|
| Status |
Public on May 05, 2011 |
| Title |
Dark, biological rep1 |
| Sample type |
RNA |
| |
|
| Source name |
Arabidopsis Thaliana under dark
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
stress: Dark
sample type: cell suspension culture
|
| Treatment protocol |
An incubation of 30 min at high light or 1-h at dark were selected as the optimum time to monitor the changes in the transcription profile in the microarray experiments.
|
| Growth protocol |
Arabidopsis cell suspension culture was maintained in 200 mL of liquid growth medium (Jouannea and Peaudlen, 1967; Axelos et al., 1992) by gentle agitation at 120 rpm at 24 ºC under continuous illumination (50 microE/m2/s) in an incubator shaker. Cells were sub-cultured with a 1/20 dilution factor every 7 days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted with the acid guanidine isothiocyanate-phenol-chloroform method using Trizol reagent. Total RNA was treated with TURBO DNase to eliminate traces of contaminating genomic DNA.
|
| Label |
biotin
|
| Label protocol |
Biotin-labelled cRNA was produced by in vitro transcription using GeneChip® 3' IVT Express Kit. The biotin-labelled cRNA was degraded by alkaline digestion and used for hybridization with ATH1 arrays.
|
| |
|
| Hybridization protocol |
Technical steps as target hybridization, washing and staining of the arrays were performed sequentially as described in the Affymetrix GeneChip expression analysis technical manual using the Affymetrix once-cycle target labelling and control reagents, an Affymetrix GeneChip hybridization oven 640, and Affymetrix Fluidics Station 450
|
| Scan protocol |
Microarrays were scanned using Affymetrix GenChip Scanner 3000 7G.
|
| Description |
Gene expression data from Arabidopsis Thaliana under dark
|
| Data processing |
Data was standardized from R using the affy Bioconductor package. Methods: Robust Multi-array Average and quantile normalization.
|
| |
|
| Submission date |
Jul 01, 2010 |
| Last update date |
May 05, 2011 |
| Contact name |
Francisco García García |
| E-mail(s) |
fgarcia@cipf.es
|
| Organization name |
CIPF
|
| Department |
Bionformatics & Biostatistics Unit
|
| Street address |
Eduardo Primo Yúfera, 3
|
| City |
Valencia |
| ZIP/Postal code |
46012 |
| Country |
Spain |
| |
|
| Platform ID |
GPL198 |
| Series (1) |
| GSE22671 |
Gene expression from Arabidopsis under high light conditions |
|
