Affymetrix : NIDDK

Scientific Programs

Complete GeneChip® Instrument System  

GeneChip expression arrays enable researchers to simultaneously monitor genome-wide expression profiles. At The Genomic Core Facility, we support processing of several array platforms to allow flexibility for users. Currently, we support the processing of Affymetrix GeneChips along with DNA Genome-Wide SNP arrays, Whole-transcript expression (exon) and Tiling arrays too.

Microarray Core Package

The standard microarray core package will include:
  • quality control and processing of RNA samples,
  • data storage in Oracle database in sun server,
  • provision of annotations and standard statistical analysis.
  • provision of quality control metrics in powerpoint file

We may be able to provide further bioinformatics support, which will be addressed on a per user basis.



If you are considering running a microarray experiment, we can start by looking into the requirements. Decisions to be made include the type of arrays you would like to run (we only support the Affymetrix platform), number of samples, sample preparation, cost of experiment, etc... The subsequent data and analysis is only as good as the experimental design so thought at the beginning will pay dividends at the end. For example, any variation (genetic, growth rate, culture conditions) may have a larger impact on gene expression than the conditions you are testing. Therefore, it is critical to match control and experimental samples as close as possible. In addition, each condition you assay should have a minimum of three replicates from independent experiments to control for variation from sample to sample. Much of this information can be found by navigating within our website. However, if you have further questions, please don´t hesitate to call us (George:301-496-0074 or Shaila:301-594-6554). Please call Weiping Chen (301-496-0175) for the statistical experimental design and other downstream bioinformatic support.

Filling out the MIAME (Minimum Information About a Microarray Experiment (MIAME)
excel form (if not accessible please contact George) will help us analyze and track your samples, and also complies with standards currently developed by the Microarray Gene Expression Database group (MGED; The following worksheets in the MIAME form will need to be filled out: Users, Project, Experiment, RNA Sample Info, and submitted to George or Shaila.

Once samples are received in the Genomic Core Facility, we find the concentration and 260/280 ratio via the Nanodrop and RNA integrity via the Bioanalyzer. It is important that RNA be of high quality to ensure proper labeling and sufficient yield for hybridization. We highly recommend that users be informed about the specific RNA requirements, which are in FAQ. If the concentration is too low or RNA degraded we give feedback to the researchers and a decision is made to continue. We can concentrate samples to reach the requirement min. concentration of 500ng/ul per sample. Assays will be chosen according to the sample quantity. Different types of assays are as follows:

1)     Enzo- one cycle target labeling

2)     Ambion- one cycle target labeling

3)     Affymetrix Kit- two cycle target labeling

Page last updated: January 01, 0001

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For information about NIDDK programs: 301.496.3583

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