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DNA Methylation Microarray Services

The Genomics Core Facility is currently offering DNA methylation services for the NimbleGen platform. These services include the sample QC, genomic DNA sample immunoprecipitation (IP), genomic DNA target preparation and hybridization onto NimbleGen DNA methylation arrays, imaging and signal quantification.

Pricing of DNA Methylation

Sample or reference/input DNA QC: $11/sample or reference/input
Sample preparation (includes the digestion, immunoprecipitation and amplification of genomic DNA): $200/sample preparation
Target preparation: $150/microarray
Hybridization: $50/microarray
Imaging (scans and probe feature intensity quantification): $50/microarray

How to Submit Samples for DNA Methylation Array Services

  1. All samples must pass Quality Control (QC) tests (service provided by MCF) before sample immunoprecipitation or target preparation.
  2. For DNA methylation array service, please submit 10 µg of genomic DNA for sample immunoprecipitation.
  3. If the customer performs their own immunoprecipitation, please submit 4 µg (concentration 25-1000 ng/µL is needed) of both immunoprecipitated-amplified sample and input-amplified reference sample for sample target preparation.
  4. All samples need to be transported to the MCF at designated times only (Tuesday and Thursdays 1:30 p.m. to 4 p.m.).
  5. 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).
  6. Make sure that your first initial and last name are on all vials along with your sample identifier.
  7. At the time of submission, user must inform the technician if leftover sample should be discarded or returned.

Purchasing Microarrays

User is required to purchase the microarrays. For questions regarding choice of the appropriate type of array for your experiment, and most recent MD Anderson pricing, user should contact Roche-NimbleGen at 1-877-NIMBLEGEN (1-877-646-2534).

Sample Submission for QC

MCF will perform QC of any samples submitted to the MCF for the DNA methylation microarray service for concentration and quality requirements. The user is required to submit a 6-µL aliquot (>210 ng/µL) of each sample for QC if he/she is planning to submit samples for sample preparation or a 4-µL aliquot if he/she is planning to submit samples for target preparation (>25 ng/µL) where the DNA methylation immunoprecipitation protocol has already been performed.

Sample Submission for Sample Preparation (DNA Methylation Immunoprecipitation Protocol)

The DNA methylation immunoprecipitation procedure requires 6 µg genomic DNA at a concentration of >210 ng/µL.

Sample Submission for Target Preparation

Users that have done their own immunoprecipitation procedure and are submitting samples for target preparation need to submit 2-3 µg of DNA (>25 ng/µL) for each sample.

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/DVD). 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.

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


© 2012 The University of Texas MD Anderson Cancer Center