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DNA Array Core Facility

Frequently Asked Questions

1. What do I need to do before submitting my samples?

Most questions regarding sample submittal can be answered in the Sample Submittal section of our website. To begin the process of sample submittal, we strongly recommend appropriately designing your microarray experiment. Once the experiment has been planned and you have isolated your RNA to be processed and placed on a chip, you must fill out our Sample Submittal Form. When you are ready to drop off your samples and chips, please call the Core Facility at (858) 784-2263 and arrange for a drop off date and time. Please do not leave samples with people who are not members of the DNA Array Lab.

2. What happens if the quality of my RNA is not adequate?

If the quality of submitted RNA appears to be less than optimal, the Core Facility will contact you and ask you to make a decision whether to continue with the processing of the sample(s). Please note: If you decide to process a sample which we deem is of questionable quality, we are not responsible for poor yields in probe synthesis. A second probe synthesis will NOT be done free of charge. If you have questions or would like more information about the quality analysis we perform, please see the Quality Control section of our website, or call the Core Facility at (858) 784-2263.

3. What if the concentration of my RNA does not meet the stated requirement?

Different instrumentation will almost always result in different measured concentrations for a given sample. Upon receipt of your sample, the Core Facility will measure the concentration and compare our values with the ones you have included in your submittal form. If the differences between the concentrations you submit and the ones we measure are not substantial, we will proceed with the processing of your sample. If there is a discrepancy, you will be contacted and the sample processing protocol will be terminated until the proper sample concentrations are obtained.

4. What if I do not have the minimum required amount of starting material?

Recent developments in RNA amplification and labeling technology have allowed for less starting material than was previously necessary. The DNA Array Core Facility offers a variety of protocols that are suited to the amount of RNA you are able to extract. We recommend a starting amount of 500-1000ng. However, we are currently able to amplify and label a minimum of 5ng. Please contact the Core Facility to discuss the appropriate labeling protocol before beginning your experiment.

5. When can I expect to have my data?

Samples are handled on a first come first serve basis! GeneChip data is usually 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 expected 2 weeks.

6. What happens to any leftover cRNA and hybridization cocktail?

The DNA Microarray 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 collect your total RNA, cRNA and hybridization cocktail when you pick up your data.

7. What sort of data does the Core Facility provide me with?

When you come to the lab to pick up your data, you will receive a CD with the following files for each chip: .DAT (a raw GeneChip image file), .CEL (a processed image file with calculated signal intensities assigned to each oligonucleotide "cell" on the GeneChip), .CHP (a text-based file containing the relevant signal values, absolute calls and p-values assigned to each gene on the GeneChip), .TXT (data in text format), .RPT (a text-based file containing the quality control numbers for the experiment including percent present, presence of spiked controls, background, noise, etc.), and .EXP (a text-based file containing general experiment information such as sample name, date, etc.). Please be aware that only the .TXT file can be opened outside of the GeneChip Operating Software (GCOS). To view the other files you may schedule a time to come into the lab and use a computer that has the appropriate software installed. Please call the Core Facility at (858) 784-2263 for scheduling or other questions.

8. How can I get help with the analysis of my data?

The Core Facility has computers installed with the GeneChip Operating Software available for use by investigators. We also have other data analysis programs (shareware and commercial) available, and technicians are available for assistance upon request. Please call the Core Facility at (858) 784-2263 to schedule a date and time if you need help with data analysis. We strongly suggest visiting the Data Analysis section of our website to get an idea of the analysis options and programs that are available.

9. What happens if I have a defective chip? How can I tell if a chip is defective?

Defective chips are replaced by Affymetrix free of charge. You will be informed by the Core Facility when a chip is suspected of being defective. The replacement chip will be the exact chip type that was found to be defective. You may not "trade in" your defective chip for another chip type. Please be aware that the replacement of a chip can take up to one month. You will be notified when your replacement chip comes in, and you may either keep it at the Core Facility or pick it up and store it in your own lab. For more information please contact the Core Facility.

10. Can I buy Affymetrix chips from the Core Facility?

The Core Facility keeps a LIMITED number of commonly used chips (e.g. HU133A, MOE430A, etc.) in stock. Occasionally special arrangements can be made and an Investigator can use GeneChips that are kept by the Core Facility depending on the current 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 see the Pricing section of our website for more information on GeneChip costs.

11. If I have any leftover chips, can I sell them back to Affymetrix or to the Core Facility?

Unfortunately, it is not possible to resell your unused chips. We are sensitive to the fact that these are expensive/perishable items and research money is tight. The best option we can offer is that investigators post messages to members of Scripps via the wetlab email. This will allow labs to exchange chips or pay via interdepartmental vouchers. Alternatively, researchers not needing all the chips available in a box can team up with another lab so that all the chips get used upon purchase.