|
| Status |
Public on Jan 13, 2011 |
| Title |
FlagLeaf_Sterile_3WAH_rep_2 |
| Sample type |
RNA |
| |
|
| Source name |
Flag Leaf, Sterile plant, 3 weeks after heading, replicate 2
|
| Organism |
Oryza sativa Japonica Group |
| Characteristics |
synonym: Oryza sativa L. ssp. japonica
organ/tissue: Flag leaf
phenotype: Sterile
stage: 3 weeks after heading
accession: NC0122 (Tos17 mutant line)
genotype: PAIR2 (-/-)
|
| Growth protocol |
All plants were grown in paddy field in Tsukuba, Japan (~36o N latitude) during normal rice growing season in 2009.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using RNeasy Plant Mini Kit (QIAGEN) according to the manufacturer's protocol, quantitied using NanoDrop ND-1000 UV-VIS spectrophotometer (NanoDrop) and quality-checked using Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA).
|
| Label |
Cy3
|
| Label protocol |
400 ng of total RNA was added with one-color spike-mix and labeling was performed using Quick Amp Labeling Kit, One-Color (Agilent) in the presence of cyanine-3-CTP accoring to the manufacturer's protocol. The cyanine-3-labeled cRNA was purified by RNeasy Mini Kit (QIAGEN), and quantified using NanoDrop ND-1000 UV-VIS spectrophotometer.
|
| |
|
| Hybridization protocol |
For hybridization, 1650 ng of cyanine 3-labeled cRNA was fragmented and hybridized with the rice 4x44K microarray RAP-DB (G2519F#15241) at 65°C for 17 hours using the Agilent Gene Expression Hybridization Kit.
|
| Scan protocol |
Slides were scanned on an Agilent G2505B DNA microarray scanner using one-color scan setting for 4x44K array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green PMT: XDR Hi 100%; XDR Lo 10%).
|
| Description |
Gene expression of flag leaf at 3 weeks after heading in the sterile plant, pair2 mutant
|
| Data processing |
The scanned images were analyzed with Feature Extraction Software 9.5.3.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended processed signal intensities. The processed signal intensities were used for 75 percentile normalization and log2 transformation with GenespringGX11(Agilent).
|
| |
|
| Submission date |
Apr 20, 2010 |
| Last update date |
Jan 13, 2011 |
| Contact name |
Baltazar Antonio |
| E-mail(s) |
antonio@nias.affrc.go.jp
|
| Organization name |
National Institute of Agrobiological Sciences
|
| Department |
Genome and Biodiversity Research
|
| Lab |
Genome Resource Center
|
| Street address |
Kannondai 2-1-2
|
| City |
Tsukuba |
| State/province |
Ibaraki |
| ZIP/Postal code |
305-8602 |
| Country |
Japan |
| |
|
| Platform ID |
GPL6864 |
| Series (2) |
| GSE21398 |
Comparison of gene expression profile of flag leaf from fertile and sterile lines of rice |
| GSE21494 |
Transcriptomic analysis of rice |
|
