|
| Status |
Public on Apr 02, 2010 |
| Title |
AP1-GRap1cal_12hr Dex vs. Mock_set3 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
AP1-GRap1cal_12hr Dex_set3
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
genome/variation: AP1-GR ap1 cal inflorescences
treatment group: Dex
treatment time: 12hr
|
| Treatment protocol |
For all experiments, we used approximately 4 week-old 35S:AP1-GR ap1-1 cal-1 plants. For each sample, inflorescence tissue from ~25 plants was collected using jeweler’s forceps. Four biologically independent sets of samples were generated. Inflorescences were treated with a solution containing 10 μM dexamethasone (Sigma-Aldrich), 0.01% (v/v) ethanol, and 0.015% (v/v) Silwett L-77 (De Sangosse), or with an identical mock solution that lacked dexamethasone. We then collected inflorescence tissue after 2, 4, 8, and 12 hours, as well as from untreated plants (0 hour time point).
|
| Growth protocol |
Plants were grown on a soil:vermiculite:perlite (2:1:1) mixture at 20ºC under constant illumination with cool white fluorescent light.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from tissue samples using the Plant Total RNA kit (Sigma-Aldrich) according to the manufacturer’s instructions. Quality of RNA samples was evaluated using a Bioanalyzer and a RNA Nano 6000 kit (Agilent). RNA concentrations were determined using a Nanodrop ND-1000 spectrophotometer (Thermo Fisher Scientific).
|
| Label |
Cy3
|
| Label protocol |
Agilent microarrays were used following manufacturer's instructions. RNA samples were labeled with fluorescent dyes using the Quick Amp Labeling Kit (Agilent).
|
| |
|
| Channel 2 |
| Source name |
AP1-GRap1cal_12hr Mock_set3
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
genome/variation: AP1-GR ap1 cal inflorescences
treatment group: Mock
treatment time: 12hr
|
| Treatment protocol |
For all experiments, we used approximately 4 week-old 35S:AP1-GR ap1-1 cal-1 plants. For each sample, inflorescence tissue from ~25 plants was collected using jeweler’s forceps. Four biologically independent sets of samples were generated. Inflorescences were treated with a solution containing 10 μM dexamethasone (Sigma-Aldrich), 0.01% (v/v) ethanol, and 0.015% (v/v) Silwett L-77 (De Sangosse), or with an identical mock solution that lacked dexamethasone. We then collected inflorescence tissue after 2, 4, 8, and 12 hours, as well as from untreated plants (0 hour time point).
|
| Growth protocol |
Plants were grown on a soil:vermiculite:perlite (2:1:1) mixture at 20ºC under constant illumination with cool white fluorescent light.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from tissue samples using the Plant Total RNA kit (Sigma-Aldrich) according to the manufacturer’s instructions. Quality of RNA samples was evaluated using a Bioanalyzer and a RNA Nano 6000 kit (Agilent). RNA concentrations were determined using a Nanodrop ND-1000 spectrophotometer (Thermo Fisher Scientific).
|
| Label |
Cy5
|
| Label protocol |
Agilent microarrays were used following manufacturer's instructions. RNA samples were labeled with fluorescent dyes using the Quick Amp Labeling Kit (Agilent).
|
| |
|
| |
| Hybridization protocol |
Agilent microarrays were used following manufacturer's instructions. Microarray hybridizations (65ºC, 16h) and washes were performed with Agilent reagents and following standard protocols.
|
| Scan protocol |
Microarrays were scanned using an Agilent DNA Microarray Scanner G2565CA, and data were acquired using Agilent's Feature Extraction Software version 9.5.3.1.
|
| Description |
GEC_251778410017_S01_GE2-v5_95_Feb07_1_4.txt
|
| Data processing |
Data were processed with the Resolver version 7.1 data analysis system (Rosetta Biosoftware, Seattle, WA), using the Agilent Ratio data processing pipeline with default settings. Resolver uses an error model-based approach to stabilize the variance estimation to improve the specificity and sensitivity in differential gene expression detection (Weng, L., Dai, H., Zhan, Y., He, Y., Stepaniants, S.B., and Bassett, D.E. (2006). Rosetta error model for gene expression analysis. Bioinformatics 22, 1111-1121).
|
| |
|
| Submission date |
Feb 01, 2010 |
| Last update date |
Jun 14, 2013 |
| Contact name |
Jose Luis Riechmann |
| E-mail(s) |
joseluis.riechmann@cragenomica.es
|
| Organization name |
Center for Research in Agricultural Genomics
|
| Street address |
Campus UAB - Edifici CRAG
|
| City |
Bellaterra |
| State/province |
Barcelona |
| ZIP/Postal code |
08193 |
| Country |
Spain |
| |
|
| Platform ID |
GPL9982 |
| Series (2) |
| GSE20139 |
Ath_Agilent_v1_Riechmann array expression profile AP1-GR ap1cal inflorescences - time series (hours) |
| GSE20184 |
Orchestration of floral initiation by APETALA1 |
|
