|
| Status |
Public on Nov 15, 2007 |
| Title |
Mock day 3 (day3E1) |
| Sample type |
RNA |
| |
|
| Source name |
inflorescence tips, 3 days after mock-treatment
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
ap1-1 and cal-1, 35S:AGGR background, L-er accession, grown in controlled environment room at 18 C, 16h light/8h dark
|
| Treatment protocol |
Dexamethasone (Sigma, stock solution 10 mM in ethanol) was used at a final concentration of 10 μM in Silwet L-77 0.015%, applied directly on the inflorescence tips; for mock treatments, the solution contained the same amount of ethanol (0.1%) and Silwet L-77. After treatment, RNA was extracted from inflorescence apices and stored at -70 C until activation of AGGR was confirmed (2 weeks later).
|
| Growth protocol |
Plants were grown on a mix of vermiculite:soil:sand at 18°C with 16 hours light/8 hours dark cycles.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using TRI reagent (Sigma) according to the manufacturer’s instructions. For array hybridisation, the RNA was cleaned up with RNeasy columns (Qiagen) and precipitated to increase final concentration.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
|
| |
|
| Hybridization protocol |
Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 50C on GeneChip Arabidopsis ATH1 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
|
| Scan protocol |
GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
|
| Description |
mock treatment was ethanol 0.1%, Silwet L-77 0.015%
|
| Data processing |
The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500. To calculate p-values for expression changes after steroid treatmen at each time point, the Wilcoxon signed-rank test was applied to each of the four pairwise combinations of steroid-treated X control sample, using MAS 5.0.
|
| |
|
| Submission date |
Nov 14, 2007 |
| Last update date |
Aug 28, 2018 |
| Contact name |
Robert Sablowski |
| E-mail(s) |
robert.sablowski@jic.ac.uk
|
| Phone |
+44 1603 450530
|
| Organization name |
JIC
|
| Department |
CDB
|
| Street address |
The John Innes Centre
|
| City |
NORWICH |
| State/province |
Norfolk |
| ZIP/Postal code |
NR4 7UH |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL198 |
| Series (1) |
| GSE9605 |
Target genes of AGAMOUS during early flower development in Arabidopsis |
|
| Relations |
| Reanalyzed by |
GSE118579 |
| Reanalyzed by |
GSE119083 |
