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SRX8686140: GSM4661609: VT50-b; Vitis vinifera; RNA-Seq
1 ILLUMINA (HiSeq X Ten) run: 22.6M spots, 6.8G bases, 2.7Gb downloads

Submitted by: NCBI (GEO)
Study: Comparative study on berry development of two grape cultivars by transcriptomic analyses [Victoria]
show Abstracthide Abstract
Grape berry development is a highly coordinated, intricate and complex process with many morphological, biochemical and physiological changes occurring during the ripening process. Equally, ripening is an organoleptic characteristic linked to fruit development. The fruits Seedless (FS) and Victoria (VT) grape varieties exhibit many morphological and phytochemical differences, but genetic mechanisms underlying them remain poorly explored. Herein, we comparatively analysed the phenotypic and transcriptomic patterns of Victoria (VT) and Flame Seedless (FS) grape varieties during berry development. We studied the physiological analysis and transcriptomic profiles sequencing were performed at four berry developmental stages time-points (40, 50, 60 and 80 DPA). Notably, the VT variety berry size was comparatively larger to the FS variety. At maturity, 80DPA, the FS soluble solids were 61.8% higher than VT. Further, a total of 4889 and 2802 DEG's were identified from VT and FS 40 DPA to 80 DPA development stages, respectively. 1386 DEGs were common in the two varieties. GO analysis identified Cysteine biosynthetic process, response to red light, chlorophyll binding, polysaccharide biosynthetic process and chloroplast thylakoid membrane as some of the dominant terms under the biological processes, molecular function and cellular component categories. Overall design: Transcriptome analysis for berry development of two grape cultivars,in triplicate, using Illumina HiSeq X-ten.
Sample: VT50-b
SAMN15473291 • SRS6964994 • All experiments • All runs
Organism: Vitis vinifera
Library:
Instrument: HiSeq X Ten
Strategy: RNA-Seq
Source: TRANSCRIPTOMIC
Selection: cDNA
Layout: PAIRED
Construction protocol: Total RNA was extracted using a Plant RNA EASYspin Plus Kit (aidlab, Peking, China) according to the instructions of the manufacturer, and treated with RQ1 DNase (Promega) to remove DNA. The quality and quantity of the purified RNA were determined by measuring the absorbance at 260 nm and 280 nm (A260 and A280) using SmartSpec Plus (BioRad, USA). RNA integrity was further verified by electrophoresis using a 1.5% agrose gel. To avoid individual variation, we selected three biological replicates for each sample, and extracted total RNA separately, and then we pooled the replicates together for the following experiments. Construction of cDNA library was independently prepared using 10 ug of total RNA. Polyadenylated RNAs were purified and concentrated with oligo (dT)-conjugated magnetic beads (Invitrogen) before being used for the directional RNA-seq library preparation. Purified mRNAs were iron fragmented at 95oC followed by end repair and 5' adaptor ligation. Then reverse transcription was performed with RT primer harboring 3' adaptor sequence and randomized hexamer. The cDNAs were purified and amplified and PCR products corresponding to 200-500 bps were purified, quantified and stored at -80 oC until used for sequencing.
Experiment attributes:
GEO Accession: GSM4661609
Links:
Runs: 1 run, 22.6M spots, 6.8G bases, 2.7Gb
Run# of Spots# of BasesSizePublished
SRR1217132422,645,5576.8G2.7Gb2023-07-01

ID:
11302192

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