|
| Status |
Public on Nov 01, 2014 |
| Title |
Berry_pulp_25˚brix |
| Sample type |
RNA |
| |
|
| Source name |
Vitis vinifera L. cv. Cabernet Sauvignon (clone 8 scion on 1130 Paulsen rootstock) berry pulp
|
| Organism |
Vitis vinifera |
| Characteristics |
cultivar: Cabernet Sauvignon (clone 8 scion on 1130 Paulsen rootstock)
tissue: berry pulp
brix level: 25
year: 2008
vineyard name: J. Lohr Vineyards & Wines
vineyard location: Paso Robles, CA, USA
|
| Treatment protocol |
IBMP concentrations of berries during maturation were determined. Twenty bunches per row were picked at each harvest date. Samples were collected from six assigned rows at each harvest date in the first five harvest dates and from three assigned rows in the last harvest. Two clusters per vine were sampled from the west arm on the cordon every ten plants (six biological replicates per harvest date). Clusters were carried in a cooler with dry ice to the laboratory and stored at -80 °C until analysis.
|
| Growth protocol |
A vineyard from a commercial winery (J. Lohr Vineyards & Wines) in Paso Robles, CA, planted with Vitis vinifera L. cv. Cabernet Sauvignon (clone 8 scion on 1130 Paulsen rootstock), was dedicated to the study. Thirty-three vineyard rows, established as three separate blocks of 11 consecutive rows, were assigned to the project based on a completely randomized block design. The orientation of the vineyard was north-south.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Skins were peeled from frozen berries with a razor blade for all berries on the clusters of each biological replicate. Separated skins and pulp of all the berries of each biological replicate were pooled (without seeds) and ground in a frozen mortar and pestle. Total RNA was extracted from the finely ground skins and pulp in liquid nitrogen using Qiagen RNeasy Plant MidiKit columns . The total RNA was further purified using a Qiagen RNeasy Plant Mini Kit according to the manufacturers’ instructions. RNA quality and quantity were determined using a Nanodrop 2000 spectrophotometer (Thermo Scientific) and a Bioanalyzer Chip RNA 7500 series II (Agilent).
|
| Label |
Cy3
|
| Label protocol |
cDNA synthesis and labeling reactions were performed according to the NimbleGen Arrays User's Guide (V 3.2).
|
| |
|
| Hybridization protocol |
Labeled cDNA was hybridized to a NimbleGen microarray 090818 Vitis exp HX12 (Roche, NimbleGen Inc., Madison, WI, USA), which contains probes targeted to 29,549 grapevine genes predicted from the V1 annotation of the 12x grapevine genome (http://srs.ebi.ac.uk/), and 19,091 random probes as negative controls.
|
| Scan protocol |
Each microarray was scanned using an Axon GenePix 4400A (Molecular Devices, Sunnyvale, CA, USA) at 532 nm (Cy3 absorption peak) and GenePix Pro7 software (Molecular Devices) according to the manufacturer’s instructions.
|
| Description |
This sample is from Vitis vinifera L. cv. Cabernet Sauvignon berry pulp. six biological replicates used in this experiment, each from twenty bunches harvested from six rows at 25˚Brixs.
|
| Data processing |
Images were analyzed using NimbleScan v2.5 software (Roche), which produces pair files containing the raw signal intensity data for each probe and calls files with normalized expression data derived from the average of the intensities of the four probes for each gene.
|
| |
|
| Submission date |
Feb 24, 2014 |
| Last update date |
Nov 01, 2014 |
| Contact name |
Grant Cramer |
| E-mail(s) |
[email protected]
|
| Phone |
7757844204
|
| Organization name |
University of Nevada, Reno
|
| Department |
Biochemistry & Molecular Biology
|
| Street address |
1664 N. Virginia St
|
| City |
Reno |
| State/province |
Nevada |
| ZIP/Postal code |
89557 |
| Country |
USA |
| |
|
| Platform ID |
GPL17894 |
| Series (1) |
| GSE55302 |
Transcriptomic analysis of the late stages of grapevine (Vitis vinifera cv. Cabernet Sauvignon) berry ripening indicates significant induction of ethylene signaling and flavor pathways in the skin. |
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