|
| Status |
Public on Aug 23, 2011 |
| Title |
time: 1 h - treatment: cold (5 C) - rep1 |
| Sample type |
RNA |
| |
|
| Source name |
time: 1 h - treatment: cold (5 C)
|
| Organism |
Vitis vinifera |
| Characteristics |
time point: 1 h
treatment: cold (5 C)
organism part: po: 0009006##
development stage: A vegetative growth PO:0007134
growth media: hydroponic drip 0.1 hoagland
|
| Growth protocol |
Growth Description: plants were grown in a greenhouse with supplemental lighting providing 16 hr light, 8 hr dark (6:30 to 22:30). Day temperature 25-34 C, night 18-20 C. Plants were grown in a hydroponic drip system with LECA (lightweight expanded clay aggregate), and a nutrient solution of modified 0.1 Hoagland with full strength micronutrients. Experimental time 0 was at approximately 9 am.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNeasy Midi
|
| Label |
biotin
|
| Label protocol |
Affy-Eukaryotic Target Preparation
|
| |
|
| Hybridization protocol |
Affy- Eukaryotic Target Hybridization
|
| Scan protocol |
Affy- Array Scanning
|
| Description |
plants were grown in a greenhouse with supplemental lighting providing 16 hr light, 8 hr dark (6:30 to 22:30). Day temperature 25-34 C, night 18-20 C. Plants were grown in a hydroponic drip system with LECA (lightweight expanded clay aggregate), and a nutrient solution of modified 0.1 Hoagland with full strength micronutrients. Experimental time 0 was at approximately 9 am. . Development stage: [4 weeks after pruning 2 year old plants to 4 nodes]. Part of organism: [shoot tips to 4th leaf including leaves, stem, tendrils, buds]. Treatment application type: [temperature shock].
|
| 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 |
Aug 23, 2011 |
| Last update date |
Aug 23, 2011 |
| 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 |
GPL1320 |
| Series (1) |
| GSE31594 |
short term abiotic stress Cabernet Sauvignon |
|
