Affymetrix Exon Arrays
These arrays assay all exons (detected or putative) in the human, mouse and rat genomes. These are the most comprehensive expression arrays available with ~1.5 million probes per array. Each array is designed to contain one to four 25mer oligonucleotides that is a perfect match for each exon. As a result, each transcript is assayed across its entire length with large numbers of probes, typically ~40 probes per transcript. These arrays can give very high quality data at both the whole transcript level and the exon level to identify unsuspected splicing variations. Note that because the probes for these arrays are exon specific and do not cover splice junctions, it is still possible to miss some splicing events. To search the arrays for your gene of interest or to download complete gene lists for the Affymetrix arrays, please visit NetAffx*.
For additional information see:

affymetrix.com*

Preparation of target
Total RNA samples are isolated using standard methods and assayed using the Agilent 2100 BioAnalyzer to confirm quality. Next, double stranded cDNA is prepared using random-T7 RNA polymerase primers. Biotinylated cRNA is prepared by in vitro transcription and then converted back to ssDNA. The ssDNA is fragmented and end labeled with biotin. As a result prepared samples represent the entire transcript and are resistant to problems due to RNA degradation. The minimum amount of starting material for these arrays is 1 ug total RNA.