genotype: Wild-type phenotype: normal cultivar: ILMI treatment: under 2 days water withdrawal
Growth protocol
Wild type and transgenic rice (Oryza sativa L. cv. ILMI) plants were grown under the conditions specified. Sterilized seeds were germinated in Murashige-Skoog (MS) solid medium in a growth chamber in the dark at 28°C for three days followed by in the light at 28°C for one day, transplanted into soil, and grown in a glasshouse (16 h light/8 h dark cycle) at 28-30°C. Each plant was grown in a pot (4x4x5 cm3; six plants per pot) filled with rice nursery soil (Bio-media, Kyeongju, Korea) for 6-week-old after germination. For drought stress, water was removed from the pots of 6-week-old plants, which is treated by water withholding for two days.
Extracted molecule
total RNA
Extraction protocol
Total and polysomal RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA) and the RNAprotect reagent (Qiagen) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen).
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
Wild type Oryza sativa L. cv. ILMI under 2 days water withdrawal (replicate2)
Data processing
The raw data (.pair 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.).
