Arabidopsis plants (ecotype Ler) were grown under short day conditions (8h cool white fluorescent light at 100 uE, 16h dark) at 20 °C and ambient humidity in PGW36 phytochambers (Controlled Environment Ltd., Winnipeg, MB, Canada). Plants were grown in Redi soil (Grace & Co, Ajax, ON, Canada) in 12 cm pots at a density of five plants per pot without fertilization for 8 weeks. Light conditions were then changed to long day (16h light, 8h dark), and plants were fertilized once with standard 10-15-10 plant fertilizer (150 ul in 300 ml water per pot) (Schultz, St. Louis, MO, USA). Twelve and 14 days after changing to long day conditions we harvested sections from stems totalling 4-6cm (“5cm stem”) and 9-11cm (“10cm stem”) in length, respectively. All flowers, siliques, cauline leaves, and secondary branches were discarded and the remaining bolting stems were cut with a razor blade to generate the following sections: 0-2cm and 2-4cm from 5cm stems; and 0-3cm, 3-5cm, 5-7cm, and 7-9cm from 10cm stems. For array hybridizations, labelled cDNA derived from each section was co-hybridized with cDNA from 0-2cm sections as a reference. Microarrays were scanned with a ScanArray Express (Perkin Elmer, Woodbridge, ON, Canada) scanner with laser power set to 90% and photo-multiplier-tube set to 62 (channel 1) and 60 (channel 2). This file describes results for replicate 1 of 4 comparing 0-3 cm sections (Channel 2, Cy5) with 0-2 cm sections (Channel 1, Cy3)
