normalization data transformation protocol
The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100. ID_REF = VALUE = MAS5.0 signal intensity.
array scanning protocol
GeneChips were scanned with Affymetrix GeneChip® Scanner 3000 7G.
Following fragmentation, 10 ug of cRNA were hybridized for 16 h at 45°C using an Affymetrix GeneChip Hybridization Oven 640. GeneChips were washed and stained at Affymetrix GeneChip Fluidics Station 450.
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
Rice seeds were surface-disinfected and then soaked in distilled sterile water for germination at 28°C for 2 days. rice seedlings with similar size were selected and transplanted into 8 L plastic containers containing nutrient solution(Yoshida et al., 1976) in a controlled climate chamber at 16-h-light (30°C)/8-h-dark (26°C) cycle.
nucleic acid extraction protocol
Trizol extraction of total RNA was performed according to the manufacturer's instructions.