|
| Status |
Public on Sep 16, 2008 |
| Title |
protocol: Cot filtration (CF) - genotype: Mo17 maize inbred - rep1 |
| Sample type |
genomic |
| |
|
| Source name |
leaf (protocol: Cot filtration (CF) - genotype: Mo17 maize inbred)
|
| Organism |
Zea mays |
| Characteristics |
Mo17 (Germplasm Name); PO:0009025 leaf, (Organism Part); PO:0007134 A vegetative growth, PO:0007071 2.02 main shoot and axillary shoots visible at two nodes (Development Stage); 2 week old (Age); Scotts MetroMix 200 (Growth Media).
|
| Growth protocol |
Growth Description: glasshouse
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cot Filtration (CF)
|
| Label |
biotin
|
| Label protocol |
BioPrime DNA labeling system for CF/MF
|
| |
|
| Hybridization protocol |
Affy- Eukaryotic Target Hybridization
|
| Scan protocol |
Affy- Array Scanning
|
| Description |
Plants grown in glasshouse for 2 weeks. Array data is low quality. The data has low correlation (0.5) with other Mo17-CF arrays.
|
| 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 |
Sep 13, 2008 |
| Last update date |
Sep 15, 2008 |
| 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 |
GPL4032 |
| Series (1) |
| GSE12770 |
Evaluation of Target Preparation Methods for Single-Feature Polymorphism Detection in Large Complex Plant Genomes |
|
