|
| Status |
Public on Dec 23, 2009 |
| Title |
necrotic synthetic wheat-seedling leaf-replicate2 |
| Sample type |
RNA |
| |
|
| Source name |
synthetic hexaploid wheat
|
| Organism |
Triticum aestivum |
| Characteristics |
tissue: leaf
phenotype: hybrid necrosis
|
| Growth protocol |
Plants were grown at 23°C for 3 weeks
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from the 1st (lowest) leaves of WT and necrosis synthetic lines, using an RNeasy Plant Mini kit (Qiagen). RNA quality was checked using an Agilent 2100 BioAnalyzer.
|
| Label |
Cy3
|
| Label protocol |
Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions. Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
|
| |
|
| Hybridization protocol |
Hybridization of the Cy3-labeled cRNA to the microarrays and washing were performed using a Gene Expression Hybridization kit and Gene Expression Wash Pack (Agilent Technologies) according to the manufacturer's instructions.
|
| Scan protocol |
Signal intensities were detected by Feature Extraction software (Agilent Technologies). Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).
|
| Description |
Gene expression in 3-week-old seedling leaves
|
| Data processing |
The scanned images were analyzed with Feature Extraction Software 9.5 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
|
| |
|
| Submission date |
Dec 22, 2009 |
| Last update date |
Dec 22, 2009 |
| Contact name |
Shigeo Takumi |
| Organization name |
Kobe University
|
| Department |
Graduate School of Agricultural Science
|
| Lab |
Plant Genetics
|
| Street address |
Rokkodai 1-1, Nada
|
| City |
Kobe |
| State/province |
Hyogo |
| ZIP/Postal code |
657-8501 |
| Country |
Japan |
| |
|
| Platform ID |
GPL9805 |
| Series (1) |
| GSE19613 |
Expression profiling of hybrid necrosis in triploid hybrids crossed between tetraploid wheat and Aegilops tauschii |
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