|
| Status |
Public on Jan 13, 2011 |
| Title |
Root_27DAT_12:00_rep3 |
| Sample type |
RNA |
| |
|
| Source name |
Root, 27 days after transplanting, 12:00, replicate 3
|
| Organism |
Oryza sativa Japonica Group |
| Characteristics |
synonym: Oryza sativa L. ssp. japonica
cultivar: Nipponbare
organ/tissue: Root
growth/development stage: 27 days after transplanting
sampling time: Daytime 12:00
|
| Growth protocol |
All plants were grown in paddy field in Tsukuba, Japan (~36o N latitude) during normal rice growing season in 2008.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For leaf blade, leaf sheath, root, stem, inflorescence, pistil, anther, lemma, palea, ovary and embryo samples, total RNA was extracted using RNeasy plant minikit (QIAGEN). For endosperm samples, total RNA was extracted with phenol and purified using the RNeasy mini spin column of the RNeasy plant mini kit. The extracted RNA was quantified 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 |
One-color spike-mix was added to the RNA prior to labeling reaction. Labeling was performed using Quick Amp Labeling Kit, One-Color (Agilent Technologies) in the presence of cyanine-3-CTP according 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 microarray hybridization, 1650 ng of cyanine 3-labeled cRNA (or entire labeled cRNA for samples with low yield) were 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 root at daytime 27 days after transplanting
|
| 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) |
| GSE21396 |
Spatio-temporal gene expression of various tissues/organs throughout entire growth in rice |
| GSE21494 |
Transcriptomic analysis of rice |
|
