cultivar: Oryza sativa subsp. japonica var. Nipponbare age: three-month-old rice flag leaves, Day 2, 8:00pm
Treatment protocol
Flag leaves were harvested at 8:00pm
Growth protocol
For flag leaf samples, the rice plants were grown in the field under natural conditions, within the May-October growing season, on an experimental farm in Zhejiang, China. Three-month-old rice plants were entrained into the greenhouse under the regular condition (32/30°C and 12/12 h of light/dark).
Extracted molecule
total RNA
Extraction protocol
Total RNA was isolated using TRIZOL® reagent (Invitrogen, CA, USA) and purified using Qiagen RNeasy columns (Qiagen, Hilden, Germany)
Label
biotin
Label protocol
8 µg of total RNA was used for making biotin-labelled cRNA targets; cDNA and cRNA synthesis; cRNA fragmentation, hybridization, washing and staining; and scanning, following the GeneChip Standard Protocol (Eukaryotic Target Preparation). In this experiment, a Poly-A RNA Control Kit and a One-Cycle cDNA Synthesis kit were applied.
Hybridization protocol
Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45? on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
Scan protocol
GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
Description
Gene expression data from 17-day-old rice seedling leaves, Day 1, 8:00am, the end of night
Data processing
The data were analyzed with GCOS software (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.
Submission date
Mar 23, 2011
Last update date
Mar 24, 2011
Contact name
Wenying Xu
Organization name
Institute of Genetics and Developmental Biology, Chinese Academy of Sciences
Street address
Institute of Genetics and Developmental Biology, Chinese Academy of Sciences
