La Jolla Interdisciplinary Neuroscience Center Cores - Gene Analysis Core BU

基因分析核心 一、主要目标和新方向 拟议的基因分析资源的任务是提供常规服务，如DNA 测序和小鼠基因分型，但主要关注点是更尖端的基因分析 通过实时定量聚合酶链式反应和全基因组芯片表达分析。 BIMR核心设施由克雷格·毛瑟领导，目前是伯纳姆国立卫生研究院资助的 癌症中心，但目前的Q-PCR和微阵列分析能力刚刚足以满足 癌症中心的需求。因此，La Jolla神经科学社区即使有的话，也非常有限 访问这些服务。核心提供的微阵列和Q-PCR服务位于 BMIR将为La Jolla神经科学界提供独特而宝贵的资源。 BIMR核心使用Illumina BeadStation平台执行微阵列分析，该平台已经 被发现为全球基因表达分析提供了出色的高质量数据。这一分析是远远不够的 比斑点阵列更具重现性，并且可以以大约总成本的一半来执行 位于La Jolla的Affymetrix或安捷伦核心设施，或通过神经科学微阵列 财团所在地。除了阵列技术，BIMR基因的一个重要组成部分 分析核心是它与信息学核心的紧密结合。此信息学资源提供 协助数组数据分析，不仅是对在核心中生成的数组数据，而且 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面的服务分析，其中 调查人员提供核糖核酸，并在其信息和统计分析方面获得数据和协助。 除了提供对Illumina和Affymetrix微阵列设施的访问外，创建La 与阵列核心相关的Jolla神经科学微阵列用户组将获得最大的提升 微阵列分析的挑战性部分：下游信息和直观分析需要 将海量数据转化为神经科学知识。因此，除了数据共享之外，它还 预计共享有关分析方法和资源的信息将显著 在这个社区加快从微阵列分析的进展。 基因分析核心将提供的实时定量聚合酶链式反应(Q-PCR)服务 BIMR独有的，但其对基于SYBR Green的Q-PCR分析的关注和专业知识有别于 拉霍亚地区的其他资源。在BIMR癌症进行的&gt；14,000个Q-PCR反应中 中心核心在去年，&gt；95%的分析是与SYBR绿色。另一个选择 基于杂交探针(Taqman)的Q-PCR方法在更广泛的应用是一种很好的定量方法 基因表达，而索尔克的核心在这方面拥有专业知识。然而，这笔费用 杂交探针使得使用这种方法查询大分子的表达是不切实际的 基因的数量。在适当的控制下，基于SYBR Green的Q-PCR几乎同样敏感和 具体如TaqMan，但更快，分析每个基因所需的材料成本几乎是 少了一个数量级。因此，对于许多建议的方法(例如，微阵列跟踪、基因 家庭特征分析、假设检验、组织样本特征分析)BIMR Q-PCR核心将提供 为神经学家量化基因表达提供了重要支持。除了提供专家 这两个核心设施都将为希望进行自己的质量控制审查的调查人员提供培训。 核心的管理将由现任BIMR经理Dianne Foster执行 癌症中心基因分析核心。一位致力于满足微阵列和Q-PCR的技术人员 BIMR核心设施将增加神经科学家的需求。同样，另一名技术人员在 索尔克实验室将致力于提供基因表达分析和其他基于微阵列的 拉荷亚地区神经学家的分析。这将有效地增加这些至关重要的 由于限制能力的是人员，而不是仪器设备，因此这些领域的能力受到了限制。除了正在进行的工作之外 在基因表达分析方面，预计后续将有新的研究领域 由神经科学核心实现的将需要大幅增加微阵列/Q-PCR分析 被神经学家发现。这方面的例子包括识别受影响的通路和推断机制 从新发现的生物活性化合物中分离出来，并对发育标志物进行分析 在干细胞中沿着神经路径分化。总体而言，基因分析核心将提供 具有中坚力量的调查人员的日常服务，以及获得新服务的途径日益重要 先进的基因表达分析设备。

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.