|
| Status |
Public on Nov 15, 2010 |
| Title |
genetic line: SM89010 - treatment: Mock - rep2 |
| Sample type |
RNA |
| |
|
| Source name |
(genetic line: SM89010 - treated or untreated: Mock)
|
| Organism |
Hordeum vulgare |
| Characteristics |
genetic line: SM89010
tissue: seedling
|
| Growth protocol |
Growth Description: Seedlings were grown in the greenhouse for 9 days. Nine-day old seedlings were inoculated with stem rust isolate TTKS (Ug99), placed in a mist chamber for 16 hours in the dark, then 5 hours of light in the mist chamber, then the greenhouse for 2 hours until harvesting of tissue. Environmental Conditions: St. Paul 2007, Cereal Disease Lab GH#1 & #10
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol RNA extraction followed by RNeasy purification
|
| Label |
biotin
|
| Label protocol |
Affymetrix standard protocol: Eukaryotic Target Preparation
|
| |
|
| Hybridization protocol |
Affymetrix standard protocol: Eukaryotic Target Hybridization
|
| Scan protocol |
Affymetrix standard protocol: Array Scanning
|
| Description |
sm89010 (germplasm name); po: 0009025 (Organism Part); PO:0007098 (Development Stage); 1st leaf; 10 das (Age); garden soil (Growth Media).
Seedlings were grown in the greenhouse for 9 days. Nine-day old seedlings were inoculated (INOC) with stem rust isolate TTKS (Ug99) in Soltrol oil (inoculum per plant weight of 0.25 mg) or just Soltrol oil (MOCK), placed in a mist chamber for 16 hours in the dark, then 5 hours of light in the mist chamber, then the greenhouse for 2 hours until harvesting of tissue.
|
| 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 |
Feb 18, 2010 |
| Last update date |
Nov 15, 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) |
| GSE20416 |
Genetic regulation of gene expression of barley in response to stem rust (Pgt isolate TTKS) |
|
