|
| Status |
Public on Apr 12, 2016 |
| Title |
Hybrid weakness, root of a parental cultivar, Jamaica, biological rep3 |
| Sample type |
RNA |
| |
|
| Source name |
Root, two-week old seedling of Jamaica
|
| Organism |
Oryza sativa Japonica Group |
| Characteristics |
subspecies: japonica
cultivars: Jamaica
|
| Treatment protocol |
Collected biological samples were frozen in liquid nitrogen and kept at -80˚C until RNA extraction.
|
| Growth protocol |
Plants were aseptically germinated and cultivated on MS medium at 25˚C under continuous light (20 Em–2 s–1). After two weeks cultivation, seedlings were used for measurement.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted with RNeasy plant mini kit (Qiagen) according to manufacturer's protocol.
|
| Label |
Cy3
|
| Label protocol |
Cy3-labeled cRNA were prepared from 100 ng of total RNA using Quick-Amp Labeling Kit (Agilent) according to manufacturer's protocol.
|
| |
|
| Hybridization protocol |
Fragmentation and hybridization was carried out with Gene Expression Hybridization Kit (Agilent). 400 ng of labeled and fragmented cRNA was hybridized to microarray using hybridization oven G2545A (Agilent), and wash step was performed with Gene Expression Wash Buffer Kit (Agilent). All operations were performed according to manufacturer's protocol.
|
| Scan protocol |
Microarrays were scanned using Agilent DNA microarray scanner G2565BA.
|
| Description |
Gene expression of normal roots of a parental cultivar, 'Jamaica'.
|
| Data processing |
Scanned tiff image files were analyzed with FeatureExtraction 9.5.3.1 (Agilent). We slightly modified manufacturer's default extraction protocol called 'GE1-v5_95_Feb07' as follows: 'Background Subtraction Method' was set to 'Average of Negative Control Features', and 'Use Surrogates' was set to 'False'. Then 'gBGSubSignal' columns were extracted from the text data files produced by FeatureExtraction, and introduced into GeneSpring 7.3.1 (Agilent). Positive and negative control features (such as spike-in or dark corner) were removed before data introduction into GeneSpring. Introduced signal intensities were scaled to median per chip, and the lowest value of scaled signal intensity was set to 0.01. Normalized signal intensities of some probes locating multiple positions on a array were average values of all corresponding probes.
|
| |
|
| Submission date |
Apr 21, 2009 |
| Last update date |
Apr 12, 2016 |
| Contact name |
Nori Kurata |
| E-mail(s) |
nkurata@nig.ac.jp
|
| Phone |
+81-55-981-6808
|
| Organization name |
National Institute of Genetics
|
| Lab |
Plant genetics Lab.
|
| Street address |
1111 Yata
|
| City |
Mishima |
| State/province |
Shizuoka |
| ZIP/Postal code |
411-8540 |
| Country |
Japan |
| |
|
| Platform ID |
GPL8852 |
| Series (1) |
| GSE15755 |
Microarray analysis of a hybrid weakness in the cross between rice cultivars |
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