|
| Status |
Public on Jun 01, 2016 |
| Title |
WT P1 |
| Sample type |
RNA |
| |
|
| Source name |
Arabidopsis, leaf, control, replicate 1
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
genotype: wild type Col-0
tissue: leaves
age: 10 weeks
|
| Treatment protocol |
no special treatment, 2 source leaves from 4 different plants formed 1 pool (P), quick frozen with liquid nitrogen
|
| Growth protocol |
Arabidopsis thaliana seeds were sown on soil and stratificated at 4°C for 2 days to synchronize germination. Following stratification, plants were cultivated under short-day conditions (SD; 8 h light at 22°C, 16 h dark at 19°C), 10 weeks old plants
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction after Logemann (1987)
|
| 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)
|
| |
|
| 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)
|
| Scan protocol |
Microarrays were scanned using Agilent G2565B Microarray Scanner. Data were extracted using Feature Extraction Version: FE Version 12.5.1 (Agilent Technologies Germany). Data extraction using protocol GE1_v5_95_Feb07
|
| Description |
Gene expression after 10 weeks under shortday conditions
|
| Data processing |
After importing text files via feature extraction software (Version12.5.1; Agilent Technologies) into GeneSpring GX 11.0 (Silicon Genetics) microarray data were log2-transformed followed by normalization to the 75th percentile and corrected to the median of all samples. The identification of differentially regulated genes between cher1-4, cher1-5 and control plants with >2.0-fold change and P < 0.05 was achieved by using T-test unpaired and Benjamini–Hochberg multiple test correction (Benjamini and Hochberg, 1995).
|
| |
|
| Submission date |
Sep 20, 2014 |
| Last update date |
Jun 01, 2016 |
| Contact name |
Uwe Sonnewald |
| Organization name |
Friedrich-Alexander-University
|
| Department |
Biology, Biochemistry
|
| Street address |
Staudtstr. 5
|
| City |
Erlangen |
| ZIP/Postal code |
91058 |
| Country |
Germany |
| |
|
| Platform ID |
GPL12621 |
| Series (1) |
| GSE61595 |
Choline transporter-like1 is required for plasmodesmal targeting of Potato leafroll virus movement protein MP17 and long-distance assimilate transport |
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