germplasm name: cv. nipponbare organism part: PO:0009006 shoot development stage: PO:0007106 LP.03 three leaves visible age: 2 weeks after sowing growth media: LC-1 Soil Mix
Extracted molecule
total RNA
Extraction protocol
Hot Phenol/Guanidine Thiocyanate and RNeasy Clean up
Label
biotin
Label protocol
Affy-Eukaryotic Target Preparation
Hybridization protocol
Affy- Eukaryotic Target Hybridization
Scan protocol
Affy- Array Scanning
Description
R2XOO24H Replication 2, Xoo-inoculated rice, tissue collected at 24HAI
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
Jun 24, 2009
Last update date
Jun 25, 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)
