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| Status |
Public on Jun 28, 2017 |
| Title |
Moscatobianco_Pea_3 |
| Sample type |
SRA |
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| Source name |
berry pericarp
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| Organism |
Vitis vinifera |
| Characteristics |
cultivar: Moscato bianco
growth stage: Pea-sized berries
tissue: berry pericarp
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| Growth protocol |
Grape berries were collected from five white-skin-coloured Vitis vinifera cultivars, all cultivated in the same experimental vineyard (Conegliano, Veneto region, Italy), during the 2011 season.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from approximately 400 mg of berry pericarp tissue (entire berries without seeds) ground in liquid nitrogen, using the Spectrum™ Plant Total RNA kit (Sigma-Aldrich) with some modifications. The sixty non-directional cDNA libraries were prepared from 2,5 µg of total RNA using the Illumina TruSeq RNA Sample preparation protocol
RNA 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 1000 |
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| Data processing |
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence
Sequenced reads were aligned onto Vitis vinifera reference genome PN40024 (12x), using the program TopHat v2.0.6, with default parameters.
Mapped reads were used to reconstruct the transcripts using the program Cufflinks v2.0.2 and the V1 version of the 12x draft annotation of the grapevine genome. For each reconstructed transcript, Cufflinks also calculated its normalized expression in FPKM (Fragments Per Kilobase of Mapped reads)
Reconstructed transcripts were merged into a single non-redundant list of 29287 transcripts, using the program Cuffmerge, from the Cufflinks package. Using this novel list of transcripts, the normalized mean expression of each transcript was calculated in FPKM (Fragments Per Kilobase of Mapped reads) for each triplicate using the geometric normalization method.
Genome_build: Vitis vinifera reference genome PN40024
Supplementary_files_format_and_content: tab-delimited text file including mean FPKM values of the biological triplicate for each variety at each stage
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| Submission date |
Oct 27, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Mélanie Massonnet |
| E-mail(s) |
[email protected]
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| Phone |
+390458027991
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| Organization name |
University of Verona
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| Department |
Biotechnology Department
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| Lab |
Pezzotti Lab
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| Street address |
Strada Le Grazie, 15
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| City |
Verona |
| State/province |
Verona |
| ZIP/Postal code |
37134 |
| Country |
Italy |
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| Platform ID |
GPL19359 |
| Series (1) |
| GSE62745 |
Transcriptome analysis of 5 white Italian grapevine varieties during berry development |
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| Relations |
| BioSample |
SAMN03144943 |
| SRA |
SRX744197 |
| 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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