Background correction, normalisation, and calculation of probe set summaries were done using RMA (Irizarry et al., 2003) implemented in the Aroma.Affymetrix package (Bengtsson et al., 2008). Data were log2-transformed by RMA.
Leaves were harvested into liquid nitrogen. RNA was extracted using Trizol (Invitrogen) according to manufacturer’s instructions. The RNA was subjected to a DNase treatment.
Three successive experiments were carried out using seeds of the Arabidopsis thaliana accession Col-0, clf-29, ft-10 and lhp1-6 ft-10. For each experiment, rosette leaf 6 was harvested from 10 plants per genotype. Plants were grown under short-day conditions (8 h light and 16 h darkness) at 21°C for 48d.
RNA was amplified and labelled with the GeneChip WT Sense Target Labeling Assay (Affymetrix, Santa Clara, CA).