Affymetrix Whole Transcript Arrays (e.g. Human Gene 1.0 ST array)
These arrays assay all well annotated transcripts (~28K per array) in human, mouse or rat. Each array is designed to contain a single 25mer oligonucleotide that is a perfect match for each exon in every transcript. As a result, each transcript is assayed across its entire length with large numbers of probes, typically >25 probes per transcript. These arrays can give you high quality data for well annotated genes, but may not be helpful for poorly annotated genes or ESTs. 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 100 ng total RNA.

Array Comparisons