Labelled using protocol described in Affymetrix manual "3' IVT Express Kit User Manual"
Hybridization protocol
Biotin Labelled cRNA using "Affymetrix GeneChip Hybridization, Wash and Stain Kit", according to guidelines set out by Affymetrix, Santa Clara, CA
Scan protocol
Scanned according to guidelines set out by Affymetrix, Santa Clara, CA.
Description
Two days at 4C, 1 min 70% EtOH, 5 min 50% bleach, 0.5% Tween-20. Rinse with water 3 times. Seeds were germinated in tubes filled with 0.7% agarose, tubes, tubes were transferred to hydroponic cultures after germination.The hydroponic cultures were not kept sterile. The media used is a basic nutrient solution as previously described (Somerville and Ogren, 1982) but at half strength [2.5 mM KNO3, 1.25 mM KH2PO4 (pH5.6), 1 mM MgSO4, 1 mM Ca(NO3)2, 25 microM Fe-EDTA and the reported micronutrient mix at 1x concentration. 23 ðC average, 23 ðC day, 23 ðC night not controlled % average, not controlled % day, not controlled % night
Data processing
Raw data from the microarrays was normalized at probe-level using MAS5 algorithm. The detection calls (present, marginal, absent) for each probe set was obtained using the GCOS system
