Microarray FAQs

  • What should I do to start an experiment?
    You should first contact us via e-mail and be sure to provide your phone number. This allows us to get back to you as quickly as possible to discuss the specifics of your experiment, give you a quote, and establish time lines. Once you have agreed to your quote and a purchase order number has been assigned to your experiment, arrangements will be made for you to send your samples to our facility on dry ice. All samples should be accompanied by a completed sample submission form and a picture of an agarose gel or bioanalyzer report of your samples.

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    What type of arrays can the Genomics Core Facility process?
    We can prepare and process all Affymetrix GeneChip® arrays (both eukaryotic and prokaryotic samples). We generally use standardized Affymetrix protocols. However, if you need special services or protocols, please discuss this with us.

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    What type of starting material does the Genomics Core Facility accept?
    This depends on the type of Affymetrix array you plan to use in your experiment. In general, we accept user-isolated total RNA, mRNA, genomic DNA, and/or fragmented samples for the partial services.

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    Does the Genomics Core Facility isolate RNA and DNA from tissue or cells?
    Yes, although a separate per-sample fee will be applied to extract these starting materials.

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    What happens if my RNA quality is not optimal?
    All samples submitted will be analyzed on the Agilent Bioanalyzer. If the quality of your RNA is less than optimal, we will contact you and ask you to make a decision regarding the processing of your samples. If you ask us to process a sample that we consider to be of poor quality, we are not responsible if poor yields are obtained, leading to unsuccessful hybridization and scan results. A second sample preparation and hybridization will NOT be done free of charge. Please contact us if you would like more information about the types of quality metrics we perform.

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    What if the submitted samples do not meet the concentration requirement?
    We understand that slight variations in concentrations occur when different people measure concentrations. Unless the difference between the concentrations you submit and the ones we measure are significant, we will continue with the processing. If the discrepancy is significant, you will be contacted. Please see our “Quantity” sections about providing additional starting material. If we have to manipulate the sample in order to attain the required concentrations, a per-sample surcharge will be applied.

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    What does the Genomics Core Facility suggest as a minimum amount of starting material to submit for the full service?
    Please review our “Quantity” and “Quality” sections about minimum amounts of starting material. If you need further clarification, feel free to contact us.

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    What amount of fragmented material should I submit for the partial service?
    Since the answer to this question is array-dependent, we suggest that you contact us regarding the particular array type you would like to use for your experiments.

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    Should I choose the full or partial service?
    This usually depends on your needs and budget. However, allowing the core to perform the full service reduces technical variation and leads to the best results.

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    Do I need to run a test3 array?
    The test3 array from Affymetrix has hybridization controls from various species. We recommend using the test3 array especially if you have never done a study with us. The test3 array is priced less than the standard arrays and allows us to make sure the hybridization protocol is optimal for your sample. It is less expensive to modify a protocol for a failed test3 array experiment than to have a failed genome array experiment.

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    What is my turn-around time?
    Samples are handled in the order they are received. Once we start your experiment, we will usually have results in less than one business week. You can usually expect to receive a DVD copy in less than two business weeks.

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    What does the Genomics Core Facility do with leftover DNA, RNA, hybridization cocktails, and GeneChips?
    We store all leftover DNA, RNA, and hybridization cocktails at -80°C for one month from the finishing date of your experiment. Your GeneChip arrays will also be stored at 4°C for one month from the finishing date of your experiment. Please let us know if you desire to collect your leftover DNA, RNA, hybridization cocktails, and/or GeneChips before the one-month deadline. Please note that we will discard your sample materials once the deadline has passed. You will receive notification when your one month deadline approaches.

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    What format of data will I receive?
    We will extract data from individual chips for you. We will give you the .EXP (general experimental information), .DAT (.jpg image), .CEL (averaged cell intensity), and the .CHP (data in Affymetrix software format) files for each sample of your experiment. A .RPT (report) file containing all the signal data can be produced using Affymetrix GeneChip Operating Software (GCOS) or some other second- or third-party software.

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    Can I get additional analysis of my data?
    The Genomics Core Facility has a statistician and computers with software licenses for GCOS and Data Mining Tool software (e.g. GeneSpring®, SpotFire®, and Partek®). If you want further analysis of your data, please contact us for a cost estimate.

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    I think my chip was defective. How can I be sure and what do I do?
    Defective chips are replaced free of charge by Affymetrix. We will contact you if we suspect that your chip is defective. Affymetrix will request a copy of the .DAT and .EXP files for a defective chip and on confirmation, replace the defective chip. Please note that it usually takes a month for the replacement.

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    Can I buy chips from the Genomics Core Facility?
    We can buy chips for you from Affymetrix at prices significantly cheaper than list prices. You may also buy the chips yourself and provide them to us prior to the study. Please note that if you provide us the chips, you are responsible for obtaining the replacements for any defective chips.

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    Can I sell any leftover chips back to Affymetrix or the Genomics Core Facility?
    No. Unfortunately, chips are sold in packs of 2, 5, 6, or 30 which leads to leftover chips if you do not have enough samples. We realize that chips are expensive and budgets are tight. We suggest teaming up with another lab to use up all the chips.

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