Labelled using the protocol described in the Affymetrix manual "3' IVT Express Kit User Manual".
Hybridization protocol
Biotin-labelled cRNA using the "Affymetrix GeneChip Hybridization, Wash and Stain Kit" according to the guidelines set out by Affymetrix, Santa Clara, CA.
Scan protocol
Scanned according to the guidelines set out by Affymetrix, Santa Clara, CA.
Description
Plants were grown individually in 26 by 60 mm tubes and watered and fertilized optimally. Plants were grown in a split growth chamber (providing uniform temperature and PPFD but allowing for differential R:FR) with 18 h photoperiods (185 microMoles m-2 s-1 PPFD provided by T12 VHO CW fluorescent lamps) and 24oC/18oC day/night temperatures. 3 days at 4oC. 22.5°C average, 24°C day, 18°C night 50% average, 50% day, 50% night Hoagland ampapos;s No.2 basal salt mixture.
Data processing
Raw data from the microarrays was normalized at probe-level using the MAS5 algorithm. The detection calls (present, marginal, absent) for each probe set was obtained using the GCOS system.
