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Gene Expression Arrays

Our microarray-based gene expression services are supported by an Affymetrix Gene Chip system 3000 7G and an Illumina iScan.

The Affymetrix system is comprised of a hybridization oven, three fluidics stations, and a scanner equipped with an autoloader. The system is capable of scanning older Affymetrix gene chips, in addition to newer higher density arrays. Affymetrix has a broader range of species-specific arrays available. For human, mouse and rat Affymetrix arrays, while we still have access to older arrays, the newer Gene 1.0 ST and Exon 1.0 ST arrays are currently the most widely used Affymetrix arrays.

The Illumina system is capable of running any of the Illumina BeadChip arrays, which currently is limited to human, mouse or rat species. On average, the cost for running Illumina arrays can be significantly lower on a ‘per sample’ basis, but often requires a minimum number of samples to be run in order to see this cost savings. Please inquire for more specific details.

Full service includes evaluation of the RNA provided by the investigator using an Agilent 2100 Bioanalyzer. RNA that is deemed not to be of sufficient quality will not be processed. Samples are labeled, hybridized, washed, scanned, and normalized data is provided back to the investigator.

Guidance is also provided to investigators on experimental design, and methods for RNA extraction based on the source of the RNA. Arrangements can be made for BSS staff to perform the RNA extraction as necessary. Normalized data generated by the Biopolymer/Genomics Core Facility is provided to the investigator to perform the data analysis.

Bioinformatics support for data analysis is available through the Institute for Genome Sciences. They will be happy to assist you with your analysis needs for expression and genotyping studies.

Our facility has extensive experience running human, mouse, and rat arrays, although we have also had great success running a number of other species-specific arrays. Investigators who request the Biopolymer/Genomics Core staff to perform gene expression experiments must purchase gene chips directly from Affymetrix or Illumina and provide them along with their RNA. THE FACILITY DOES NOT STOCK AFFYMETRIX GENE CHIPS OR ILLUMINA BEADCHIPS. We can however, provide you with the University pricing, so please contact us for pricing information.

The Biopolymer/Genomics Core Facility also has extensive experience in processing custom (glass slide) arrays. These arrays, which can be purchased through a variety of commercial vendors. Typical protocols for processing these arrays includes generation of cRNA that is labeled with either cy3 or cy5 dyes (usually one label for each of two conditions), hybridized to the slides, washed and scanned on an Axon Genepix 4000B scanner, using GenePix Pro6.0 software. As with the Affymetrix arrays, the Biopolymer/Genomics Core does not stock any glass slide arrays.  

Array Type
Cost/Array for Processing
Affymetrix Gene 1.0 arrays $350.00
Affymetrix Exon 1.0 arrays $350.00
Illumina arrays $125.00
Glass slide arrays $250.00*
(Re)Hybridization, washing, staining, scanning only $75.00
Bioanalyzer run only (included in full service prices) $25.00/chip

* A volume discount is available for this service for 6 or more samples submitted simultaneously.

If you do not see a specific array listed in the price list above, please contact us; it does not signify that we do not work with that array!