|
| Status |
Public on Oct 07, 2010 |
| Title |
genotype: Excel - time: 3 days - rep2 |
| Sample type |
RNA |
| |
|
| Source name |
seed (genotype: Excel - time: 3 days)
|
| Organism |
Hordeum vulgare |
| Characteristics |
germplasm name: hv cv. excel
organism part: po: 0009010 seed
development stage: PO:0001170 seed
growth media: not specified
age: 3 days
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol RNA extraction followed by RNeasy purification
|
| Label |
biotin
|
| Label protocol |
Affymetrix one-cycle target labeling
|
| |
|
| Hybridization protocol |
Affy- Eukaryotic Target Hybridization
|
| Scan protocol |
Affy- Array Scanning
|
| Description |
Excel grains after 3 days of germination replication 2
|
| 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 |
Oct 05, 2010 |
| Last update date |
Oct 06, 2010 |
| 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 |
GPL1340 |
| Series (1) |
| GSE24534 |
Transcriptome analysis of a breeding program pedigree |
|
