Five replicates for each sample category were generated, and compared with a global reference, generated from an equimolar mix of amplified RNAs from each of the 15 plants. RNA from each individual sample, plus the reference, were amplified, and used for labeling. For each category, three samples were labeled with Cy5 and two with Cy3, and compared with the corresponding reversed-labeled reference mix. Long 70-mers oligonucleotide microarrays, provided by Dr. D. Galbraith (Univ. Arizona), contain 29,110 probes from the Qiagen-Operon Arabidopsis Genome Array Ready Oligo Set (AROS) Version 3.0. This oligo set represents 26,173 protein-coding genes, 28,964 protein-coding gene transcripts and 87 miRNAs and is based on the ATH1 release 5.0 of the TIGR Arabidopsis genome annotation database (www.tigr.org/tdb/e2k1/ath1/) and release 4.0 of the miRNA Registry at the Sanger Institute (www.sanger.ac.uk/Software/ Rfam/mirna/index.shtml). Further information can be found at the Operon website (omad.operon.com/download/index.php). Oligos were rehydrated and immobilized by UV irradiation. Slides were then washed twice in 0.1% SDS, 4 times in water, dipped in 96% ethanol for 1 min, and dried by centrifugation. Slides were prehybridized 30 min at 42uC with 100 mL of 66 SSC, 1% BSA and 0.5% SDS, under a 60622 mm coverslip LifterSlip (Erie Scientific) in an ArrayIt microarray hybridization cassette (TeleChem). Slides were then rinsed five times in H 2 O and dried by centrifugation. Slides were hybridized immediately. Labeled RNA was used to hybridize the slides basically as described in [40] . After hybridization and wash, slides were scanned at 532 nm for the Cy3 and 635 nm for the Cy5 dyes, with a GenePix 4000B scanner (Axon Molecular Devices), at 10 nm resolution and 100% laser power. Photomultiplier tube voltages were adjusted to equal the overall signal intensity for each channel, to increase signal-to-noise ratio, and to reduce number of spots with saturated pixels. Spot intensities were quantified using GenePix Pro 6.0 (Axon Molecular Devices).