|
| 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.
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| |
|
| 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 |
