|
| Status |
Public on Apr 28, 2023 |
| Title |
CS14_C_3_9 |
| Sample type |
SRA |
| |
|
| Source name |
Cabernet Sauvignon berry sample collected at time point 9 (replicate 3) over ripening season 2014 - Crop thinned 75%
|
| Organism |
Vitis vinifera |
| Characteristics |
cultivar: Cabernet Sauvignon
tissue: grape berry pericarp
year: 2014
time point: 9
time point replicate: 3
day after veraison: 42
sugar content (g/100ml): 25.16
treatment (cluster thinning): Crop thinned 75%
|
| Treatment protocol |
Cluster thinning treatments: Moderate thinning (50% crop load reduction) was achieved removing clusters to maintain one cluster per shoot; severe thinning (75% crop load reduction) consisted in mantaining one cluster every other shoot; control (0% crop load reduction) was unthinned vines.
|
| Growth protocol |
Vineyard Features: Vitis vinifera cultivar Cabernet Sauvignon (clone FPS 8 grafted on 5C rootstock and planted in 1997) was grown nearby Modesto (USA, CA) in sandy clay loam in an east-west orientation with 10 foot row spacing and 5 foot vine spacing.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using the Spectrum Plant Total RNA kit (Sigma-Aldrich) following the manufacturer’s instructions with some modifications (Fasoli et al., 2012). RNA quality and quantity were determined using a Nanodrop 2000 spectrophotometer (Thermo Scientific) and a Bioanalyzer Chip RNA 7500 series II (Agilent).
206 non-directional cDNA libraries were prepared from 2.5 μg of total RNA using the Illumina TruSeq RNA Sample preparation protocol (Illumina Inc., San Diego, CA, USA). Library quality was determined using the Agilent High Sensitivity DNA kit on the Agilent 2100 bioanalyzer, and the quantity was determined by quantitative PCR using the KAPA Library Quantification kit (KapaBiosystems).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1000 |
| |
|
| Data processing |
The reads were aligned onto the grapevine 12x reference genome PN40024 using TopHat v2.0.6 with default parameters
Mapped reads were used to reconstruct the transcripts using Cufflinks v2.0.2 and the reference genome annotation V1
The normalized expression of each transcript was calculated as RPKM (Reads Per Kilobase per Million mapped reads) for each sample.
Genome_build: 12X reference genome PN400024
Supplementary_files_format_and_content: tab delimited text file containing the normalized reads counts RPKM for all the samples.
|
| |
|
| Submission date |
Sep 27, 2017 |
| Last update date |
Apr 28, 2023 |
| Contact name |
Marianna Fasoli |
| E-mail(s) |
[email protected]
|
| Phone |
+39 045 842 5625
|
| Organization name |
University of Verona
|
| Department |
Biotechnology
|
| Lab |
Molecular Viticulture
|
| Street address |
Via della Pieve 70
|
| City |
San Pietro in Cariano |
| State/province |
Verona |
| ZIP/Postal code |
37029 |
| Country |
Italy |
| |
|
| Platform ID |
GPL19359 |
| Series (1) |
| GSE104316 |
Cluster thinning effect on Cabernet Sauvignon berry ripening |
|
| Relations |
| BioSample |
SAMN07709514 |
| SRA |
SRX3219420 |
