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Sample GSM270866 Query DataSets for GSM270866
Status Public on Jun 02, 2008
Title Arabidopsis cell culture, 4 h_response to phytoprostane A1_rep1
Sample type RNA
 
Source name cell culture, 4 h treatment with 75µM phytoprostane A1, first replicate
Organism Arabidopsis thaliana
Characteristics mixotrophic cell culture, 4 h treatment with 75 µM phytoprostane A1
Extracted molecule total RNA
Extraction protocol For microarray analysis total RNA was extracted using the RNeasy plant mini kit (Qiagen) according to the manufacturer’s protocol.
Label biotin
Label protocol 1 µg of total RNA was linearly amplified and biotinylated using the One-Cycle Target Labeling Kit (Affymetrix, Santa Clara, CA) according to the manufacturer’s instructions. Labelling and hybridization were conducted by the microarray facility of the Universitaetsklinikum Tuebingen, Germany.
 
Hybridization protocol 15 µg of labeled and fragmented cRNA was hybridized to Arabidopsis ATH1 Gene Chip® arrays (Affymetrix). After hybridization the arrays were washed and stained in a Fluidics Station 450 (Affymetrix) with the recommended washing procedure. Biotinylated cRNA bound to target molecules was detected with streptavidin-coupled phycoerithrin, biotinylated anti-streptavidin IgG antibodies and again streptavidin-coupled phycoerithrin according to the protocol.
Scan protocol Arrays were scanned using the GCS3000 Gene Chip scanner (Affymetrix) and GCOS 1.3 software. Scanned images were subjected to visual inspection to control for hybridization artifacts and proper grid alignment and analyzed with Microarray Suite 5.0 (Affymetrix) to generate report files for quality control.
Description Three independent replicates were done for each treatment.
Data processing For statistical data analysis the CEL-files were imported into Genespring 7.1 (Agilent Technologies, Santa Clara, CA) using Genesprings implementation of GC-RMA for normalization and probe summarization (Wu et al., 2003). Additionally, genes were median centered by dividing all signal values for a gene by the median of all signals for that gene. Transcripts with a high variance in replicate measurements were removed. From the remaining set genes that show an at least two-fold increase or decrease in average expression were analyzed in a Welsh’s t-test for significant differences and corrected for multiple testing according to Benjamini and Hochberg (1995). Functions of differentially expressed transcripts were annotated using the NetAFFX analysis center.
 
Submission date Mar 04, 2008
Last update date Aug 28, 2018
Contact name Susanne Berger
E-mail(s) berger@biozentrum.uni-wuerzburg.de
Phone 49 931 318 6170
Organization name Julius-von-Sachs-Institute
Department Pharmaceutical Biology
Street address Julius-von-Sachs-Platz 2
City Wuerzburg
ZIP/Postal code 97082
Country Germany
 
Platform ID GPL198
Series (2)
GSE10719 Response of Arabidopsis cell culture to phytoprostane A1
GSE10749 Response of Arabidopsis cell culture to cyclopentenone oxylipins
Relations
Reanalyzed by GSE118579
Reanalyzed by GSE119083

Data table header descriptions
ID_REF
VALUE value
ABS_CALL detection call
DETECTION P-VALUE detection p-value

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
AFFX-BioB-5_at 78.898 P 0.00141043
AFFX-BioB-M_at 72.9929 P 6.02111e-05
AFFX-BioB-3_at 45.4278 P 0.000195116
AFFX-BioC-5_at 201.314 P 6.02111e-05
AFFX-BioC-3_at 173.913 P 6.02111e-05
AFFX-BioDn-5_at 437.198 P 4.42873e-05
AFFX-BioDn-3_at 630.231 P 4.42873e-05
AFFX-CreX-5_at 2247.22 P 4.42873e-05
AFFX-CreX-3_at 3287.7 P 4.42873e-05
AFFX-DapX-5_at 63.256 P 9.4506e-05
AFFX-DapX-M_at 166.501 P 0.000126798
AFFX-DapX-3_at 253.932 P 4.42873e-05
AFFX-LysX-5_at 11.0555 M 0.0584438
AFFX-LysX-M_at 15.769 A 0.275146
AFFX-LysX-3_at 38.7201 P 4.42873e-05
AFFX-PheX-5_at 22.322 M 0.0542134
AFFX-PheX-M_at 23.1609 P 0.0044838
AFFX-PheX-3_at 39.5364 P 0.00687065
AFFX-ThrX-5_at 26.9718 P 0.00110197
AFFX-ThrX-M_at 34.8128 P 0.000146581

Total number of rows: 22810

Table truncated, full table size 678 Kbytes.




Supplementary file Size Download File type/resource
GSM270866.CEL.gz 2.2 Mb (ftp)(http) CEL
GSM270866.CHP.gz 123.4 Kb (ftp)(http) CHP
Processed data included within Sample table
Raw data provided as supplementary file
Processed data provided as supplementary file

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