germplasm name: cabernet sauvignon organism part: PO 0009001 fruit development stage: UD 0000039 38E-L age: 6 tissue: fruit growth media: field soil
Extracted molecule
total RNA
Extraction protocol
Tris-LiCl
Label
biotin
Label protocol
Affymetrix one-cycle target labeling
Hybridization protocol
Affymetrix GeneChip Hyb
Scan protocol
GeneChip Expression Wash
Description
Uninfected and GLRaV-3-infected V. vinifera cv. Cabernet Sauvignon grapevines were obtained from the nursery of the Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile. Four uninfected and three virus infected vines were maintained separately in the field under similar growing conditions in the same experimental block. Uninfected plants in this study were defined as plants without any detectable levels of the following thirteen viruses as determined by RT-PCR: Grapevine virus A (GVA), Grapevine virus B (GVB), Grapevine fanleaf virus (GFLV), Grapevine fleck virus (GFkV), Tomato ringspot virus (ToRSV), Grapevine rootstock stem lesion associated virus (GRSLaV) and Grapevine leaf-roll-associated viruses (GLRaV) 1, 2, 3, 4, 5, 6 and 7. In addition, all uninfected plants were free of bacterial, fungal or viroids disease symptoms.
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
Aug 25, 2011
Last update date
Aug 26, 2011
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)
