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miRNA Profiling Services

The MCF is currently offering miRNA profiling services on the Exiqon's miRCURY LNA miRNA platform. The MCF provides QC (quality control), target preparation, hybridization and imaging services for this platform. Users are required to perform miRNA extraction in their own laboratories using any of the several kits available (e.g., Qiagen, Ambion, etc.) for miRNA extraction. For Exiqon platform, we recommend extracting total RNA including the miRNA fraction for performing target preparation.

Pricing of miRNA

Sample or reference/input RNA QC: $11/sample or reference
Target preparation: $150/microarray
Hybridization: $50/microarray
Imaging (scans and probe feature intensity quantification): $50/microarray

How to Submit Samples for miRNA Profiling Services

  1. All samples must pass quality control (QC) tests (services provided by MCF) before target preparation.
  2. Please submit 1-5 µg (minimum concentration allowed is 500 ng/µL) of both total RNA (which includes miRNA) and a reference total RNA.
  3. All samples need to be transported to the MCF using appropriate storage conditions (preferably on dry ice) at designated times only (Tuesday and Thursdays 1:30 p.m. to 4 p.m.).
  4. All sample aliquots need to be in either a 0.5-mL or 1.5-mL tube. Please do not submit your samples in PCR tubes (0.2 mL).
  5. Make sure your first initial and last name are on all vials along with your sample identifier. Please make sure that you inform the technician which species your RNA samples were extracted from (e.g., human, mouse, rat).
  6. At the time of submission, user must inform the technician if leftover sample should be discarded or returned.

Purchasing Microarrays

Users are required to purchase the microarrays. There is a choice of 3-, 6- or 24-microarray packs. For further questions regarding ordering or customizing microarray, users can contact Exiqon sales representative, Dwight Navis, by e-mail at Dwight.Navis@exiqon.com, or contact Exiqon at 1-888-mirCURY or the Exiqon Web site. MD Anderson users should ask for the MD Anderson discounted pricing when purchasing the kits.

Sample Submission for QC

We will QC any samples submitted to the MCF for miRNA analysis. Users need to provide 4 µL (>500 ng/µL) aliquot of each sample for QC prior to submitting any requests for target prep and hybridization. If this volume amount is difficult to supply, please call the MCF to make other arrangements.

Sample Submission for Target Preparation

Users are required to submit 1-5 µg of RNA sample at a concentration no lower than 500 ng/µL for target preparation. Users need to indicate what species the samples were generated from, since this information will be required for the analysis step.

Office Hours

We have office hours every Tuesday and Thursday from 1:30-4:00 p.m. All samples should be submitted to the MCF in a 0.5-ml or 1.5-ml microfuge tube and have the user's last name and sample ID# written legibly on each tube. In case a user cannot submit samples during our office hours, he/she should call the MCF to make an appointment for bringing in the samples.

Data

Users will receive a copy of their TIF images and GFF files for each microarray (burned to a CD). The GFF, which contains the intensity raw data of the probe features, can be opened up in Excel but it is recommended to use NimbleGen's SignalMap software (that users will receive with the microarray purchase) for data analysis.

Bioinformatics Assistance

Dr. Li Zhang in the Department of Bioinformatics and Computational Biology (lzhangli@mdanderson.org) is currently assisting users with further analysis of the microarray data generated for these applications.

Please contact David Pollock at the MCF for further questions.

Genomics Core Facility
MD Anderson Cancer Center
BSRB Room S15.8425
Phone: 713-834-6199


© 2012 The University of Texas MD Anderson Cancer Center