Rice (Oryza sativa, japonica cultivar Zhonghua 11), was cultivated at day/night temperatures (28/22 °C) in phytotron
RNA was extracted using the TRIzol method (Invitrogen).
RNA was labeled for use with the Affymetrix GeneChip Rice Genome array according to the manufactures protocol. (Expression Analysis Technical Manual, 2004, Affymetrix).
Affymetrix® GeneChip® Operating Software Version 1.0 was used for washing, staining, and scanning as described in the supplier’s protocol.
Scanning procedures of the arrays were carried out using Affymetrix GeneChip Scanner 3000 as described in the Affymetrix technical manual.
The data was 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 500.