Frequently Asked Questions

Questions & Answers



I can't get a lot of RNA from my samples.

What can I do?

Two rounds of in vitro transcription can be used to amplify very small RNA samples. The Core does not currently offer this as a service, but prior users have been successful performing this procedure themselves and then submitting the labeled sample for hybridization to us.


I want to analyze specific cell types from a tissue specimen, is this possible?

Yes, you will need use Laser Capture Microdissection (LCM) first, then isolate and amplify the RNA. Contact the Tissue Acquisition Shared Service for access to LCM instrument and contact us to discuss your experiment.


Will you charge me if the microarray hybridization/Real Time PCR analysis of my sample does not work?

No. Our goal is to provide quality data to further your research goals. We will only charge you for hybridizations that work. The most likely source of failure is poor quality sample - this is why the Core runs all samples through quality control before using them. The second most likely source of failure is manufacturing defects in the microarrays or the kits we use to run them. The manufacturers usually reimburse the researchers for these types of failures.


Does the Genomics Shared Service perform RNA amplifications on investigator provided samples?

Yes, single round amplification is integrated into all our expression platforms.


Where can I get a list of the genes on the Core's spotted cDNA and oligonucleotide microarrays?

The gene lists for the human and mouse cDNA and oligonucleotide arrays are available here.


How is my data returned to me?

Your raw data will be archived on the password protected portion of this web site The GSS also archives the raw image files from each hybridization should you need access to them later. Data analysis can be performed in consultation with the Informatics/Bioinformatics Shared Service (Contact David Mount, Director of Bioinformatics).


Will you help me analyze my data?

Yes - the Informatics/Bioinformatics Shared Service will. We recognize that microarray data analysis poses a challenge for our users. Interested users are encouraged to Contact David Mount to set up an appointment to analyze their data.


Can I buy microarrays from the Core and do the hybridizations myself?

Yes. Protocols for fluorescent target preparation are available. Please contact George Watts. We have found that the microarray process can take time to learn and get working well. Thus, the technique does not reward the casual user. If you believe you will be doing a significant amount of microarray work, we can arrange to provide arrays, access to the scanner, training, and protocols.


How much do Affymetrix/Agilent/Nimblegen arrays cost?

If you are a user at an academic institution in the state of Arizona we can provide you with the academic pricing for the microarrays offered by our commercial platforms. See our price list above.


Will you help me analyze my data?

Yes. We recognize that microarray data analysis poses a challenge for our users. Interested users are encouraged to contact George Watts for consultation and analysis using Silicon Genetics' GeneSpring software.


Where do I get the primer/probe sets for real time RT/PCR for a gene of interest?

Assays can be searched for in the Assays-on-Demand section of the ABI web site


My gene(s) of interest are not available from Assays-by-Design, now what?

If your gene of interest does not have an assay-on-demand yet, you can request an assay (primer pair) be made for you via the Assays-by-Design portion of the Applied Biosystems web site For more information, please contact Amber May at (520) 626-0267.


What kind of results do I get back from the real time RT-PCR service?

Once your samples have been run you will receive an amplification plot of your data and a report showing the cycle threshold (Ct) of each sample and your controls. Using this information you can calculate relative expression levels between your samples.