|
| Status |
Public on Sep 22, 2008 |
| Title |
Nipponbare, 4 days after infection with S. hermonthica, biological replicate #1 |
| Sample type |
RNA |
| |
|
| Source name |
Oryza sativa roots infected with Striga hermonthica at 4 days post-inoculation
|
| Organism |
Oryza sativa Japonica Group |
| Characteristics |
synonym: Oryza sativa subsp. japonica
cultivar: Nipponbare
Age: 25 days
|
| Treatment protocol |
Twenty one day-old seedlings were infected with 25 mg of preconditioned and pre-germinated Striga hermonthica seeds by aligning them along the roots. Control plants were treated in a similar manner (mock-inoculated).
|
| Growth protocol |
Seedlings of the rice cultivars Nipponbare and IAC 165 (Oryza sativa subspecies japonica) were grown for three weeks in a controlled environment growth room under a 14 hour photoperiod with an irradiance of 400 μmol m-2 s-1, a daytime and night-time temperature of 27 oC and 23 oC respectively and 60% relative humidity.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using TRI reagent (Ambion) and then purified using an RNA purification column kit (Qiagen) according to manufacturer’s instructions.
|
| Label |
biotin
|
| Label protocol |
3'IVT Affymetrix protocol using 5 ug total RNA
|
| |
|
| Hybridization protocol |
Following fragmentation, 5 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Rice Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
|
| Scan protocol |
Chips were scanned using an Affymetrix GeneChip scanner 3000 7G
|
| Description |
Gene expression data from Oryza sativa (cultivar Nipponbare) roots infected with Striga hermonthica at 4 days post-inoculation
|
| Data processing |
Data were analysed using Affymetrix GCOS, with global scaling to a target of 100
|
| |
|
| Submission date |
Feb 04, 2008 |
| Last update date |
Sep 22, 2008 |
| Contact name |
Julie Scholes |
| Organization name |
University of Sheffield
|
| Department |
Animal and Plant Sciences
|
| Street address |
Western Bank
|
| City |
Sheffield |
| ZIP/Postal code |
S10 2TN |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL2025 |
| Series (1) |
| GSE10373 |
Rice cultivars undergoing a susceptible and resistant interaction with the parasitic plant Striga hermonthica |
|
