Microarray Core Facility

Frequently Asked Questions (FAQ)

  1. Which microarray platform should I choose?
    Currently we provide Affymetrix, Illumina and high density spotted arrays for you to choose. While most labs are still using Affymetrix arrays, the Illumina platform is getting more and more users because of its high specificity and sensitivity, low input RNA requirement and very low cost. We got good feedback from users of all platforms. Literatures regarding pros and cons can also be used for your choice. We will be happy to discuss with you for details of each platform.
  2. Do I need to do replicates when doing microarray?
    Generally no. Previous study has shown very consistent and highly correlated data for technically replicated samples. However, biologically replicated samples (at least 3 for each biological condition) are required for statistical analysis.
  3. When, where and how should I submit samples?
    After you place an online order, you can send samples in ice, dry ice or LN, to us (ND6.504) anytime from 9am to 5pm on any workday.
  4. How much total RNA is required?
    Depending on which service, Affymetrix, Illumina, spotted arrays require at least 2ug, 500ng and 1ug respectively, in RNase-free water, with concentration greater than 100ng/ul. Bioanalyzer or OD check needs about 50ng in 2ul. Extra amount is always helpful, especially when first trial is failed, although the chance is small.
  5. Do you keep my remaining samples?
    Yes, please indicate in your order form, and ask them back after you get the data. Your leftover samples will be thrown away after 2 weeks.
  6. Is chip cost included in the service fee?
    No, service fee covers reagents and labor. Chips are expensive, different types of chips have different price, and some labs bring their own chips. So please remember to order chips when order microarray service. Check our price listing to know the chip and service costs.
  7. For microarray service, do I have to order bioanalyzer check as well?
    It's an option, but we strongly recommend you order the bioanalyzer check on your samples unless you already did the quality check by yourself. We need prove (such as a gel picture) that your samples are in good quality before we process.
  8. What??s the turn-around time?
    Normally about two weeks for microarray full service (from total RNA to data), a week for hyb and scanning, a few days for bioanalyzer check or OD measurements, etc. If it takes longer, you will be told when submit samples. For faster service, 20% more service fee (minimum $20) is charged.
  9. How do I get data?
    You data will be stored in our data server for one month free of charge for you to download. You also have the choice of CD/DVDs with a small fee.
  10. Do I need to bring you an IDR?
    No, no paperwork is required. All we need is a req# / acct# from your order.
  11. I can??t get a req#/acct# now, can I still place order?
    Yes, just enter ??to give?? in the fields, and email them later.
  12. Can I use a blanket IDR or use the same req# for all orders?
    Yes, just use the same req# / acct# if your account administrator agrees.
  13. Can I pay first, and do service later?
    Yes, but due to school fund policies, service must be done within 6 months.
  14. Do you provide data analysis software training?
    Yes, please place an order for GeneSpring, Genetraffic or BeadStudio software training, and make an appointment with Yun.Lian@utsouthwestern.edu.
  15. Can I use your GeneSpring software in after-hours?
    Yes, please contact us for computer reservation and a door code.
  16. Do you do service for non-UTSW labs? Is there a price difference?
    Yes, but the service fee will be different from on-campus users (contact us for details). A check is the only payment method for outside-campus users.
  17. I still have questions, what should I do?
    You can call extension 56071 or email jinchun.zhou@utsouthwestern.edu.
    Email is preferred, and will be replied quickly.