Rice seeds were sterilized and germinated on 2N6 media in a growth chamber with a 16 hr light (28°C), 8 hr dark (26°C) photoperiod for 7 dats. The seedling were transferred to individual pots and grown in a greenhouse under the controlled conditions
Extracted molecule
total RNA
Extraction protocol
Total RNA from frozen wild-type and mutant leaves was prepared as previously described [Davis, KR & Ausubel, FM (1989) Mol. Plant-Microbe Interact 2: 363-368). Genomic DNA contamination was removed by DNase I at 37°C for 30 min and cDNA was generated by commercial cDNA synthesis kit according to the manufacturer's guidelines.
Label
Cy3
Label protocol
Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.
Hybridization protocol
Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.
Scan protocol
Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.
Description
PM_HM_ABFT9
Data processing
The raw data (.probe file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).
