|
| Status |
Public on Jul 16, 2009 |
| Title |
Pokkali root, salt-treated, biological replicate 1 |
| Sample type |
RNA |
| |
|
| Source name |
root, Pokkali, salt-treated
|
| Organism |
Oryza sativa Indica Group |
| Characteristics |
salt-tolerant
|
| Treatment protocol |
On day 22 after germination, salt treatment commenced by adding NaCl and CaCl2 (5:1 molar concentration) in two steps over a period of 3 days to the nutrient solution reservoir. Salinity in the treatment reservoir reached 7.4 dS/m. Plants were harvested on day 30.
|
| Growth protocol |
Plants were grown in sand-filled tanks and irrigated with nutrient solution (for details see Walia et al (2005), Plant Physiol. 139:822-35) for 30 days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using TRIzol and subsequently purified using an RNeasy spin column (Qiagen) and an on-column DNase treatment.
|
| Label |
biotin
|
| Label protocol |
Approx. 8 µg of total RNA was processed to produce biotinylated cRNA targets.
|
| |
|
| Hybridization protocol |
Standard Affymetrix procedures.
|
| Scan protocol |
Standard Affymetrix procedures.
|
| Description |
Pokkali salt-treated
|
| Data processing |
The data were normalized using the Robust Multichip Average method of background correction, quantile normalisation, and summarisation of cell signal intensities (Irrizary et al., 2003).
|
| |
|
| Submission date |
Jan 13, 2009 |
| Last update date |
Mar 11, 2009 |
| Contact name |
Ute Baumann |
| E-mail(s) |
ute.baumann@adelaide.edu.au
|
| Phone |
++61 8 83037388
|
| Organization name |
University of Adelaide
|
| Department |
Australian Centre for Plant Functional Genomics
|
| Street address |
Hartley Grove
|
| City |
Glen Osmond |
| State/province |
SA |
| ZIP/Postal code |
5064 |
| Country |
Australia |
| |
|
| Platform ID |
GPL2025 |
| Series (1) |
| GSE14403 |
Root-specific transcriptional profiling of contrasting rice genotypes in response to salinity stress |
|
