|
| Status |
Public on Dec 09, 2010 |
| Title |
WT Shoot-Pi, biological rep3 |
| Sample type |
RNA |
| |
|
| Source name |
shoots from wild type plants grown in media lacking Pi
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: shoots
genotype: wild type
genetic background: Columbia-5
|
| Growth protocol |
Plants were grown for 7 days in solid Johnson medium containing 2% sucrose and either 2mM Pi (KH2PO4) for complete medium (+Pi) or in phosphate-lacking medium (-Pi).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The RNA from root and shoot samples processed separately was isolated using RNeasy plant mini kit from Quiagen
|
| Label |
biotin
|
| Label protocol |
Each RNA preparation was tested for degradation using the Agilent 2100 Bioanalyzer (Agilent technologies, Palo Alto, CA). 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.
|
| |
|
| Hybridization protocol |
10µg of fragmented cRNA were hybridized to the Arabidopsis ATH1 Genome array (Affymetrix, SantaClara, CA), containing 22500 transcript variants from 24000 well -characterized Arabidopsis thaliana genes. 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 |
Gene expression data from shoots of wild type plants grown in Johnson solid media lacking Pi.
|
| 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).
|
| |
|
| Submission date |
Jun 19, 2009 |
| Last update date |
Aug 15, 2018 |
| Contact name |
Regla Bustos |
| Organization name |
CNB-CSIC
|
| Street address |
Darwin 3
|
| City |
Campus de Cantoblanco |
| State/province |
Madrid |
| ZIP/Postal code |
28049 |
| Country |
Spain |
| |
|
| Platform ID |
GPL198 |
| Series (1) |
| GSE16722 |
Expression data from Arabidopsis thaliana under phosphate starvation stress |
|
| Relations |
| Reanalyzed by |
GSE118579 |
