|
| Status |
Public on May 09, 2007 |
| Title |
Col-O_LL_C |
| Sample type |
RNA |
| |
|
| Source name |
Col-O, control
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
Col-O, 7 d old seedlings
|
| Growth protocol |
Arabidopsis thaliana seeds were sterilized (75 % ethanol, 0.01 % Triton X-100) for 15 min and washed three times with 95 % ethanol before spreading onto 0.27 % phytoagar plates containing 1x Murashige and Skoog basal salt mixture including vitamins (Duchefa) and 2 % sucrose. The plates were stratified two days in darkness at 4°C and then placed 7 d into continuous white light (100 micro mol quanta m-2 s-1, 22 °C).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For total RNA isolation the RNeasy Plant Mini Kit (QIAGEN) was used according to the manufacturer’s instructions. The concentration of total RNA was determined with a Nanodrop ND-1000 spectrophotometer; quality of RNA was checked by agarose gel electrophoresis
|
| Label |
Biotin
|
| Label protocol |
5 μg of total RNA was used in a reverse transcription reaction (Ambion MessageAmp kit) to generate first-strand cDNA. After second-strand synthesis, double-stranded cDNA was used in an in vitro transcription reaction to generate biotinylated cRNA. The quality of purified and fragmented cRNA was assessed by spectrophotometry and agarose gel electrophoresis.
|
| |
|
| Hybridization protocol |
15 μg of fragmented, biotinylated cRNA was used for hybridization. Hybridization was performed as in the Affymetrix technical manual.
|
| Scan protocol |
Washing, staining, and scanning procedures were performed as described in the Affymetrix technical manual. A Hybridization Oven 640, a Fluidics Station 450 and a GeneChip Scanner 3000 were used.
|
| Description |
Part of an experiment investigating transcriptome changes in of wt, cry1 and hy5 after high light and in wt after blue light treatment.
|
| Data processing |
Normalization and expression estimate computation were calculated from the .CEL output files from the Affymetrix GCOS 1.1 software using gcRMA implemented in R using standard settings. Statistical testing for differential expression was performed with logit-t analysis (p < 0.025). The .CHP and logit-t files were loaded into GeneSpring 7.3 (Agilent Technologies). Affymetrix present, marginal and absent flags were used as an indicator of whether or not a gene was expressed. Genes called absent in both of the
compared conditions were removed from subsequent analyses.
|
| |
|
| Submission date |
May 03, 2007 |
| Last update date |
Aug 28, 2018 |
| Contact name |
Tatjana Kleine |
| E-mail(s) |
[email protected]
|
| Organization name |
Ludwig-Maximilians-Universität München
|
| Department |
Biologie I, Botanik
|
| Lab |
Dario Leister
|
| Street address |
Großhaderner Straße 2
|
| City |
Planegg |
| ZIP/Postal code |
82152 |
| Country |
Germany |
| |
|
| Platform ID |
GPL198 |
| Series (1) |
| GSE7743 |
Genome-wide gene expression analysis reveals a critical role for CRY1 in the Response of Arabidopsis to High Irradiance |
|
| Relations |
| Reanalyzed by |
GSE118579 |
| Reanalyzed by |
GSE119083 |
