Genomics Core Briefs
Sept 23, 2009: Increase in rates - As you are undoubtedly aware, the economy is poor. As a result one of our funding institutions has had to eliminate support for the Genomics service. To compensate for this loss, we will be raising our rates 20% as of Oct 1, 2009. We regret this increase in costs and hope that funding will return once the economy recovers.
Jan 26, 2009: Micorarray-based RNAi analysis - The Genomics Shared Service now offers RNAi analysis through Affymetrix, Agilent, and Nimblegen microarrays. contact us for more information about the microarrays available and RNA isolation protocols.
June 23, 2008: Full service DNA Methylation analysis - The Genomics Shared Service now provides a complete service for analysis of DNA methylation. The service is based on the MeDIP approach to ChIP-chip. If you want to perform genome-wide DNA methylation analysis contact (our contact info. link is at the top of the page) us so we can discuss your project.
May 10, 2007: Data Analysis through Bioinformatics - The Bioinformatics Shared Service has formally taken over analysis of all microarray data. We will still meet with users to discuss experimental issues. If you want to contact Bioinformatics for analysis of your microarray data, email: bioinf@email.arizona.edu or call 621-2464.
October 10, 2007: New Affymetrix Arrays - We have sucessfully implemented the new Affy ST arrays for human, mouse, and rat. When purchased in packs of 10, these arrays can be run for $425 per sample. This is a 41% discount compared to running a 3-prime GeneChip!
Feb 12, 2007: Acknowledge the Core - please acknowledge the Genomics Core is papers using data generated by us, we use these acknowledgements to justify our funding which in turn lowers the price we have to charge for services. Sample acknowledgement: "Microarray data generated by the Genomics Core at the Arizona Cancer Center; supported by the Southwest Environmental Health Sciences Center, NIEHS grant ES06694, and the Arizona Cancer Center, NIH grant CA23074."
Introduction
What Are Microarrays?
Introductory information on microarrays can be found at here.
Our Name(s)
The Genomics Shared Service/Genomics Facility Core is referred to by different names in the grants that support it, but will be referred to as the Genomics Core, or just "the Core", on this web page.
Our Purpose
The goal of the Core is to provide Genomics services centered on microarray technology. The Core serves the research community with priority given first to members of our funding centers, then to other federally funded investigators at the University of Arizona, and then all other research investigators. The Core provides complete support for gene expression profiling, as well as support for DNA-based applications including: comparative genomic hybridization (CGH), chromatin immunoprecipitation on chip (ChIP on chip), single nucleotide polymorphism (SNP) analysis, and re-sequencing. The Core also provides sample quality control services, real time PCR service, consultation in experimental design, and data archiving.
Our Supporting Institutions
The Core is supported by the Arizona Cancer Center (National Institutes of Health Cancer Center Support Grant P30CA23074), the Southwest Environmental Health Sciences Center (National Institute of Environmental Health Science Center Grant ES06694), and the BIO5 Institute.
Overview Of the Service
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 and archiving, and finally, data confirmation. The Genomics Core provides solutions to all the steps of microarray analysis including protocols for isolating samples, sample quality control, Real-Time PCR confirmation of results. The Core's microarray platforms, applications, and associated services are broken 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).
Experiment 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. Questions regarding power and statistical analysis should be referred to the Bioinformatics Shared Service (click here to contact).
Applications for microarray:
RNA expression
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, hybridization, 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 have 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
Results are loaded to the Core's website and user's are notified automatically that their data are ready. Analysis of microarray data is offered by the Bioinformatics Shared Service at the Arizona Cancer Center. (click here to contact)
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 Gene Expression 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.
Recommendations for Sample Preparation
It is critical to provide high quality RNA or DNA as the starting material for microarray analysis. Problems we have found with user samples include: RNA or DNA degradation, incorrect concentration, and contaminants (proteins, salt, phenol, etc), and finally the presence of RNA in DNA preparations or vice versa. To help you provide good quality sample, we recommend isolation kits available from Qiagen. For total RNA isolation use the RNeasy Mini or Midi kit. RNA yields vary, but 10 million cells in culture will yield approximately 100-300 micrograms of total RNA. Ten milligrams of tissue will yield approximately 20-80 micrograms of total RNA. For genomic DNA isolation use the QIAamp DNA Mini or Midi kit. DNA yields vary, but are approximately 30 micrograms per 10 million cells in culture. Ten milligrams of tissue will yield approximately 5-20 micrograms of genomic DNA. These Qiagen kits are available to all University of Arizona researchers from University Stores.