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Comparative Genomic Hybridization (CGH) and Chromatin Immunoprecipitation on Chip (ChIP-chip) Array Services

The Genomics Core Facility is currently offering CGH and ChIP-on-chip services on the NimbleGen platform. These services include the sample QC, genomic DNA target preparation and hybridization onto NimbleGen CGH and ChIP-on-Chip arrays, imaging and signal quantification.

Pricing of CGH or ChIP-chip

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

How to Submit Samples for Array CGH and ChIP-on-Chip Services

  1. All samples must pass Quality Control (QC) tests (service provided by MCF) before target preparation.
  2. For CGH array service, please submit 4 µg (concentration 25-1000 ng/µL is needed) of both genomic sample DNA and reference (both sonicated appropriately) for sample target preparation.
  3. For ChIP-on-chip service, please submit 4 µg (concentration 25-1000 ng/µL is needed) of both immunoprecipitated-amplified sample and input reference sample for sample target preparation.
  4. All samples need to be transported to the facility 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

Genomics Core Facility will perform QC of any samples submitted to the facility for CGH or ChIP-on-chip array service for concentration and sufficient base pair size requirements. User is required to submit 4-mL aliquot (>25 ng/mL) of each sample for QC prior to submitting samples for target preparation and hybridization.

Sample Submission for Target Preparation

Users need to submit 4 µg DNA (>25 ng/ µL) for each test and reference sample. If a user is planning to use the same reference for all test samples, then that user will need to submit 4 mg multiplied by how many test samples are submitted (e.g., if you have five test samples and plan to use the same reference for each test, you would submit 20 µg of reference DNA). Users need to perform sample sonication for array CGH and chromatin immunoprecipitation and LM-PCR amplification for ChIP-on-chip application in their own laboratory, prior to submitting samples to the facility.

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. NimbleGen’s SignalMap software (that users will receive with the microarray purchase), will assist the users in 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 Pollack at the facility 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