Seeds were surface sterilized for 8min in 5% sodium hypochlorite, 0.15% Tween 20, excessively rinsed in distilled water, and germinated on MS medium (0.8% Select Agar (Life Technologies, Inc., Rockville, MD), 0.5X Murashige-Skoog (MS) salts (Life Technologies, Inc.), 0.5mM MES, pH5.7, 1% sucrose, 1X B5 vitamins. After cold treatment at 4 C for 2 days, the plates were incubated at 25 C under 16h light / 8h for 10 days.
Extracted molecule
total RNA
Extraction protocol
Total RNA was prepared using RNAqueous RNA isolation kit with Plant RNA isolation aid (Ambion, Austin, TX). After LiCl precipitation, RNA was purified using RNeasy columns (Qiagen, Valencia, CA) and re-precipitated with LiCl. RNA pellets were washed with 70% EtOH (three times), and resuspended in DEPC-treated water.
Label
biotin
Label protocol
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA
Hybridization protocol
10 microgram of cRNA were hybridized to the GeneChip® Arabidopsis ATH1 Genome Array chip according to the protocols provided by the manufacturer. GeneChips were scanned with the default settings using the > GeneChip® Scanner 3000 7G.
Scan protocol
GeneChips were scanned with the default settings using the GeneChip® Scanner 3000 7G.
