normalization data transformation protocol
Analysis performed using the BioConductor suite in R. All 12 arrays were pre-processed together using GCRMA. Expression data were filtered to remove probe sets which reported low transcript abundance and low variance across all arrays (minimum intensity of 100 on at least two arrays, minimum inter-quartile range of 0.5 on the log2-scale). The pre-processed data were analysed as a 2 X 2 factorial complete randomized ANOVA using the linear model for microarray (limma) package in R (R Development Core Team, 2009). The linear model was parameterized by group means with a manually defined sum-to-zero contrast matrix to test directly for the contrasts of interest: the main and interaction effects overall, as well as the effect of the co-treatment with sucrose and SMX. A Benjamini-Hochberg false discovery rate of 0.1 was applied to the output of all tests (Benjamini and Hochberg, 1995). ID_REF = VALUE = log2 scale, GCRMA signal
array scanning protocol
Affymetrix protocol: GeneChip Scanner 3000 7G Affymetrix 00-0073.
Affymetrix protocol: Eukaryotic target preparation: Eukaryotic target hybridization.
Affymetrix protocol: Eukaryotic target preparation: One-cycle target labeling assay.
Wild-type Arabidopsis thaliana (Col) seeds were sown in sterile liquid MS growth media in 24-well plates and wrapped in light-blocking foil. Plates were cold-stratified at 4C for three days, then exposed to light for six hours to promote germination. Seedlings were grown for three days at 21C prior to RNA extraction.
nucleic acid extraction protocol
Total RNA extracted using RNeasy extraction kit (Qiagen).