|
| Status |
Public on Apr 25, 2014 |
| Title |
Wild type, 30μM phosphate, 8 hours. Rep1 |
| Sample type |
RNA |
| |
|
| Source name |
Wild type, 30μM phosphate, 8 hours
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype: Col-0
genotype: Wild Type
supplement: Phosphate (30μM)
time: 8 hours
|
| Treatment protocol |
Plants were transferred to liquid medium supplemented with 30 μM As(V), 30 μM Pi, 1mM Pi (or not supplemented) for indicated times.
|
| Growth protocol |
Plants were grown on Johnson medium with 1 mM Pi (7 days), transferred to -Pi medium (2 days).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated from three independent biological samples for each condition using the RNeasy Plant Mini Kit (Qiagen). Each RNA preparation was tested for degradation using the Agilent 2100 Bioanalyzer (Agilent technologies, Palo Alto, CA).
|
| Label |
Biotin
|
| Label protocol |
cDNA was synthesized from 4 µg of total RNA using One-cycle target labeling and control reagents(Affymetrix, Santa Clara, CA) to produce biotin-labeled cRNA. The cRNA preparations (15 µg) were fragmented at 94ºC for 35 min into 35-200 bases in length.
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| |
|
| Hybridization protocol |
10µg of fragmented cRNA were hybridized to the Arabidopsis ATH1 Genome array (Affymetrix, SantaClara, CA). Each sample was added to a hybridization solution containing 100mM2-(N-morpholino) ethanesulfonic acid, 1M Na+,and 20mM of EDTA in the presence of 0.01% of Tween-20 to a final cRNA concentration of 0.05µg/ml. Hybridization was performed for 16 h at 45ºC . Each microarray was washed and stained with streptavidin-phycoerythrin in a Fluidics station 450 (Affymetrix).
|
| Scan protocol |
Each microarray was scanned at 2.5 µm resolution in a GeneChip® Scanner 3000 7G System (Affymetrix)
|
| Description |
Wild type plants supplemented with 30μM phosphate (8 hours). Replicate 1
|
| Data processing |
Analysis was performed using the affylmaGUI R package (Wettenhall et al, 2006). Robust Muti-array Analysis (RMA) algorithm was used for background correction, normalization and expression levels summarization (Irizarry et al., 2003).
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| |
|
| Submission date |
Jul 19, 2013 |
| Last update date |
Apr 25, 2014 |
| Contact name |
Juan Carlos Oliveros |
| Organization name |
CNB, CSIC
|
| Street address |
Darwin 3
|
| City |
Cantoblanco |
| State/province |
Madrid |
| ZIP/Postal code |
28049 |
| Country |
Spain |
| |
|
| Platform ID |
GPL198 |
| Series (1) |
| GSE49037 |
WRKY6 Transcription Factor Restricts Arsenate Uptake and Transposon Activation in Arabidopsis |
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