ID_REF = VALUE = log2 RMA signal
The software program Affymetrix 'GeneChip Command Console (v3.1)' was used to operate the staning, washing and scanning of the GeneChips and visual inspection of the array images. Chips were scanned using the Affymetrix 3000G scanner
Data were processed using the Bioconductor packages in R and using the RMA normalization algorithm.
The (#900720) GeneChip Hybridization, Wash and Stain Kit was used for hybridization, washing, staining and scanning of the chips.
The Affymetrix 3'IVT-Express Labeling Kit was used to synthesize Biotin-labeled cRNA. From each RNA sample 100 ng was used as input for the labelling reactions.
Plants were put in each of the four conditions (control light with mock spray, control light with 0.5 mM SA spray, low R:FR (0.2) with mock spray, low R:FR (0.2) with 0.5 mM SA spray) for 2h. One petiole (approx. 5 mm length) per plant was harvested in liquid N2. 3 petioles/biological replicate were pooled.
Total RNA was isolated from homogenized material using the RNeasy plant mini kit (Qiagen) with on-column DNA digestion following the company’s instructions
Arabidopsis thaliana plants were sown, stratified (4˚C) for 3 days and then transferred to a growth chamber (9 h. light (180 �mol / m2 / s, 20�C, 70% RH, R/FR = 2.2), 15 h dark) where they were transferred to individual pots after 10 d and gwon until 4 weeks old.