The Genomics Shared Service (GSS) also known as The Genomics Facility Core is housed on the third floor of the Arizona Cancer Center (AZCC). The GSS Core is supported by the Arizona Cancer Center CCSG (Cancer Center Support Grant P30CA23074) and the Southwest Environmental Health Sciences Center (SWEHSC) (National Institute of Environmental Health Science grant ES06694), and the BIO5 Institute.

The Core is continually updating and expanding its services to keep up with advances in microarray technology and its applications. Microarray analysis can be broken down into the following components: array design and manufacture, experiment design, sample isolation, target labeling, hybridization, data collection, data analysis and archiving, and finally, data confirmation. The Genomics Core provides solutions to all these steps in microarray analysis including protocols for isolating samples, sample quality control, Real-Time PCR confirmation of results, workshops on data analysis for users, and one-on-one consultation during data analysis. The Core's microarray platforms, applications, and associated services break down as follows:

Preparation:

       Sample Quality Control

RNA and DNA samples are checked for quality and quantity. The Core checks every sample before use to ensure success of the microarray analysis. Samples are run on the Agilent Bioanalyzer which simultaneously quantitates the sample as well as measuring sample integrity. In the case of RNA, sample integrity is quantitated as a RNA integrity number (RIN)

      Experimental Design

The Core provides free consultation aimed at defining experimental goals and then matching those goals to the researcher's budget and appropriate microarray platform. Research goals and budget are also considerations in selecting samples, references, controls, and sample isolation procedures.

Experiment:

      RNA expression 

XXX The original application of microarrays, expression analysis is the application for which the researcher has the most options. The Core offers "complete service" for analysis of RNA expression meaning that the researcher need only provide sample RNA and the Core handles all other aspects of the process: sample quality control, labeling, purification, hybbridization, data collection, data analysis, and data archiving. Researchers have the following platforms from which to choose: spotted cDNA microarrays, spotted oligonucleotide microarrays, Affymetrix GeneChips, Agilent microarrays, and Nimblegen microarrays. These platforms have been chosen to serve the widest possible research community. A key part of the service is consultation with the researcher to determine which platform is appropriate for their goals during the preparation stage (see above).
 

      RNA regulation 

By designing probes to non-coding regions of the genome, microarrays can be used to survey genomic DNA with chromatin immunoprecipitation (ChIP on chip) and comparative genomic hybridization (CGH). ChIP on chip and CGH can detect factors affecting RNA expression including: transcription factor binding, chromatin structure, DNA methylation, copy number, deletions, and amplifications. The Core provides full service for researchers wishing to use the Core's CpG island microarrays for DNA methylation analysis. For all other microarrays the researcher will be responsible for isolating the genomic DNA sample and labeling it for hybridization. The Core will then perform the remainder of the process from the hybridization onwards. Researchers hava the following platforms from which to choose: spotted cDNA microarrays, spotted oligonucleotide microarrays, Affymetrix GeneChips, Agilent microarrays, and Nimblegen microarrays. As with RNA expression analysis, the Core will consult with the user to match experimental goals with the appropriate platform.  

      DNA analysis 

Several platforms offered by the Core can be used by the researcher to compare DNA sequences between samples to identify sequence variation (re-sequencing arrays), including single nucleotide polymorphisms. Platforms to choose from include Affymetrix GeneChips, Agilent microarrays, and Nimblegen microarrays As with applications for analysis of RNA regulation, the researcher will isolate the genomic DNA sample and prepare it for hybridization at which point the Core will perform the remaining steps.

Data analysis and confirmation:

      Data analysis

The Core will meet with researchers one on one to analyze their data. The Core uses BRB ArrayTools and GeneSpring GX software to perform data analysis. Results are loaded and examined to determine that the data is good quality. Samples are grouped and analyzed according to the experimental design. The Core can perform various analyses including ANOVA, class prediction, class comparison, and various types of clustering and visualization analyses.

      Data confirmation

The Core provides a full real time PCR service for confirmation of microarray results. Real time RT/PCR to confirm differences in RNA expression can be performed using the ABI TaqMan GeneExpression Assays or a locked nucleic acid Universal Probe Library from Roche. Real time PCR can also be used to confirm results found by DNA based applications such as ChIP on chip and CGH.

More Information on the Core can be found at the following links:

• Services & Platforms
• Real-Time PCR
• Pricing
• Data Analysis
• FAQ
• Contact Information

Thank you for your interest in the

Genomics Shared Service!

Please contact George Watts, Ph.D. to discuss your project's genomic needs

,The Genomics Shared Service/Genomics Facility Core is housed on the third floor of the Arizona Cancer Center, and

suThe GSS offers a full line of services on the Affymetrix and Codelink commercial microarray platforms as well as spotted oligonucleotide-based and cDNA-based microarrays

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