|
Status |
Public on May 09, 2007 |
Title |
Col-O_HL_A |
Sample type |
RNA |
|
|
Source name |
Col-O, 3 hours high light
|
Organism |
Arabidopsis thaliana |
Characteristics |
Col-O, 7 d old seedlings
|
Treatment protocol |
For high light treatment seedlingswere transferred for 3 h 1000 micro mol quanta m-2 s-1 (metal halide HQI-T 400 W daylight light bulbs, Osram).
|
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.
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|
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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.
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Description |
Part of an experiment investigating transcriptome changes in of wt, cry1 and hy5 after high light and in wt after blue light treatment.
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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; (21)). 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.
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|
|
Submission date |
May 03, 2007 |
Last update date |
Aug 28, 2018 |
Contact name |
Tatjana Kleine |
E-mail(s) |
tatjana.kleine@lmu.de
|
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 |