|
| Status |
Public on Jan 01, 2020 |
| Title |
WT plants under normal growth condition, biological rep3 [re-analysis] |
| Sample type |
RNA |
| |
|
| Source name |
The youngest fully expanded leaves from 2.5-month-old WT plants under normal condition
|
| Organism |
Oryza sativa |
| Characteristics |
genotype background: Oryza sativa ssp. Japonica. cv. Dongjin
genotype/variation: wild type
age: 2.5-month-old
treatment: normal
tissue: fresh leaves
|
| Treatment protocol |
For drought treatment, pairs of 10-week-old osnadk1 and WT plants were each grown in the same pot to ensure an identical water-stress condition. The youngest fully expanded leaf from each osnadk1 and WT plant was harvested 0 and 15 days after the commencement of the drought treatment. At these two time points, the soil moisture percentages were 47.3 ± 1.9% and 8.5 ± 2.1%, respectively.
|
| Growth protocol |
After germination, rice seeds were transferred into a tray and watered daily with Hoagland’s nutrient solution. After 2 weeks, when the fourth leaf of each seedling had fully expanded, every four seedlings was transferred into a plastic pot, which were each filled with 12.5 kg of soil from a paddy field and cultivated in a greenhouse with a day/night temperature cycle of 36 ℃/28℃, light intensity of 800 μmol m-1 s-1, 16 h day/8 h dark, and 60%–65% relative humidity. The seedlings were watered at 2–3 d intervals to keep the soil submerged in water until the drought treatments were applied.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
|
| |
|
| Hybridization protocol |
Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip rice genome arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
|
| Scan protocol |
GeneChips were scanned using the GeneChip Scanner 3000 (P/N 00-00212, Affymetrix)
|
| Description |
BH2010393_2_WT-control-3
|
| Data processing |
The data were read with Command Console Software 3.1 (Affymetrix) and normalized using GeneSpring Software 11.0 (Agilent) and the MAS5.0 algorithm. Data quality was assessed and statistical analysis was performed as described in the Affymetrix GeneChip Expression Analysis and Statistical Algorithms Description Documents. The data were analyzed using Student’s t-test.
|
| |
|
| Submission date |
Jan 22, 2017 |
| Last update date |
Jan 01, 2020 |
| Contact name |
Kunming Chen |
| E-mail(s) |
[email protected]
|
| Organization name |
Northwest A&F University
|
| Department |
College of Life Sciences
|
| Lab |
State Key Laboratory of Crop Stress Biology in Arid Area
|
| Street address |
Xinong Road 22#
|
| City |
Yangling |
| State/province |
Shaanxi |
| ZIP/Postal code |
712100 |
| Country |
China |
| |
|
| Platform ID |
GPL2025 |
| Series (1) |
| GSE93917 |
The NAD kinase OsNADK1 affects the redox and enhances the tolerance to drought in rice |
|
| Relations |
| Reanalysis of |
GSM1315900 |
