Supplementary Methods
Transcriptional analysis of flagellin response in wild-type and mkk1 mutant plants.
The seedlings were treated as described in Methods using flg22 to a final concentration of
1 μM. Plants from different plates were pooled and treated independently to account for
biological variation. RNA was extracted from snap-frozen samples using RNeasy Plant
Mini Kit from Qiagen (Crawley, UK). Processing of the RNA samples, hybridization to
ATH1 arrays, washing and scanning of the arrays followed standard Affymetrix protocol
and were performed by VBC Genomics (Vienna, Austria). Signal intensities were
normalized using the global scaling method. Expression signals lower than 50 were
floored to 50 to eliminate noise and the number of minor significant changes. Expression
ratios were calculated by comparing the signal intensities in Col-0 versus mkk1, or
control versus flg22-treated. Flagellin-responsive genes showing a different expression in
mkk1 background were chosen for detailed analysis using quantitative RT-PCR.