Trizol total RNA extraction, Qiagen RNeasy column purification
Affy-Eukaryotic Target Preparation
Affy- Eukaryotic Target Hybridization
Affy- Array Scanning
regina (germplasm name); po: 0009005 root, (Organism Part); PO:0007520 root development stages (Development Stage); sand (Growth Media). Four day old barley cv. Regina roots inoculated with zoospore-free buffer (0.1 g L-1 Phostrogen, 0.5% Bovine serum albumen) as mock inoculation control. Sample prepared for roots collected from ten seedlings from each of the ten time points (15’, 30’, 45’ 1h, 2h, 3h, 4h, 5h, 6h, 7h) were combined for each treatment to give a time course pool. RNA was extracted from this time course pool and used for subsequent experiments.
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.
Jul 21, 2009
Last update date
Jul 23, 2009
PLEXdb Curator, Sudhansu Dash
Iowa State University
Virtual Reality Application Center
1023 Crop Genomes Informatics Lab (Iowa State University)