|
| Status |
Public on Oct 10, 2014 |
| Title |
crown of 4C 2 |
| Sample type |
RNA |
| |
|
| Source name |
hexaploid wheat_crown_4C
|
| Organism |
Triticum aestivum |
| Characteristics |
tissue: shoots containig shoot apical meristem
|
| Treatment protocol |
low templature treatment
|
| Growth protocol |
Plants were grown at 24°C for 3 weeks, and then moved and grown at 4°C for 6 or 12 weeks.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from the leaf tissues and crown tissues of hexaploid wheat, 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 6-week cold-treated crown tissues
|
| 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. For normalization, first, trimmed-mean was calculated excluding control probes and 2% of the probe sets with the highest and the lowest intensity values. Then, scaling factor was calculated dividing 2500 (target signal) by trimmed-mean. Normalized signal intensities (gScale Signal) were obtained multiplying the signal values by the scaling factor. No filtering was applied at this step.
|
| |
|
| Submission date |
Sep 22, 2014 |
| Last update date |
Oct 10, 2014 |
| 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) |
| GSE61621 |
Gene expression profiles during long-term low-temperature treatment and cold acclimation in synthetic wheat hexaploids |
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