|
| Status |
Public on Aug 11, 2009 |
| Title |
tissue type: seedling, root - rep3 |
| Sample type |
RNA |
| |
|
| Source name |
tissue type: seedling, root
|
| Organism |
Triticum aestivum |
| Characteristics |
PO:0009005## (Organism Part); root PO:0009005 (Cell type); vegetative growth PO:0007134 (Development Stage); 10 days after planting (Age); vermiculite (Growth Media).
|
| Growth protocol |
Growth Description: Three seeds were planted in a single 10 cm pot containing vermiculite. 20 pots were sown for each replicate. When seedlings reached 10 cm (9-11 cm above surface of vermiculite) they were sampled randomly and vermiculite was removed by washing in RO water. Roots from 10 plants per collection were excised at the base and frozen in liquid Nitrogen.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA Isolation Using Trizol And Qiagen RNAeasy Columns
|
| Label |
biotin
|
| Label protocol |
Affy-Eukaryotic Target Preparation
|
| |
|
| Hybridization protocol |
Affy- Eukaryotic Target Hybridization
|
| Scan protocol |
Affy- Array Scanning
|
| Description |
Three seeds were planted in a single 10 cm pot containing vermiculite. 20 pots were sown for each replicate. When seedlings reached 10 cm (9-11 cm above surface of vermiculite) they were sampled randomly and vermiculite was removed by washing in RO water. Roots from 10 plants per collection were excised at the base and frozen in liquid Nitrogen. Development stage: [10 cm seedling]. Sample type: [root]. Individual genetic trait genotype: [Chinese Spring]. Treatment application type: [No Treatment].
|
| 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 20, 2008 |
| Last update date |
Aug 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) |
| GSE12508 |
Transcription patterns during wheat development |
|
