Gene Expression Arrays

Our microarray-based gene expression services are supported by an Affymetrix Gene Chip system 3000 7G. This 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 the newer V2.0 higher density arrays.

Our 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. Labeled, fragmented cRNA used to hybridize to Affymetrix Gene Chips is made using the Affymetrix One-Cycle or Two-Cycle kits, depending on the amount of total RNA or mRNA provided.

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.

Our facility has extensive experience running human, mouse, and rat arrays, although we have also had great success running a number of different prokaryotic directed arrays, and custom arrays developed by Nimblegen. Investigators that request the Biopolymer/Genomics Core staff to perform Affymetrix gene chip experiments must purchase gene chips directly from Affymetrix and provide them along with their RNA. THE FACILITY DOES NOT STOCK AFFYMETRIX GENE CHIPS.

TheBiopolymer/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.

Our facility also has a Cartesian Spotter for printing custom oligo- or cDNA-directedarrays. These arrays are typically represented as small, focused oligonucleotides arrays, not whole-genome. Oligonucleotides or cDNAs are attached to glass slides whose surfaces have been derivatized with poly-L-lysine. These slides are processed in a similar manner to the custom glass slide arrays (above). Typical spotted arrays consist of 48 to 384 spots, which are printed on glass slides in triplicate. Investigators can provide us with their oligos or cDNAs; alternatively, the Biopolymer/Genomics Core Facility can synthesize the oligonucleotides for an additional fee. Larger, cDNA arrays are no longer printed in the facility, as it is more cost effective to purchase them commercially.

Array Type	Cost/Array for Processing
Affymetrix; one cycle apmplification (older chips)	$300.00
Affymetrix; two cycle amplification (older chips)	$350.00
Affymetrix Gene 1.0 arrays	$350.00
Affymetrix Exon 1.0 arrays	$350.00
Glass slide arrays	$250.00*
(Re)Hybridization, washing, staining, scanning only	$75.00
Bioanalyzer run only (included in full service prices)	$25.00/chip
Slide printing (Does not include cost of oligos)	By Quote
Glass slide scanning (Axon 4000B)	$25.00/slide

* 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!