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Series GSE72421 Query DataSets for GSE72421
Status Public on Nov 12, 2015
Title Five Omic Technologies Are Concordant in Differentiating the Biochemical Characteristics of the Berries of Five Grapevine (Vitis vinifera L.) Cultivars
Organism Vitis vinifera
Experiment type Expression profiling by array
Summary Background: Grape cultivars and wines are distinguishable by their color, flavor and aroma profiles. Omic analyses (transcripts, proteins and metabolites) are powerful tools for assessing biochemical differences in biological systems.

Results: Berry skins of red- (Cabernet Sauvignon, Merlot, Pinot Noir) and white-skinned (Chardonnay, Semillon) wine grapes were harvested near optimum maturity from the same experimental vineyard and ˚Brix-to-titratable acidity ratio. Identical sample aliquots were analyzed for transcripts by grapevine whole-genome oligonucleotide microarray and RNA-seq technologies, proteins by nano-liquid chromatography-mass spectroscopy, and metabolites by gas chromatography-mass spectroscopy and liquid chromatography-mass spectroscopy. Principal components analysis of each of five Omic technologies showed similar results across cultivars in all Omic datasets. Comparison of the processed data of genes mapped in RNA-seq and microarray data revealed a strong Pearson's correlation (0.80). The exclusion of probesets associated with genes with potential for cross-hybridization on the microarray improved the correlation to 0.93. The overall concordance of protein with transcript data was low with a Pearson's correlation of 0.27 and 0.24 for the RNA-seq and microarray data, respectively. Integration of metabolite with protein and transcript data produced an expected model of phenylpropanoid biosynthesis, which distinguished red from white grapes, yet provided detail of individual cultivar differences.

Conclusions: The five Omic technologies were consistent in distinguishing cultivar variation. There was high concordance between transcriptomic technologies, but generally protein abundance did not correlate well with transcript abundance. The integration of multiple high-throughput Omic datasets revealed complex biochemical variation amongst five cultivars of an ancient and economically important crop species.
Overall design Vitis vinifera L. cv. Cabernet Sauvignon, Chardonnay, Merlot, Pinot Noir, Semillon berries were harvested from Nevada Agricultural Experiment Station Valley Road Vineyard, Reno, NV, USA. Whole-genome microarray analysis was used to assess the transcriptomic response of berry skins at harvest, approximately 24 °Brix (2011 vintage). Vines were grown under water deficit and well-watered conditions. At least two clusters harvested from non-adjacent vines were used for each of five experimental replicates.
Web link
Contributor(s) Ghan R, Van Sluyter SC, Hochberg U, Degu A, Hopper DW, Tillet R, Schlauch K, Fait A, Haynes PA, Cramer GR
Citation(s) 26573226
Submission date Aug 26, 2015
Last update date May 31, 2016
Contact name Grant Cramer
Phone 7757844204
Organization name University of Nevada, Reno
Department Biochemistry & Molecular Biology
Street address 1664 N. Virginia St
City Reno
State/province Nevada
ZIP/Postal code 89557
Country USA
Platforms (1)
GPL17894 NimbleGen 090918 Vitus vinifera exp HX12 [090918_Vitus_exp; GENE_CALL_ID version]
Samples (50)
GSM1862195 Berry_skin_CS-WW-rep2
GSM1862196 Berry_skin_CS-WW-rep3
GSM1862197 Berry_skin_CS-WW-rep4
BioProject PRJNA294008

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE72421_RAW.tar 116.0 Mb (http)(custom) TAR (of PAIR)
GSE72421_annotation.txt.gz 324.7 Kb (ftp)(http) TXT
Processed data included within Sample table

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