Data

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 processed microarray data in this study.

Heenam Kim, Erik C. Snesrud, Brian Haas, Foo Cheung, Christopher D. Town, and John Quackenbush. 2003. Gene expression analyses of Arabidopsis chromosome 2 using a genomic DNA amplicon microarray. Genome Research, in press.

Primer sequences and PCR validation scores for the Arabidopsis nuclear, chloroplast, and mitochondrial genomes.

Primers used in this project were synthesized and are available from Invitrogen.

pick_primer.pl: A perl script used for primer selection for genomic amplicon arrays.