|
| Status |
Public on Jul 15, 2008 |
| Title |
Red soft berry C16 from plant 1 cluster distal position, biological rep 2 |
| Sample type |
RNA |
| |
|
| Source name |
grape berry near maturation
|
| Organism |
Vitis vinifera |
| Characteristics |
Cultivar: Cabernet sauvignon
|
| Treatment protocol |
Seleted grape berries were snap frozen upon harvest, prior to RNA extraction.
|
| Growth protocol |
Dormant shoot cuttings of V. vinifera cv. Cabernet Sauvignon clone 15 were collected from a commercial vineyard near Osoyoos, BC, in January, 2006, and then transported on wet ice and stored at 4ºC.For fruit cluster propagation, a technique similar to that reported by Mullins and Rajasekaran (1981) was employed, as follows. The basipetal ends of several cuttings were scored with a razor blade and then placed in heated soil within a 4ºC walk-in cooler to promote root formation but inhibit bud break. After adventitious roots became visible, cuttings were moved to the greenhouse and potted in a mixture of 75% peat and 25% perlite (pH 7.0). On average, after nine days at 20-25ºC under a 16 h photoperiod, bud break occurred and a single cluster formed on the resulting shoot. Two shoots bearing healthy clusters were selected for experimentation.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated as described in Reid et al. 2006 (PMID: 17105665). One RNA extraction was done for each of 32 berries.
|
| Label |
biotin
|
| Label protocol |
Biotin -labeled cRNA was prepared according to the manufacturer’s protocol (Affymetrix, Santa Clara, CA).
|
| |
|
| Hybridization protocol |
Following fragmentation, 14 µg of cRNA from one berry was hybridized for 16 hr at 45ºC on each GeneChip Vitis (Grape) Genome Arrays . GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
|
| Scan protocol |
GeneChips were scanned with an Affymetrix GeneArray 3000 7G scanner.
|
| Description |
One goal of this study was to determine the association between the global transcriptome state and phenotypic variables frequently used in berry staging such as color and firmness, so we defined the four time-points (development series) by color/firmness combinations: green hard (GH), green soft (GS), pink soft (PS) and red soft (RS)
|
| Data processing |
The raw data were background adjusted, normalized and log2-transformed using the Bioconductor GCRMA package.
|
| |
|
| Submission date |
May 09, 2008 |
| Last update date |
Jul 15, 2008 |
| Contact name |
Steven T. Lund |
| E-mail(s) |
stlund@interchange.ubc.ca
|
| Phone |
604-822-5708
|
| Fax |
604-822-5143
|
| URL |
http://www.landfood.ubc.ca/wine/lund/lund.html
|
| Organization name |
The University of British Columbia
|
| Department |
Wine Research Centre
|
| Street address |
241 - 2205 East Mall
|
| City |
Vancouver |
| State/province |
BC |
| ZIP/Postal code |
V6T 1Z4 |
| Country |
Canada |
| |
|
| Platform ID |
GPL1320 |
| Series (1) |
| GSE11406 |
Expression data in individual grape berries during ripening initation |
|
