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Gene Expression Arrays

Biopolymer microarray-based gene expression services are supported by an Affymetrix Gene Chip system 3000 7G.

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 2.0 ST and Exon 1.0 ST arrays are currently the most widely used Affymetrix arrays.

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. Our Laboratory DOES NOT STOCK AFFYMETRIX GENE CHIPS. 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 can be purchased through a variety of commercial vendors. The standard 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.

Array Type 
Cost/Array for Processing 
Affymetrix Gene arrays $225.00
Affymetrix Exon arrays $225.00
Affymetrix 3' IVT arrays $225.00
Affymetrix Specific arrays $225.00
Affymetrix SMiRNA $120.00
(Re)Hybridization, washing, staining, scanning only $75.00
Bioanalyzer run only (included in full service prices) $40.00/chip

* A volume discount is available for this service for 25 or more samples submitted simultaneously. This volume discount must be arranged prior to the start of the project. 

Note: If you do not see a specific array listed in the description above, please contact a member of the Biopolymer team.