Affymetrix GeneChip Analysis System

Affymetrix GeneChips are oligonucleotide microarrays that provide a platform for full genome gene expression analysis. Affymetrix has developed this platform based on stringent probe-selection algorithms and a manufacturing technology that uses a combination of photolithography and solid-phase combinatorial chemistry. Cell and tissue specific gene expression profiles are generated utilizing biotinylated cRNA samples that are hybridized to Affymetrix GeneChips.

The Core Facility has extensive experience running a variety of arrays including human, mouse, rat, Rhesus, Arabidopsis, and Drosophila. The core provides extensive support and advice to customers on topics including preparation of the samples, downstream analysis, and data storage. 

Our services include:

  • Sample Labeling
  • Microarray Hybridization and Scanning
  • Sample Quality Control
  • Data Analysis
  • Assistance with Experimental Design


For standard RNA labeling investigators are required to submit 100-500 nanograms of high quality total RNA with 260/280 readings from a spectrophotometer and gel images of each sample submitted. Users must also provide the appropriate Affymetrix GeneChips.

For hybridizations on 3' expression arrays, investigators are required to provide 15 ug of high quality, labeled, and fragmented cRNA and the appropriate Affymetrix GeneChips. For hybridizations on Gene 1.0 and Exon 1.0 arrays, we require 5ug of fragmented ssDNA. We also require gel images of each sample submitted, showing the initial RNA extraction and both the unfragmented and fragmented cRNA preps. Copies of the sample preparation protocols are available from the Affymetrix website.