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Sample GSM270868 Query DataSets for GSM270868
Status Public on Jun 02, 2008
Title Arabidopsis cell culture, 4 h_response to phytoprostane A1_rep2
Sample type RNA
Source name cell culture, 4 h treatment with 75µM phytoprostane A1, second 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
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
Reanalyzed by GSE118579
Reanalyzed by GSE119083

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

Data table
AFFX-BioB-5_at 116.002 P 0.000146581
AFFX-BioB-M_at 140.959 P 4.42873e-05
AFFX-BioB-3_at 91.0538 P 4.42873e-05
AFFX-BioC-5_at 310.442 P 5.16732e-05
AFFX-BioC-3_at 268.417 P 4.42873e-05
AFFX-BioDn-5_at 690.394 P 4.42873e-05
AFFX-BioDn-3_at 887.386 P 4.42873e-05
AFFX-CreX-5_at 2906.16 P 4.42873e-05
AFFX-CreX-3_at 3611.82 P 4.42873e-05
AFFX-DapX-5_at 73.4794 P 4.42873e-05
AFFX-DapX-M_at 138.784 P 0.000126798
AFFX-DapX-3_at 215.616 P 4.42873e-05
AFFX-LysX-5_at 13.2146 P 0.0125468
AFFX-LysX-M_at 10.8434 A 0.147939
AFFX-LysX-3_at 38.5773 P 0.000169227
AFFX-PheX-5_at 20.334 P 0.00618711
AFFX-PheX-M_at 15.484 A 0.0780018
AFFX-PheX-3_at 28.89 P 0.0012475
AFFX-ThrX-5_at 20.2847 P 0.000753643
AFFX-ThrX-M_at 32.989 P 4.42873e-05

Total number of rows: 22810

Table truncated, full table size 680 Kbytes.

Supplementary file Size Download File type/resource
GSM270868.CEL.gz 2.1 Mb (ftp)(http) CEL
GSM270868.CHP.gz 123.6 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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