|
| Status |
Public on Sep 30, 2009 |
| Title |
Control seed_Rep1 |
| Sample type |
RNA |
| |
|
| Source name |
Well-watered barley plants
|
| Organism |
Hordeum vulgare |
| Characteristics |
organ: Seed
treatment: Control
|
| Treatment protocol |
Drought stress was initiated at Zadok stage 71 (kernel watery-ripe; Zadoks et al., 1974) by withholding water for 4 days. Non-stressed (control) plants received 500 ml water every day.
|
| Growth protocol |
Barley plants (Hordeum vulgare L. cv. Morex) were grown in a controlled environment chamber at 22°C/18°C day/night temperatures, 60% RH and a 16 h photoperiod. Plants were grown in 20 cm x 25 cm pots and fertilized using Osmocote® slow release fertilizer.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA from the lemma, palea and awn was extracted with guanidinium thiocyanate (Chirgwin et al. 1979). Total RNA from the seed was extracted using Tri Reagent (Molecular Research Center Inc., Cincinnati, OH), followed by precipitation of starch with 0.8 M sodium citrate and 1.2 M NaCl according to the manufacturer’s recommendation.
|
| Label |
Biotin
|
| Label protocol |
Biotinylated cRNA was prepared from total RNA according to the the Affymetrix One-Cycle Target Labeling protocol.
|
| |
|
| Hybridization protocol |
The labeled cRNA was purified and fragmented. Then, hybridization controls were added to the resulting cRNA and hybridized to the Barley1 GeneChips for 16 h at 45°C. Arrays were washed using the GeneChip® Fluidics Station 450.
|
| Scan protocol |
GenChips were scanned using the GeneChip® 3000 Scanner.
|
| Description |
Gene expression data from well-watered seed
|
| Data processing |
Cell intensity (CEL) files were imported into Expression Console v 1.1 (Affymetrix) for background correction, normalization and summarization using the Microarray Analysis Suite v 5.0 (MAS5) algorithm. Background intensity was corrected as the difference between the perfect match (PM) and mismatch (MM) pair of each probe set. Summarised values were normalized using global scaling. The mean signal of each array was scaled to 500
|
| |
|
| Submission date |
Aug 17, 2009 |
| Last update date |
Sep 30, 2009 |
| Contact name |
Tilahun Abebe |
| E-mail(s) |
[email protected]
|
| Phone |
319-273-7151
|
| Organization name |
University of Northern Iowa
|
| Department |
Biology
|
| Street address |
191 McCollum Hall
|
| City |
Cedar Falls |
| State/province |
IA |
| ZIP/Postal code |
50614 |
| Country |
USA |
| |
|
| Platform ID |
GPL1340 |
| Series (1) |
| GSE17669 |
Gene expression in the barley spike during drought stress |
|
