|
| Status |
Public on Dec 10, 2010 |
| Title |
WT mock treated_biological rep 2 |
| Sample type |
RNA |
| |
|
| Source name |
4 day old seedlings, mock-treated 10 hr
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype: Columbia
tissue: whole seedling
agent: control
biological rep: 2
|
| Treatment protocol |
Plates were flooded with water or 7 mM dicamba (Cadence 0.325 g/mole, Syngenta) for 40 minutes. The treatments were poured off and the plates incubated for an additional 9 hr 20 min at RT.
|
| Growth protocol |
WT (a Columbia line containing a -800GSTF8::LUC reporter) Arabidopsis seeds were surface sterilzed and sown on MS-media plates. Plates were vernalized 3 days at 4C in dark before being transferred to controlled growth room set at 21ºCwith a 16 hour ligh
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using the Qiagen RNeasy Mini Kit, following the manufacturer’s instructions.
|
| Label |
Biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
|
| |
|
| Hybridization protocol |
cRNA was hybridized to the GeneChip® Arabidopsis ATH1 Genome Array using a Genechip instrument system with scanner 3000 7G and autoloader for expression array processing and analysis, following manufacturer's protocol. Labeling, hybing and scanning were
|
| Scan protocol |
Genechips were scanned Affymetrix GeneChip scanner 3000 7G
|
| Description |
Gene expression data from WT seedlings that contain the GSTF8::LUC reporter treated with water (mock)
|
| Data processing |
The raw data files underwent background correction, normalization, probe specific correction, and summary value computation using the Robust Multichip Average (RMA) method in the Bioconductor package. To find the differentially expressed genes we utilized the limma package for R to calculate the Log2 fold change, the moderate t-statistic, B value, and the adjusted p value (BenjaminiHochberg FDR) for each array probe.
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| |
|
| Submission date |
Sep 09, 2010 |
| Last update date |
Dec 10, 2010 |
| Contact name |
Cynthia Gleason |
| E-mail(s) |
cynthia.gleason@csiro.au
|
| Phone |
+61 08 9333 6358
|
| Organization name |
CSIRO
|
| Department |
Plant Industry
|
| Street address |
Private Bag #5
|
| City |
Wembley |
| State/province |
WA |
| ZIP/Postal code |
6319 |
| Country |
Australia |
| |
|
| Platform ID |
GPL198 |
| Series (1) |
| GSE24052 |
Expression data in whole Arabidopsis seedlings after treatment with the herbicide dicamba |
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