|
| Status |
Public on Dec 07, 2010 |
| Title |
rosettes_drought_rep2 |
| Sample type |
RNA |
| |
|
| Source name |
vegetative rosettes, water deficit
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
Cultivar:Columbia-0
|
| 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 (reaction at 37C for 16h) from 15 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
|
| |
|
| Hybridization protocol |
Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C, refer to GeneChip Expression Analysis Technical Manual (www.affymetrix.com). GeneChips were washed and stained with streptavidin-phycoerythrin conjugate on an Affymetrix Fluidics Station 450
|
| Scan protocol |
GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G; Pixel size: 1.56 um; Filter: 570 nm
|
| Description |
Soil water deficit stress was imposed on four week old plants by withholding water until plants reached a relative water content (RWC) of 65%.
|
| Data processing |
The data was analysed using Rosetta Resolver 6.0, creating ratio-experiments using control reps as one pool, and treatment reps as the other pool. Resulting log ratios and p-values are calculated using Rosetta's proprietary ratio error model.
|
| |
|
| Submission date |
May 22, 2008 |
| Last update date |
Dec 07, 2010 |
| Contact name |
Jean-Jack M. Riethoven |
| E-mail(s) |
jeanjack@unl.edu
|
| Organization name |
University of Nebraska-Lincoln
|
| Department |
Beadle Center for Biotechnology
|
| Lab |
Bioinformatics Core Research Facility
|
| Street address |
1901 Vine Street
|
| City |
Lincoln |
| State/province |
NE |
| ZIP/Postal code |
68588-0665 |
| Country |
USA |
| |
|
| Platform ID |
GPL198 |
| Series (2) |
| GSE11538 |
The association between gene expression and whole genome histone H3K4 mono-, di, and trimethylation: expression data |
| GSE11658 |
The association between gene expression and whole genome histone H3K4 mono-, di, and trimethylation |
|
