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| Status |
Public on Jun 30, 2015 |
| Title |
St Col-0 control replicate 1 |
| Sample type |
RNA |
| |
|
| Source name |
St Col-0 control replicate 1
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype: Col-0
tissue: Stomata of leaves
age: 5-week old plants
treatment: 5 weeks under control conditions
|
| Treatment protocol |
Six week old plants were exposed to mild drought stress (5 days). Mild drought stress was applied according to Prasch and Sonnewald, 2013. Harvest of plant material was realized at the end of the light period. After determine the fresh weight of each plant, stomata-specific and total RNA of leaves has been prepared.
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| Growth protocol |
After two days overnight 4°C treatment for stratification plants were grown on soil under short-day conditions (8 h light, 16 h dark), 60% humidity and 22°C (day) or 18/19°C (night). 14 days later young seedlings were further cultivated in single plant pots containing 160g soil and plants were watered with defined volumes of water as described by Prasch and Sonnewald, 2013. Controlled plant cultivation was achieved by a temperature regime followed the light/dark cycle with 22°C/18°C and a diurnal rhythm of 12h of light at approximately 80 µmol m-2 s-2 and exactly 60% humidity at day and night provided by a plant climate chamber (Plant-Master PGR 3045, CLF Plant Climatics GmbH, Germany).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
After plants have been treated with drought stress (5 days) 5-8 plants were grouped for one biological replicate. The stomata extraction procedure was performed as described by Bauer et al., 2013. After sampling, material was immediately frozen in liquid nitrogen. Stomatal RNA was isolated using the RNeasy Plant Mini Kit (www.quiagen.com) according to the manufacturer’s protocol. Two to three biological replicates were used for microarray hybridization.
|
| Label |
Cy3
|
| Label protocol |
Cy3-labeled cRNA were prepared according to the agilent protocol from 80mg total RNA after the method published by Logemann et al. (1987) (One-Color Microarray-based gene expression analysis v.5.5)
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| |
|
| Hybridization protocol |
following fragmentation, 1.65 µg of Cy3-labeled cRNA were hybridisied for 17h at 65°C on 4x44K Agilent Arabidopsis_v4 arrays. Arrays were washed according to the protocol (One-Color Microarray-based gene expression analysis v.5.5)
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| Scan protocol |
Microarrays were scanned using Agilent G2565B Microarray Scanner. Data were extracted using Feature Extraction Version: FE Version 11.7.1 (Agilent Technologies Germany). Data extraction using protocol GE1_v5_95_Feb07
|
| Description |
Experiment3: Stomata-specific gene expression of Col-0 plants after 5 weeks under control conditions
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| Data processing |
After importing text files via feature extraction software (Version 11.7.1; Agilent Technologies) into GeneSpring GX 12.6 (Silicon Genetics) microarray data were log2-transformed followed by normalization to Quantile and corrected to the median of all samples. After applying an one-way ANOVA (p ≤0.05, variance assumed as equal), Volcano plot analysis identified statistically significant (p ≤0.05; equal variances assumed), more than 2-fold differentially expressed genes between two conditions. For each experiment replicates of stressed plants were compared to their respective controls. Under drought stress conditions two to three replicates have been analyzed for each treatment and each genotype.
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| |
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| Submission date |
Jul 10, 2014 |
| Last update date |
Jun 30, 2015 |
| Contact name |
Christian Prasch |
| E-mail(s) |
cprasch@biologie.uni-erlangen.de
|
| Organization name |
FAU Universität Erlangen-Nürnberg
|
| Department |
Biochemistry division
|
| Lab |
Uwe Sonnewald
|
| Street address |
Staudtstrasse 5
|
| City |
Erlangen |
| ZIP/Postal code |
91058 |
| Country |
Germany |
| |
|
| Platform ID |
GPL12621 |
| Series (2) |
| GSE59315 |
ß-amylase1 mutant Arabidopsis plants show improved drought tolerance due to reduced starch breakdown in guard cells |
| GSE59321 |
ß-amylase1 mutant Arabidopsis plants show improved drought tolerance due to reduced starch breakdown in guard cells |
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