|
| Status |
Public on Feb 02, 2008 |
| Title |
7% SWC rep3 |
| Sample type |
RNA |
| |
|
| Source name |
crown
|
| Organism |
Hordeum vulgare |
| Characteristics |
drought treatment
|
| Treatment protocol |
Drought treatment began seven days after sowing and lasted for 21 days. Soil Water Content (SWC) was calculated relative to the field capacity of the soil by weighing at regular intervals. Control (91 % SWC) and stressed samples were collected at soil water contents of approximately 68%, 38%, 20%, 11% and 9% SWC.
|
| Growth protocol |
Barley (Hordeum vulgare) cv. Morex plants were grown in steam-sterilized soil in a growth chamber (Model GC-15, EGC Chagrin Falls, OH) with 12 h photopheriod (148 µmol m-2 s-1 average photosynthetic active radiation) at 23ºC, 12 h dark at 20ºC and 70% relative humidity.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using TRIzol reagent (Invitrogen) from frozen crown samples taken from above soil tissue excluding most fully extended lamina. The protocol is available on the Arabidopsis Information Resource website at http://www.arabidopsis.org/info/2010_projects/comp_proj/AFGC/RevisedAFGC/site2RnaL.htm. RNA was purified using Qiagen RNeasy spin columns with DNase treatment. Quality was assessed by running 25-250 ng on a RNA Lab-On-A-Chip (Caliper Technologies) using an Agilent Bioanalyzer 2100 (Agilent Technologies).
|
| Label |
Biotin
|
| Label protocol |
The BioArray High-Yield RNA Transcript Labeling Kit (Enzo Diagnostics) was then used to synthesize biotin-labeled cRNA from template cDNA by in vitro transcription.
|
| |
|
| Hybridization protocol |
10 µg labeled, fragmented cRNA was hybridized at 45°C with rotation for 16 hours in an Affymetrix GeneChip Hybridization Oven 320 on Affymetrix Barley1 Genechip arrays. The arrays were washed and stained using streptavidin phycoerythrin on an Affymetrix Fluidics Station 400.
|
| Scan protocol |
The arrays were scanned on a Hewlett-Packard GeneArray scanner.
|
| Description |
drought treatment
|
| Data processing |
MAS files from the GCOS software were used for determining the ‘present’ gene list. Probe set intensity values above the level set by the gcRMA normalization processor were imported into GeneSpring GX 7.3 software (Silicon Genetics, CA, USA), which was used for the rest of the analysis.
|
| |
|
| Submission date |
Feb 08, 2007 |
| Last update date |
Jul 13, 2007 |
| Contact name |
Livia Tommasini |
| E-mail(s) |
liviat@ucr.edu
|
| Phone |
951 827 3808
|
| Fax |
951 827 4437
|
| URL |
http://plantbiology.ucr.edu/research_areas/?genomics
|
| Organization name |
University of California, Riverside
|
| Department |
Botany and Plant Science
|
| Lab |
Tim Close
|
| Street address |
2150 Batchelor Hall
|
| City |
Riverside |
| State/province |
CA |
| ZIP/Postal code |
92521-0124 |
| Country |
USA |
| |
|
| Platform ID |
GPL1340 |
| Series (1) |
|
