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| Status |
Public on Mar 19, 2008 |
| Title |
Azucena root tip_Before the wax layer_Rep3 |
| Sample type |
RNA |
| |
|
| Source name |
Azucena root tip_Before the wax layer
|
| Organism |
Oryza sativa |
| Characteristics |
Rice variety Azucena, 24 day old plants, grown in sand filled chambers (internal dimensions of 10 x 5 x 25cm) with a 5mm 60% wax layer 50mm below the surface of the sand. RNA was harvested from root tips which were 5-10 mm above the wax layer. Plants were watered with nutrient solution. RNA was extracted from the last 5 mm of the root tip. Rep3.
|
| Biomaterial provider |
University of Aberdeen, Rice molecular genetic group
|
| Treatment protocol |
N/A
|
| Growth protocol |
Plants were grown in a controlled environment room with a 12 hour day and night, with a day temperature of 30oC and a night temperature of 24oC with 300 µmol m-2 s-1 PAR.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
A total of 100 mg of root tips (last 5 mm of the root) was harvested and RNA extracted using the TRIzol method (Invitrogen) followed by further purification and DNase treatment using the RNeasy clean up kit (Qiagen).
|
| Label |
Biotin
|
| Label protocol |
RNA was processed for use with the Affymetrix GeneChip Rice Genome array according to the manufactures protocol. Briefly, 5 ug of total RNA was used in the one-cycle cDNA synthesis reaction. After the generation of double stranded cDNA an in vitro transcription reaction was performed to generate biotinylated cRNA. (Expression Analysis Technical Manual, 2004, Affymetrix).
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| |
|
| Hybridization protocol |
Hybridisation, washing and staining procedures of the Affymetrix GeneChip Rice Genome arrays were carried out by the Affymetrix core facility of the University of Aberdeen, as described in the Affymetrix technical manual.
|
| Scan protocol |
Scanning procedures of the Affymetrix GeneChip Rice Genome arrays were carried out by the Affymetrix core facility of the University of Aberdeen, as described in the Affymetrix technical manual.
|
| Description |
Gene expression data from rice root tips (variety Azucena) which were above the 60% wax layer, rep3
|
| Data processing |
The data was analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.
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| |
|
| Submission date |
Mar 17, 2008 |
| Last update date |
Mar 18, 2008 |
| Contact name |
Gareth Norton |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Aberdeen
|
| Department |
Plant and Soil Science
|
| Lab |
Rice genetics
|
| Street address |
St Machar drive
|
| City |
Aberdeen |
| ZIP/Postal code |
AB24 3UU |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL2025 |
| Series (1) |
| GSE10857 |
Gene expression of rice root tips before, at and buckled by a hard layer in two rice varieties |
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