|
| Status |
Public on Jun 20, 2014 |
| Title |
Sorghum leaf_combined_R16_rep2 |
| Sample type |
RNA |
| |
|
| Source name |
Sorghum bicolor leaf, combined stress (3 day water withdrawal then 50 degree incubation for 3 hrs)
|
| Organism |
Sorghum bicolor |
| Characteristics |
variety: R16
age: 14 days after sowing
tissue: Leaf
treatment: Heat&Drought
|
| Treatment protocol |
Plants were subjected either to control (no treatment), heat, drought or combined heat and drought conditions. Drought stress was applied by withholding water from 14 days after sowing. At the point when the photosynthetic efficiency of the un-watered plants first showed a significant difference to the watered plants, they were subject to either heat shock by incubation in the dark at 50 °C for 3 h (heat and combined treatment) or 28 °C for 3 h (control and drought treatment). The youngest 3 leaves were sampled and tissue was pooled for each treatment set.
|
| Growth protocol |
Seeds of Sorghum R16 variety (Sorghum bicolor L. Moench.) were imbibed overnight in water and surface-sown singly onto soaked 42mm Jiffy peat pellets (LBS horticulture Ltd, Lancashire, UK). Seedlings were grown in a controlled growth chamber at 28°C day, 23°C night, 12 h photoperiod, 0% humidity
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using the RNeasy Mini Kit (Qiagen Sussex, UK). The integrity of the RNA was confirmed with analysis by the Agilent 2100 bioanalyzer (Palo Alto, CA) and the Agilent RNA 6000 Nano Kit (Cat no # 5067-1511)
|
| Label |
Cy3
|
| Label protocol |
RNA from Sorghum samples and Agilent One-Color RNA Spike-In RNA were labeled with reagents supplied in the Agilent Quick Amp Labeling Kit, One-Color. The labeled cRNA was then purified with the RNeasy Mini Kit (Qiagen Ltd, Crawley, UK).
|
| |
|
| Hybridization protocol |
The labeled cRNA was hybridized using Agilent's Hybridization Kit to the microarrays. The slides were then washed in Wash Solution 1 (0.005% Triton X-102), Wash Solution 2 (0.005% Triton X-102) acetonitrile and dried using Agilent's Stabilization and Drying Solution
|
| Scan protocol |
The slides were scanned with the Agilent G2505C Microarray Scanner. For data extraction and quality control, the Agilent Feature Extraction Software (v.10.7.3.1) was used.
|
| Description |
3 day not watered, followed by 50C incubation for 3 hrs
|
| Data processing |
Data was processed using default GeneSpring GX12.5 protocol: Threshold: 1.0; Logbase: 2; Data normalisation: shift to 75th percentile; Baseline transformation: median of all samples
|
| |
|
| Submission date |
Jun 21, 2013 |
| Last update date |
Jun 20, 2014 |
| Contact name |
Fei Ling Lim |
| E-mail(s) |
[email protected]
|
| Phone |
+44 (0)1234222450
|
| Organization name |
Unilever
|
| Street address |
Colworth Science Park
|
| City |
Sharnbrook |
| State/province |
Bedfordshire |
| ZIP/Postal code |
MK44 1LQ |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL17335 |
| Series (1) |
| GSE48205 |
Transcriptomic analysis of Sorghum bicolor responding to combined heat and drought stress |
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