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Browse GrapePLEX Experiment Data

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Expression data in individual grape berries during ripening initation
Steven,T.,Lund, The University of British Columbia, Vancouver , Canada (stlund@interchange.ubc.ca)
Experiment design (32 hybridizations)
developmental stage name
•green hard •green soft •pink soft •red soft
berry position
•distal •proximal
plant
•1 •2

This experiment has been imported by PLEXdb from NCBI GEO (GSE11406)

Series_summary:
We used Affymetrix microarray analyses of thirty...[complete overview]

Experiment     Expression     Hybridizations & Samples     Quality Control     Compare Treatments     Downloads    

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Experiment Name: Expression data in individual grape berries during ripening initation
Accession No: VV15
Microarray: Grape
Visibility: public
Experiment Type:
Experiment Factor(s):
developmental stage name
•green hard   •green soft   •pink soft   •red soft
berry position
•distal   •proximal
plant
•1   •2
Quality Control: biological replicates
Treatment summary:
 developmental stage name  berry position  plant  # replicates
 green hard  distal  1  2
 green hard  distal  2  2
 green hard  proximal  1  2
 green hard  proximal  2  2
 green soft  distal  1  2
 green soft  distal  2  2
 green soft  proximal  1  2
 green soft  proximal  2  2
 pink soft  distal  1  2
 pink soft  distal  2  2
 pink soft  proximal  1  2
 pink soft  proximal  2  2
 red soft  distal  1  2
 red soft  distal  2  2
 red soft  proximal  1  2
 red soft  proximal  2  2
Total hybridizations: 32
Description: This experiment has been imported by PLEXdb from NCBI GEO (GSE11406)

Series_summary:
We used Affymetrix microarray analyses of thirty-two individual Vitis vinifera cv. Cabernet Sauvignon berries sampled from two clusters at fifty-percent ripening initiation. By delineating four developmental stages of ripening initiation, we demonstrate that color is a statistically significant indicator of transcriptional state during ripening initiation. We report on clustered gene expression patterns which were mined for genes annotated with signal transduction functions in order to advance regulatory network modeling of ripening initiation in grape berries. We also demonstrated that gene expression does not differ statistically significantly at a global level in berries sampled from different plants or different positions in a cluster.

Keywords: time course (berry development series)

Series_overall_design:
Individual grape berries were selected at 4 developmental stages along ripening initiation for RNA extraction and hybridization to Affymetrix Vitis Genome GeneChips. One goal of this study was to determine the association between the global transcriptome state and phenotypic variables frequently used in berry staging such as color and firmness, so we defined the four time-points (development series) by color/firmness combinations: green hard (GH), green soft (GS), pink soft (PS) and red soft (RS). Individual berries representing each stage were collected from either the distal or the proximal position of one cluster one each of two plants used for experiments.
Publication: 'Gene expression analyses in individual grape (Vitis vinifera L.) berries during ripening initiation reveal that pigmentation intensity is a valid indicator of developmental staging within the cluster', Lund ST, Peng FY, Nayar T, Reid KE et al
Plant Mol Biol 2008 Oct;68(3):301-15
pubmed: 18642093
Created: 2009-06-30 14:48:04
Last Update: 2009-06-30 15:37:41
GEO Accession GSE11406
Submitter: PLEXdb Curator
Name: Steven,T.,Lund
Institution: The University of British Columbia, Vancouver , Canada
Head of Laboratory: --
email(s):
Homepage:

 
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