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NimbleGen Gene Expression Array Services

The Genomics Core Facility is currently offering gene expression services consisting of quality check (QC), target preparation and hybridization onto NimbleGen Gene Expression arrays, imaging and signal quantification. It will be the customer's responsibility to perform the cDNA synthesis steps from their RNA prior to submitting samples to the MCF. We can provide a copy of NimbleGen's protocol of the cDNA synthesis if one is required.

Pricing of NimbleGen Gene Expression Array

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

How to Submit Samples for Gene Expression Array Services

  1. All samples must pass quality control (QC) tests (service provided by MCF) before target preparation. A 4-µL aliquot is required before any samples will proceed to target preparation.
  2. For target preparation, please submit 2-3 µg (concentration ≥100 ng/µL) of cDNA.
  3. All samples need to be transported to the facility 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 that your first initial and last name are on all vials along with your sample identifier.
  6. 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 cDNA samples submitted for gene expression array service for concentration and sufficient base pair size requirements (>400 bp). User is required to submit a 4-µL aliquot (>100 ng/µL) of each cDNA sample for QC prior to submitting samples for target preparation and hybridization.

Sample Submission for Target Preparation

Users need to submit 2-3 µg cDNA (>100 ng/µL) for each sample for target preparation. Please call the facility if your sample yield concentrations do not meet this requirement.

Office Hours

We have office hours every Tuesday and Thursday from 1:30-4:00 p.m. All samples should be submitted to the facility 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 facility 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