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.
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