|
| Status |
Public on Jan 24, 2009 |
| Title |
5 mM B(OH)3 treatment (5B) - rep2 |
| Sample type |
RNA |
| |
|
| Source name |
leaf: 5 mM B(OH)3 treatment (5B)
|
| Organism |
Hordeum vulgare |
| Characteristics |
cultivar Hamidiye (Germplasm Name); PO:0009025 leaf, (Organism Part); PO:0007098 LP.02 two leaves visible (Development Stage); 13 days old (Age); hydroponic 1/2 strength hoagland's solution (Growth Media).
|
| Growth protocol |
Growth Description: Aseptical germination and growth on half strength Hoagland’s solution (Hoagland and Arnon, 1950) (pH 5.8) solidified with Phytagel® for 8 days and transfer to sterile hydroponic half strength Hoagland’s solution containing 5 milimolar boric acid (B(OH)3) (5B treatment) Environmental Conditions: 23±2ºC, 16 h light (400 µmol m–2 s–1) and 8 h dark photo-cycle, 70% relative humidity
|
| Extracted molecule |
total RNA |
| Extraction protocol |
TRIzol Reagent (Qiagen) and sodium acetate-ethanol precipitation
|
| Label |
biotin
|
| Label protocol |
Affy-Eukaryotic Target Preparation
|
| |
|
| Hybridization protocol |
Affy- Eukaryotic Target Hybridization
|
| Scan protocol |
Affy- Array Scanning
|
| Description |
Eight day old aseptically grown seedlings were subjected to 5 mM (milimolar) boric acid (B(OH)3) treatment (5B) for 5 days and expression profiles were determined with DNA microarrays using total RNA from leaf tissues
|
| Data processing |
The MAS5.0 Normalization is performed using the justMAS function in the simpleaffy package of Bioconductor (www.bioconductor.org). The target value is 500 for all cases. The code was developed using R2.4.1, Bioconductor 1.9, and simpleaffy 2.8.0. The CDF files were downloaded from the Bioconductor website at http://www.bioconductor.org/packages/release/AffymetrixChip.html. The normalization scripts are available from the PLEXdb team by request.
|
| |
|
| Submission date |
Jan 22, 2009 |
| Last update date |
Jan 23, 2009 |
| Contact name |
PLEXdb Curator, Sudhansu Dash |
| Organization name |
Iowa State University
|
| Department |
Virtual Reality Application Center
|
| Lab |
PLEXdb
|
| Street address |
1023 Crop Genomes Informatics Lab (Iowa State University)
|
| City |
Ames |
| State/province |
IA |
| ZIP/Postal code |
50011 |
| Country |
USA |
| |
|
| Platform ID |
GPL1340 |
| Series (1) |
| GSE14521 |
Late response to boron toxicity in barley leaves |
|
