Affymetrix WT Arrays

Important Information Regarding Sample Processing.

As of June 30, 2010, Affymetrix will discontinue the WT labeling kit for Gene and Exon arrays. The new kit from Ambion has the same chemistry, but as with any protocol change, Affymetrix recommends that Investigators try to limit the need to compare data from samples processed with different kits. We urge Investigators to try to complete any current studies with the old kit, and to begin new studies with the newer kit. Please let out technician know the status of your project when you drop off your sample. For more information, please review the following materials:

  1. WT comparison (from an Affymetrix User.)
  2. Ambion WT kit technote.
  3. Ambion WT kit whitepaper.

The WT (whole-transcript) analysis approach enables researched to detect not only the level of expression, but also the precise transcript, including alternative isoforms or genomic deletions. The WT array system provides research insights previously unattainable with the standard 3′-based microarrays.

These arrays combine a novel array design strategy with the highest density array capability. A tailored GeneChip whole transcript (WT) assay utilizes a random priming method for generating sense targets along the entire transcript. WT arrays are available for mouse, human and rat genomes.

Exon Arrays:
The Genechip Exon 1.0 ST (sense target) Arrays are the first experimental tools available to survey both gene expression and alternative splicing patterns on the whole-genome scale on a single array. There are roughly 4 probes per exon and 40 probes per gene.

Gene Arrays:
At less than half the price of Exon Arrays, the Genechip Gene1.0 ST (sense target) Arrays provide a more economical alternative to whole transcript interrogation. They utilize a subset of the probes selected from the Exon 1.0 ST Array and focus on well-annotated content at the gene level. There are 26 probes spread across the full length of each gene.