Affymetrix Microarray System
The Affymetrix GCS3000 microarray system is the flagship technology in the Genomics Centre. Affymetrix supply market-leading GeneChip arrays for analysis of gene expression, transcriptional regulation, SNP/genotyping, copy number variation, and splice variation. The GCS3000 system allows us to process these microarrays in the Centre, in terms of hybridisation and scanning.
All of the arrays are based on 25-mer oligonucleotide probes that are built directly onto the array surface using photolithography and solid-state chemistry; they also make extensive use of control probes and redundancy of measurement (by using multiple probes per "gene").
In the Genomics Centre we focus on Affymetrix's expression array products, for transcription profiling. For DNA analysis arrays (eg SNP/Genotyping) please contact the Genomics Laboratory in the Genetics Dept.
Glass-slide or spotted arrays
In-house spotted arrays are useful for people with specific applications not catered for adequately by the commercial array market (eg rarely-studied model-organisms or custom gene sets), or for people who are processing very large numbers of samples - as this can save significant costs.
We have also recently purchased a MAUI automated hybridisation system
for the array hybridisation step. This machine will improve signal to noise ratios with spotted array hybridisations, and also help to control variation between arrays at this crucial step.
Spotted arrays are scanned using a dual-laser array scanner (ProScanArray Express from Perkin Elmer). This scanner generates 5um-resolution images for high-density applications.