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| Status |
Public on Aug 09, 2022 |
| Title |
S5-CARLOS-1 |
| Sample type |
SRA |
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| Source name |
Berry
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| Organism |
Vitis rotundifolia |
| Characteristics |
tissue: Berry
genotype: Carlos
developmental stage: Berry E-L 32
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from two different cultivars of muscadine grapes, ‘Carlos’ and ‘Noble’. Grape berries from the last three developmental stages, namely bunch closure, veraison, and maturity (harvest), were collected from the research station (Citra) at University of Florida. Total RNA was isolated from each of the developmental stages using TRIZOL (Ambion, Life Technologies) followed by DNase treatment (Turbo DNA free, Thermo-Fisher).
RNA-seq libraries were constructed at the ICBR Gene Expression & Genotyping Core Lab using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, MA, USA) following the manufacturer’s recommendations.
A total of 1000 ng samples of high-quality total RNA (RNA Integrity Number, RIN ≥ 7) was used and followed by RNA library preparation with NEBNext Ultra II Directional Lib Prep (New England Biolabs, Ipswich, MA, USA, catalog #E7760) according to the manufacturer's user guide.
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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 |
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and low-quality reads were trimmed or removed. The high quality reads were then mapped to Vitis_vinifera.12X using STAR 2.7.6a
Fragments Per Kilobase of exon per Megabase of library size (FPKM), Transcript Per Million (TPM) and extimated read counts were calculated using RSEM 1.3.3
Assembly: Vitis_vinifera
Supplementary files format and content: tab-delimited text files include expected_count, TPM, and FPKM values for each Sample
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| Submission date |
May 19, 2022 |
| Last update date |
Aug 09, 2022 |
| Contact name |
Tongjun Gu |
| E-mail(s) |
tgu@ufl.edu
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| Organization name |
The University of Florida
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| Department |
ICBR
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| Street address |
2033 Mowry Road
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| City |
Gainesville |
| State/province |
FL |
| ZIP/Postal code |
32610 |
| Country |
USA |
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| Platform ID |
GPL32270 |
| Series (1) |
| GSE203347 |
Transcriptional profiling of two muscadine grape cultivars ‘Carlos’ and ‘Noble’ to reveal new genes, gene regulatory networks, and pathways that involved in grape berry ripening |
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| Relations |
| BioSample |
SAMN28544354 |
| SRA |
SRX15369715 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6167434_S5-CARLOS-1_expr.genes.results.gz |
479.3 Kb |
(ftp)(http) |
RESULTS |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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