|
| Status |
Public on Aug 11, 2009 |
| Title |
tissue type: 22 DAP embryo - rep2 |
| Sample type |
RNA |
| |
|
| Source name |
tissue type: 22 DAP embryo
|
| Organism |
Triticum aestivum |
| Characteristics |
PO:0009010## (Organism Part); seed PO:0009010 (Cell type); seed development stages PO:0001170 (Development Stage); 1 after planting (Age); Cereal mix (Growth Media).
|
| Growth protocol |
Growth Description: 20 cm pots were sown with 2 seeds at a depth of 2 cm. 14 days after germination the weaker seedling was removed. Plants were grown at 16hrs light 22oC, 8 hrs dark 16oC. 22 days after pollination the central floret was removed from 10 spikes per collection and the embryo was 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 |
20 cm pots were sown with 2 seeds at a depth of 2 cm. 14 days after germination the weaker seedling was removed. Plants were grown at 16hrs light 22oC, 8 hrs dark 16oC. 22 days after pollination the central floret was removed from 10 spikes per collection and the embryo was frozen in liquid Nitrogen. Development stage: [embryo 22 DAP]. Sample type: [embryo]. 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 |
|
