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Sample GSM187245 Query DataSets for GSM187245
Status Public on May 09, 2007
Title Col-O_LL_A
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) 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

Data table header descriptions
ID_REF
VALUE Affymetrix signal value created by GCOS 1.1
ABS_CALL Affymetrix GCOS 1.1 detection call
DETECTION P-VALUE Affymetrix GCOS 1.1 detection P-value

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
AFFX-BioB-5_at 138.445 P 0.000169227
AFFX-BioB-M_at 144.887 P 5.16732e-05
AFFX-BioB-3_at 109.413 P 4.42873e-05
AFFX-BioC-5_at 461.089 P 6.02111e-05
AFFX-BioC-3_at 285.158 P 4.42873e-05
AFFX-BioDn-5_at 890.3 P 4.42873e-05
AFFX-BioDn-3_at 1354.87 P 4.42873e-05
AFFX-CreX-5_at 4076.5 P 4.42873e-05
AFFX-CreX-3_at 5686.93 P 4.42873e-05
AFFX-DapX-5_at 222.842 P 7.00668e-05
AFFX-DapX-M_at 332.28 P 5.16732e-05
AFFX-DapX-3_at 546.61 P 4.42873e-05
AFFX-LysX-5_at 27.1319 P 0.000578906
AFFX-LysX-M_at 36.6849 P 0.00556451
AFFX-LysX-3_at 87.4361 P 6.02111e-05
AFFX-PheX-5_at 44.504 P 0.00110197
AFFX-PheX-M_at 56.0992 P 0.000340305
AFFX-PheX-3_at 72.2139 P 0.000146581
AFFX-ThrX-5_at 71.7051 P 6.02111e-05
AFFX-ThrX-M_at 105.461 P 7.00668e-05

Total number of rows: 22810

Table truncated, full table size 685 Kbytes.




Supplementary file Size Download File type/resource
GSM187245.CEL.gz 1.9 Mb (ftp)(http) CEL
GSM187245.CHP.gz 2.6 Mb (ftp)(http) CHP
Processed data provided as supplementary file

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