|
| Status |
Public on Jun 11, 2009 |
| Title |
target strand labeled: Antisense - rep1 |
| Sample type |
other |
| |
|
| Source name |
whole plant (target strand labeled: Antisense)
|
| Organism |
Triticum aestivum |
| Characteristics |
Chinese Spring (Germplasm Name); PO:0000003 whole plant, (Organism Part); PO:0007033 whole plant growth stages (Development Stage); peat/perlite/soil (Growth Media).
|
| Growth protocol |
Growth Description: For each tissue type except ‘Germinated seed’, six seeds were planted in 6-inch round pots using a potting mix (6 peat moss: 4 vermiculite with lime: 3 sand: 3 commercial potting mix: 2 perlite: 1.7 g/L lime: 3.3 g/L Osmocote: 2.2 g/L ammonium nitrate). Seedlings were grown to the appropriate growth stages for tissue collection in a greenhouse with a stable temperature of 25±2ºC and a 16 h light/8 h dark cycle.
|
| Extracted molecule |
other |
| Extraction protocol |
Trizol Plus RNA Purification (Invitrogen)
|
| Label |
biotin
|
| Label protocol |
Affy- Whole transcript target preparation
|
| |
|
| Hybridization protocol |
Affy- Eukaryotic Target Hybridization
|
| Scan protocol |
Affy- Array Scanning
|
| Description |
Mixed RNA form 5 tissue types of Chinese Spring wheat cultivar. Tissue types were; i.Germinated seed (germinated on wetted filter paper in a petri-dish in the dark for two days), ii.Shoot (Feekes 1.2, emergence with second leaf unfolded), iii.Flag leaf (Feekes 9.0, flag leaf stage with ligule emerged), iv.Spike pre-anthesis (Feekes 10.5, heading complete), and v.Spike post-anthesis (Feekes 10.5.3, flowering complete to base of spike).
|
| 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 22, 2008 |
| Last update date |
Jun 11, 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 |
GPL3802 |
| Series (1) |
| GSE12528 |
Wheat "Chinese Spring" natural antisense transcription survey |
|
