Labelled using protocol described in manual "Affymetrix GeneChip Expression Analysis Technical Manual", One-Cycle target labelling
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
The seeds were stratified at 4C for 48 hours in darkness. Seeds were rinsed in 100% ethanol and sterilized in 2.5% (v/v) sodium hypochlorite solution for 7 min, then washed with sterilized distilled water 3 times. 70-100 Seeds were plated in 10 clusters (app 10 seeds per cluster) on 1/2 MS 0.8% agar plates. Seedlings were grown in 12 h light/12 h dark (12L:12D) for 11 days at constant 19C. The light source for germination and growth was cool-white fluorescent light at 70 umol/m2/s. On the 12th day the seedlings were transferred to continuous white light conditions at 100 umol/m2/s. Autoclaved. 20 seedlings clumped together. 19 C average, 19 C day, 19 C night. 50 % average, 50 % day, 50 % night. Murashige & Skoog basal salt mixture. Constant light.
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
