Microarray hybridization and data analysis

We measured the FAC-induced gene expression changes in WT and JA-deficient plants (irAOC) using microarray analyses. The WT samples were the same as the samples used for the RNA-seq analysis. The germination and growth conditions, FAC elicitation, sample collection and RNA extraction for the analysis of the irAOC plants were the same as those described for the analysis of the WT plants. cDNA preparation and hybridizations were performed as described in Kallenbach et al. (Kallenbach et al., 2011). Quantile normalization and log₂ transformation was performed for all raw microarray data using the R package 'Agi4x44PreProcess' (http://goo.gl/TJnA6Q). Probes with 1.5-fold change and adjusted p-values less than 0.05 were considered differentially expressed. The sequences of all probes were mapped to the N. attenuata draft genome (v1.0), and only the probes that uniquely mapped to annotated gene regions were considered for downstream analysis. All microarray data were deposited in the public GEO (Gene Expression Omnibus) repository ({"type":"entrez-geo","attrs":{"text":"GSE75006","term_id":"75006"}}GSE75006).