TY  - JOUR
A1  - Kim, Heenam
A1  - Snesrud, Erik C.
A1  - Haas, Brian
A1  - Cheung, Foo
A1  - Town, Christopher D.
A1  - Quackenbush, John
T1  - Gene Expression Analyses of Arabidopsis Chromosome 2 Using a Genomic DNA Amplicon Microarray
Y1  - 2003/03/01 
JF  - Genome Research 
JO  - Genome Research 
SP  - 327 
EP  - 340 
DO  - 10.1101/gr.552003 
VL  - 13 
IS  - 3 
UR  - http://genome.cshlp.org/content/13/3/327.abstract 
N2  - 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 plantArabidopsis 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.] 
ER  -