Several factors should be considered when designing microarray experiments for measuring gene expression changes in biological systems since it is not practical to develop one experimental design that is appropriate for all microarray experiments. Please see our experimental design recommendations for more information.

We strongly recommend contacting the Core Facility to discuss the appropriate experimental design protocol before beginning your experiment. The Core Director is available to meet with you upon request. Please contact Steve Head at (858) 784-2263 for more information.

All samples to be submitted to the Core Facility for processing must be accompanied by this submittal form. Due to the recent emphasis placed on data being MIAME (Minimum Information About a Microarray Experiment) compliant, we ask that you please fill out as much information as possible.

For more information regarding MIAME compliancy, please visit the MGED Society (Microarray Gene Expression Data Society) webpage.

A minimum of 15ug total RNA at a concentration of 1ug/ul is needed to undergo the Standard Affymetrix Protocol. As little as 10-200ng may be sufficient using the Small Sample RNA Preparation Protocol. For more information on small sample preparation, please see the RNA Amplification section of our website.

RNA to be submitted must be purified using a Qiagen RNeasy column. It is highly recommended that you use our RNA Extraction Protocol on all samples to be submitted for processing. More information on RNA sample isolation and preparation is available in the RNA Isolation section of our website.

GeneChips are to be ordered by the Investigator directly from Affymetrix. Delivery time is generally around 2 weeks. Information regarding GeneChip packaging and pricing can be found in the Pricing section of our website.

Occasionally special arrangements can be made and an Investigator can use GeneChips that the DNA Array Core Facility keeps in stock. The pricing of these chips is the same as the academic discounted Affymetrix chips plus an additional 8.25% tax and 1.25% stocking charge (10% total).Please contact the Core Facility at (858) 784-2263 for more information.

GeneChip data is available approximately 2 weeks after RNA samples and GeneChips are submitted to the lab. You will be notified if turnaround time is longer than the allotted 2 weeks. When sample processing is complete and data is available, you will be contacted by the Core Facility to pick up your data (in CD format) from the lab. Software for basic and advanced data analysis is available through the Core Facility. See the Affymetrix Data Analysis section of our website for details.

The DNA Array Core Facility will store any leftover total RNA, cRNA and hybridization cocktail at -80°C for up to one month. Samples may be stored longer than the allotted month AT YOUR OWN RISK. We are NOT responsible for materials left in our possession for more than one month! If you would like to reuse your material in the future, please be sure to collect your total RNA, cRNA and hybridization cocktail when you pick up your data.

Any leftover GeneChips will be stored at 4°C until you decide to use them for another experiment. If chips are seemingly "forgotten" and/or have expired, you will be notified so that you may use them as soon as possible. The Core Facility keeps a running inventory of GeneChips being stored, so please feel free to contact us at (858) 784-2263 for any questions regarding your chips.