|
| Status |
Public on Aug 11, 2009 |
| Title |
tissue type: germinating seed, root - rep2 |
| Sample type |
RNA |
| |
|
| Source name |
tissue type: germinating seed, root
|
| Organism |
Triticum aestivum |
| Characteristics |
PO:0009005## (Organism Part); developing root (Cell type); germination PO:0007057 (Development Stage); 2 days after 2 days after germiniation (Age); 3MM filter paper (Growth Media).
|
| Growth protocol |
Growth Description: Seeds were germinated in 15 cm petri dishes on damp 3MM filter paper in a growth cabnet set at 22oC light for 16 hrs and 16oC dark for 8 hrs. A single plate containing approximately 50 seeds was sown for each replicate. For each collection for each replicate ten seeds with emerging roots and coleoptile were selected. Roots were excised 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 |
Seeds were germinated in 15 cm petri dishes on damp 3MM filter paper in a growth cabnet set at 22oC light for 16 hrs and 16oC dark for 8 hrs. A single plate containing approximately 50 seeds was sown for each replicate. For each collection for each replicate ten seeds with emerging roots and coleoptile were selected. Roots were excised and frozen in liquid Nitrogen. Sample type: [germinating seed]. 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 |
|
