|
| Status |
Public on Dec 11, 2006 |
| Title |
Rice Azucena 1ppm Arsenate Rep3 |
| Sample type |
RNA |
| |
|
| Source name |
Rice Hydroponic Roots 1 Week Old
|
| Organism |
Oryza sativa |
| Characteristics |
Rice variety Azucena, 1 week in hydroponics with 1ppm arsenate, whole root system
|
| Treatment protocol |
Germinated seedlings were grown for 1 week in hydroponics with 1ppm arsenate under 12 hr of light as described in Dasgupta T, Hossain SA, Meharg AA and Price AH. (2004) An arsenate tolerance gene on chromosome 6 of rice. New Phytologist 163: 45-49
|
| Growth protocol |
Dasgupta T, Hossain SA, Meharg AA and Price AH. (2004) An arsenate tolerance gene on chromosome 6 of rice. New Phytologist 163: 45-49
|
| Extracted molecule |
total RNA |
| Extraction protocol |
100 mg of root material was pooled from four separate plants and RNA was 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).
|
| |
|
| 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 roots (variety Azucena) grown in hydroponics for one week with 1ppm arsenate, 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.
|
| |
|
| Submission date |
Dec 11, 2006 |
| Last update date |
Dec 11, 2006 |
| 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) |
| GSE4471 |
Expression data from rice varieties Azucena and Bala grown in 0 and 1ppm arsenate |
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