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Gene Expression Analyses of Arabidopsis Chromosome 2 Using a Genomic DNA Amplicon Microarray

The Institute for Genomic Research, Rockville, MD 20850, USA.

The gene predictions and accompanying functional assignments resulting from the sequencing and annotation of a genome represent hypotheses that can be tested and used to develop a more complete understanding of the organism and its biology. In the model plant Arabidopsis thaliana, we developed a novel approach to constructing whole-genome microarrays based on PCR amplification of the 3' ends of each predicted gene from genomic DNA, and constructed an array representing more than 94% of the predicted genes and pseudogenes on chromosome 2. With this array, we examined various tissues and physiological conditions, providing expression-based validation for 84% of the gene predictions and providing clues as to the functions of many predicted genes. Further, by examining the distribution of expression along the physical chromosome, we were able to identify a region of repressed transcription that may represent a previously undescribed heterochromatic region.

[The sequence data from this study have been submitted to ArrayExpress under accession nos.: For the Array Design, A-TIGR-2. For the three subgroups of experiments: AbioticStress, E-TIGR-2; BioticStress, E-TIGR-3; Tissues, E-TIGR-4.]

² Corresponding author.

E-MAIL johnq{at}tigr.org; FAX (301) 838-0208.

Article and publication are at http://www.genome.org/cgi/doi/10.1101/gr.552003.

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