ARS | Publication request: AFFYMETRIX MAIZE PILOT EXPRESSION ARRAY

Submitted to: Plant and Animal Genome Conference Proceedings
Publication Type: Proceedings
Publication Acceptance Date: January 15, 2005
Publication Date: January 15, 2005
Citation: Williams, A., Caldo, R., Hanna, D., McLean, L., Tanimoto, G., Wise, R.P. 2005. Affymetrix maize pilot expression array. Plant and Animal Genome XIII Conference Proceedings. P897.

Technical Abstract: A pilot study was conducted to evaluate design criteria and analytical methods (particularly signal estimators) for gene expression monitoring in a selection of maize inbreds (B73, W23, Mo17, Wf9-BG) and exotic land races using the Affymetrix probe array technology. The key issue was whether eleven 25-mer probe pairs could measure transcript levels robustly despite the exceptionally high polymorphism in maize genes. As a first step in understanding how polymorphisms impact data collection, a maize pilot array containing 8,396 sets of 30 probe pairs was used. Content for the array was generated using the standard Affymetrix cDNA cluster design pipeline. Content on the array is equally divided between probe designs based on all public cDNA sequences (zm1 design) and probe sets restricted to the B73 inbred (zm3 design). Most probe sets were selected from a subset of elements in Maize Gene Discovery spotted cDNA microarray experiments. Forty-three probe sets target Glutathione S-transferases to evaluate resolution of gene expression patterns within gene families with both closely and distantly related members. The results of this pilot will be used in the design of a larger, comprehensive maize gene expression monitoring array. This larger design will be carried out under the Affymetrix Consortia Design Program.