Trizol total RNA extraction, Qiagen RNeasy column purification
Label
biotin
Label protocol
Affy-Eukaryotic Target Preparation
Hybridization protocol
Affy- Eukaryotic Target Hybridization
Scan protocol
Affy- Array Scanning
Description
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 were inoculated with a zoospore suspension of 1 x 10 6 spores mL-1 P. graminis in buffer (0.1 g L-1 Phostrogen, 0.5% Bovine serum albumen). 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.
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
Jul 21, 2009
Last update date
Jul 23, 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)
