|
| Status |
Public on Aug 26, 2011 |
| Title |
Rosette of vtc2, biological rep3 (I) |
| Sample type |
RNA |
| |
|
| Source name |
Rosette of vtc2, 42 days old
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: rosette
age: 42 days old
genotype: vtc2 (vitamin C defective 2)
|
| Treatment protocol |
Whole rosettes were harvested at the indicated stage, frozen in liquid nitrogen and stored at −80°C.
|
| Growth protocol |
Arabidopsis thaliana was grown on compost in controlled conditions. 10 h day, 60 % RH, 22 °C constant temperature, light intensity 350 µmol/ m2 s
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using RNeasy Plant Mini Kit (Qiagen) according to manufacturer’s protocol.
|
| Label |
Biotin
|
| Label protocol |
Double-stranded cDNA was generated from each of the seventeen total-RNA samples and transcribed to obtain biotin-labeled cRNA.
|
| |
|
| Hybridization protocol |
The target cRNAs were fragmented, combined with hybridization and spike controls, then hybridized to the Genechip Arabidopsis ATH1 Genome Array (Affymetrix, Inc., Santa Clara, CA) for 16 h. Following hybridization, the arrays were washed and stained with streptavidin phycoerythrin conjugate using an automated GeneChip® Fluidics Station 450
|
| Scan protocol |
GeneChips were scanned with a GeneChip® Scanner 3000 7G using a 570 nm excitation wavelength laser. Microarray quality controls were assessed using GeneChip® Operating Software (Affymetrix)..
|
| Description |
Gene expression data from rosette of vtc2.
|
| Data processing |
Raw intensity values from the scanned Arabidopsis ATH1 Genome Arrays were analyzed using RMAExpress .
A significance test was undertaken by calculating a null hypothesis through a permuted modified t-statistic across the replicates for each array comparison. The log2 means of the normalized intensity values of the biological replicates were compared as ratios, where a log2 ratio of ±1.0 and a p-value of < 0.05 was selected as worthy of further study.
|
| |
|
| Submission date |
Jul 29, 2010 |
| Last update date |
Aug 15, 2018 |
| Contact name |
Pavel Kerchev |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Leeds
|
| Street address |
Faculty of Biological Sciences University of Leeds
|
| City |
Leeds |
| ZIP/Postal code |
LS2 9JT |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL198 |
| Series (2) |
| GSE23329 |
Transcriptome analysis of vtc2, abi4-102 and the corresponding double mutant abi4 vtc2 |
| GSE23331 |
Ascorbic acid-dependent regulation of growth involves abscisic acid signalling through ABI-4 |
|
| Relations |
| Reanalyzed by |
GSE118579 |
