|
| Status |
Public on Jan 01, 2010 |
| Title |
sln1 mutant, biological rep3 |
| Sample type |
RNA |
| |
|
| Source name |
Department of Agronomy, Washington State University, Pullman, WA, USA
|
| Organism |
Hordeum vulgare |
| Characteristics |
tissue: aleurone
genome/variation: Himalaya, sln1 mutant
age: matured
treatment group: untreated
|
| Treatment protocol |
The aleurones from the half-seeds were isolated and incubated in 10 mmol/L CaCl2 (control), or in the 10 mmol/L CaCl2 solution containing 1 μmol/L GA3 (GA treatment) or 50 μmol/L ABA (ABA treatment). The isolated aleurones were treated in Petri dishes with continuously shaking (60 rpm) in darkness at 25°C, and harvested in 15 hours.
|
| Growth protocol |
The half-seeds without embryos were surface-sterilized and then imbibed in 10 mmol/L CaCl2-saturated paper tissues for three days in darkness at 25°C.To select sln1c homozygotes, the half-seeds with embryos were germinated and transferred to soil to identify the slender phenotype. The selected homozygous sln1c half-seeds without the embryo were imbibed in the same conditions as the wild type but with 5 μmol /L ABA. After imbibition for three days, the aleurones were isolated and washed 3-4 times with 10 mmol/L CaCl2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated according to a LiCl precipitation method.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA.
|
| |
|
| Hybridization protocol |
The labeled cRNA was purified, and 20 μg of the cRNA at a final concentration 0.5 µg/µL was fragmented. The fragmented cRNA (15 μg per hybridization) was used to make up the hybridization cocktail and 10 µg equivalents were hybridized to each GeneChip.
|
| Scan protocol |
The chips were washed and stained with streptavidin-phycoerythrin in the Affymetrix GeneChip fluidics station model 400. The stained chips were immediately scanned with an Agilent 2500A GeneArray scanner.
|
| Description |
Gene expression data from aleurone treated without any hormone
|
| Data processing |
The Microarray Suite (MAS) 5.0 (Affymetrix, Inc.) was used to assign present call (P<0.065) or absent call (P>0.065) for each probe sets.The trimmed mean target intensity of each array was arbitrarily set to 1000. GeneChip RMA (GCRMA) provided in GeneSpring (Agilent Technologies, Palo Alto, CA) was chosen to determine the signal intensity for probe sets for further analysis.
|
| |
|
| Submission date |
Oct 27, 2009 |
| Last update date |
Oct 27, 2009 |
| Contact name |
Kegui Chen |
| E-mail(s) |
kchen@desu.edu
|
| Phone |
608-216-5038
|
| Organization name |
University of Wisconsin
|
| Department |
Department of Agronomy
|
| Lab |
CEREAL CROPS RESEARCH UNIT
|
| Street address |
502 WALNUT STREET
|
| City |
Madison |
| State/province |
WI |
| ZIP/Postal code |
53726 |
| Country |
USA |
| |
|
| Platform ID |
GPL1340 |
| Series (1) |
| GSE18758 |
Microarray data from barley aleurone |
|
