparison of these data to other datasets. For Gene expression analysis, both the core and satellite will provide full-service analysis, where investigators provide RNA and receive data and assistance in its informatic and statistical analysis. In addition to providing access to both Illumina and Affymetrix microarray facilities, creation of a La Jolla neuroscience microarray user group associated with the array cores will enhance the most challenging part of microarray analysis: the downstream informatic and intuitive analysis required to convert vast amounts of data into neuroscience knowledge. Thus, beyond data sharing, it is anticipated that sharing information on analytical approaches and resources will significantly accelerate progress from microarray analysis in this community. The Real-time quantitative PCR (Q-PCR) service that the Gene Analysis core will provide is not unique to the BIMR, but its focus and expertise on SYBR green based Q-PCR analysis is distinct from other La Jolla area resources. Of the >1 4,000 Q-PCR reactions performed by the BIMR Cancer Center core in the last year, >95% of the analyses were with SYBR green. The alternative hybridization probe (Taqman) based Q-PCR methods in wider use are an excellent way to quantitate gene expression, and the Salk core has expertise in this approach. However, the expense of the hybridization probes makes it impractical to use this method to query the expression of a large number of genes. With the proper controls, SYBR green-based Q-PCR is nearly as sensitive and specific as taqman, but more rapid, and the materials needed to analyze each gene cost almost an order of magnitude less. Thus, for many of the proposed approaches (e.g. microarray follow-up, gene family profiling, hypothesis testing, tissue sample profiling) the BIMR Q-PCR core will provide important support for neuroscientists quantitating gene expression. In addition to providing expert service, both core facilities will provide training for investigators who wish to perform their own QPCR. Management of the core will be performed by Dianne Foster, who is the manager of the current BIMR Cancer Center Gene Analysis core. A technician dedicated to meeting the microarray and Q-PCR needs of neuroscientists will be added to the BIMR core facility. Similarly, an additional technician at the Salk facility will be dedicated to providing gene expression analysis and other microarray-based analysis for La Jolla area neuroscientists. This will effectively increase the capacity in these vital areas, as it is personnel and not instrumentation that is limiting capacity. In addition to ongoing work in the analysis of gene expression, it is anticipated that follow-up from the new research areas enabled by the neuroscience Cores will require a substantial increase in microarray/Q-PCR analysis by neuroscientists. Examples of this include identifying affected pathways and inferring mechanism from newly identified biologically active chemical compounds, and profiling of developmental markers in stem cells differentiated along neural pathways. Overall, the Gene Analysis core will provide investigators with a backbone of routine services, as well as new access to increasingly important advanced facilities for analysis of gene expression.

基因分析核心 1。主要目标和新方向 拟议的基因分析资源的使命是提供常规服务，例如DNA 测序和小鼠基因分型，但主要重点是对基因的最先进分析 通过实时定量PCR和整个基因组微阵列表达分析表达。 由Craig Mauser执导的BIMR核心设施目前是Burnham NIH资助的一部分 癌症中心，但是Q-PCR和微阵列分析的当前能力足以服务 癌症中心的需求。因此，如果有的话，La Jola Neuroscierice社区的有限 访问这些服务。位于核心提供的微阵列和Q-PCR服务 BMIR将为La Jolla神经科学社区提供独特而宝贵的资源。 BIMR核心使用Illumina BeadStation平台进行微阵列分析， 发现为全球基因表达分析产生出色的质量数据。这个分析远 比斑点阵列更可重现，可以以约一半的总成本执行 La Jolla或通过神经科学微阵列的Affymetrix或基于敏捷的核心设施 财团地点。除了阵列技术，BIMR基因的重要组成部分 分析核心是它与信息学核心的密切集成。此信息资源提供 阵列数据分析的协助，不仅为核心中生成的数组数据，而且还 将这些数据与其他数据集进行比较。 对于基因表达分析，核心和卫星都将提供全方位服务的分析，其中 研究人员提供RNA并在其信息和统计分析中获得数据和帮助。 除了提供访问Illumina和Affymetrix微阵列设施之外，还可以创建LA Jolla Neuroscience微阵列用户组与阵列核心相关联的最大增强 微阵列分析的挑战部分：所需的下游信息和直观分析 将大量数据转换为神经科学知识。因此，除了数据共享之外，它是 预计共享有关分析方法和资源的信息将大大显着 在这个社区的微阵列分析中加速进步。 基因分析核心将提供的实时定量PCR（Q-PCR）服务不是 BIMR独有的，但其对基于SYBR绿色的Q-PCR分析的重点和专业知识不同于 其他拉霍亚地区资源。 BIMR癌进行的> 1 4,000个Q-PCR反应 去年中心核心，> 95％的分析是使用SYBR Green进行的。替代方案 基于杂交探针（TAQMAN）基于更广泛使用的Q-PCR方法是定量的绝佳方法 基因表达，而Salk核心在这种方法中具有专业知识。但是， 杂交探针使使用此方法查询大型表达是不切实际的 基因数量。使用适当的控件，基于SYBR绿色的Q-PCR几乎同样敏感，并且 特定于塔克曼（Taqman），但更快，分析每个基因所需的材料几乎成本 数量级少。因此，对于许多提出的方法（例如，微阵列随访，基因 家庭分析，假设检验，组织样本分析）BIMR Q-PCR核心将提供 对神经科学家定量基因表达的重要支持。除了提供专家 服务，这两个核心设施将为希望执行自己的QPCR的调查人员提供培训。 核心的管理将由当前BIMR的经理Dianne Foster执行 癌症中心基因分析核心。致力于与微阵列和Q-PCR结识的技术人员 神经科学家的需求将添加到BIMR核心设施中。同样，一个其他技术人员 Salk设施将致力于提供基因表达分析和其他基于微阵列 La Jola地区神经科学家的分析。这将有效地增加这些重要的能力 区域是人员，而不是限制能力的仪器。除了持续的工作 在对基因表达的分析中，可以预期来自新研究领域的随访 由神经科学核启用将需要大幅度增加微阵列/Q-PCR分析 由神经科学家。其中的例子包括识别受影响的途径和推断机制 从新鉴定的生物活性化合物和发育标记的分析中 在干细胞中，沿着神经途径分化。总体而言，基因分析核心将提供 具有常规服务骨干的调查员，以及新的访问越来越重要的调查员 用于分析基因表达的高级设施。