DESIGN, PRODUCTION, AND UTILIZATION OF LONG OLIGONUCLEOTIDE MICROARRAYS FOR EXPRESSION ANALYSIS IN MAIZE

Analysis of gene expression on a genome scale can provide useful insights into plant growth and development, and an understanding of the mechanisms used by plants to cope with biotic and abiotic stress. To facilitate analysis of genome-wide gene expression in maize, we have assembled a large collection of maize EST and genomic sequences, designed a set of 57,442 maize 70-mer oligonucleotides to represent these sequences, and printed a two-slide microarray set (MOA and MOB) which is available to the maize research community at minimal cost. To monitor array quality, we have devel- oped a series of printing controls and procedures that when coupled with a 9-mer hybridization assay, allow tracking of spot morphology and printing pin carryover. An optimized hybridization protocol has been developed by testing a series of hybridization temperatures and per- forming detailed statistical analyses. To facilitate manage- ment of all long-oligonucleotide associated array data, Zeamage, a Sybase relational database has been devel- oped and is available at www.maizearray.org. Zeamage contains the appropriate tables and fields for tracking the oligonucleotide sequences and associated annotation, ar- ray design, and biological information associated with the microarray hybridizations. The www.maizearray.org web- site provides additional information on the project, array content, and data analysis tools.