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| Status |
Public on Nov 25, 2019 |
| Title |
CK-EL36-B |
| Sample type |
SRA |
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| Source name |
grape berries
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| Organism |
Vitis vinifera |
| Characteristics |
cultivar: Cabernet Sauvignon
tissue: berries
developmental stage: EL36
treatment: CK
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| Treatment protocol |
For cluster bagging treatment, an individual cluster was placed into a two-layer kraft paper bags (36 × 36 cm), yellow exterior layer with the black interior layer coated with wax), with a bent straw to keep ventilation inside the bag. Each treatment was arranged in a completely randomized experimental design with three biological replicates. In each biological replicate, treatments were applied to 15 vines randomly selected from both south and north sites of the vineyard.
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| Growth protocol |
The own-rooted vines in this vineyard were planted in 2000, arranged in north–south rows with 2.5 m × 1 m vine spacing and equipped with a furrow irrigated system, spur-pruned (15 nodes per linear metre) and trained to a modified Vertical-Shoot-Positioned (M-VSP) trellis system. Nutrition and pest managements were carried out according to industry standards for this cultivar and the region as described previously.
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| Extracted molecule |
total RNA |
| Extraction protocol |
A sub-sample of 50 berries were randomly selected from each biological replicate for RNA extraction. Total RNAs for RNA-seq analysis were isolated from frozen deseeded berries using a Plant Total RNA Extraction Kit (Sigma, St. Louis, MO, USA), and further purified by DNase I (Promega, Madison, WI, USA) digestion. RNA integrity and concentration were analyzed using the Nanodrop 2000 spectrophotometer (Thermo Fisher Scientific Inc., Wilmington, DE, USA) and the Aglient 2100 Bioanalyzer (Agilent, Santa Clara, CA, USA).
cDNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Bowtie2 v2.2.5 was used to map clean reads to reference, allowing no more than two nucleotides mismatched.
Level of gene expression was calculated using the FPKM (expected fragments per kilobase of transcript per million fragments mapped) method.
Genome_build: Vitis vinifera (PN40024) genome V2 download from Grape Genome Database (CRIBI)
Supplementary_files_format_and_content: excel file (.xlsx) include FPKM values for each sample
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| Submission date |
Apr 16, 2019 |
| Last update date |
Sep 17, 2020 |
| Contact name |
Run-Ze Sun |
| E-mail(s) |
sunrunze@ibcas.ac.cn
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| Organization name |
Chinese Academy of Sciences
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| Department |
Institute of Botany
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| Lab |
Key Laboratory of Plant Resources
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| Street address |
No.20 Nanxincun, Xiangshan, Haidian District
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| City |
Beijing |
| ZIP/Postal code |
100093 |
| Country |
China |
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| Platform ID |
GPL18740 |
| Series (1) |
| GSE129916 |
Comparative Physiological, Metabolomic, and Transcriptomic Analyses Reveal Developmental Stage-Dependent Effects of Cluster Bagging on Phenolic Metabolism in Cabernet Sauvignon Grape Berries |
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| Relations |
| Reanalyzed by |
GSM4762226 |
| BioSample |
SAMN11440997 |
| SRA |
SRX5697512 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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