|
| Status |
Public on Aug 27, 2011 |
| Title |
year: 2005 - developmental stage: UD:0000034 33E-L - rep1 |
| Sample type |
RNA |
| |
|
| Source name |
fruit_year 2005_developmental stage: UD:0000034 33E-L
|
| Organism |
Vitis vinifera |
| Characteristics |
germplasm name: clone entav 115
organism part: PO: 0009001 fruit
development stage: UD:0000034 33E-L
growth media: field soil
|
| Extracted molecule |
total RNA |
| Extraction protocol |
hot borate RNA extraction protocol
|
| Label |
biotin
|
| Label protocol |
Affy-Eukaryotic Target Preparation
|
| |
|
| Hybridization protocol |
Affy-Eukaryotic Target Hybridization
|
| Scan protocol |
Affy-Array Scanning
|
| Description |
Ten clusters of Pinot Noir, clone ENTAV 115, were collected on 07/06/2005 (5 weeks post flowering) in the study site "Ai Molini" of the IASMA Institute. 50 berries were randomly detached and immediately frozen. Three sub-pools of 8 berries each were then obtained and regarded as biological replicates. Total RNA was extracted, purified, labelled and used for Affymetrix Vitis GeneChip v1.0 hybridization.
|
| 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 27, 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)
|
| City |
Ames |
| State/province |
IA |
| ZIP/Postal code |
50011 |
| Country |
USA |
| |
|
| Platform ID |
GPL1320 |
| Series (1) |
| GSE31674 |
Pinot Noir berry transcriptome during ripening. |
|
