|
| Status |
Public on Feb 10, 2009 |
| Title |
wild type, biological rep1 |
| Sample type |
RNA |
| |
|
| Source name |
15 day old whole seedling
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
wild type control
|
| Growth protocol |
Seeds were germinated and grown vertically in MS 1/5 with Gamborg vitamins. Light condicitions: 16 hours light, 8 hours dark. Temperature: 22ºC. Light 100 μmol m−2 s−1.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the RNeasy plant mini kit (Qiagen).RNA was extracted from three sets of gapcp double mutants and wild type plants grown at the same time. RNA integrity was determined using RNA 6000 Nano Labchips® in an Agilent 2100 Bioanalyzer following the manufactures protocol. The purified RNA (8 μg) was used to generate first-strand cDNA in a reverse transcription reaction (One-Cycle Target Labeling and Control Reagents; Affymetrix). After second-strand synthesis, the double-stranded cDNAs were used to generate cRNA via an in vitro transcriptional reaction.
|
| Label |
biotin
|
| Label protocol |
The cRNA was labeled with biotin, and 20 μg of the labeled cRNA was fragmented. The size distribution of the cRNAs and fragmented cRNAs was assessed using an Eppendorf Biophotometer and electrophoresis.
|
| |
|
| Hybridization protocol |
Fragmented cRNA (15 μg) was added to 300 μL of hybridization solution, and 200 μL of this mixture was used for hybridization on Arabidopsis ATH1 Genome Arrays for 16 h at 45°C. The standard wash and double-stain protocols (EukGE-WS2v5-450) were applied using an Affymetrix GeneChip Fluidics Station 450.
|
| Scan protocol |
The arrays (three replicates of each treatment) were scanned on an Affymetrix GeneChip scanner 3000.
|
| Description |
Gene expression data from embryos younger than nuclear cycle 9, i.e. before zygotic genome activation.
|
| Data processing |
Fluorescence images were normalized with the software GCOS from Affymetrix. Data were analyzed and compared using the dChip software ( http://www.hsph.harvard.edu/~cli/complab/dchip/). A threshold criteria of 2 fold; P value <0.05 was used.
|
| |
|
| Submission date |
Feb 09, 2009 |
| Last update date |
Aug 28, 2018 |
| Contact name |
Roc Ros |
| E-mail(s) |
roc.ros@uv.es
|
| Organization name |
Universitat de Valencia
|
| Department |
Biologia Vegetal
|
| Street address |
Vicent Andres Estelles
|
| City |
Burjassot |
| State/province |
valencia |
| ZIP/Postal code |
46100 |
| Country |
Spain |
| |
|
| Platform ID |
GPL198 |
| Series (1) |
| GSE14765 |
Expression data from Arabidopsis gapcp mutant |
|
| Relations |
| Reanalyzed by |
GSE119083 |
