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Series GSE76000 Query DataSets for GSE76000
Status Public on May 22, 2016
Title Reducing sampling bias in molecular studies of grapevine fruit ripening: transcriptomic assessment of the density sorting method
Organism Vitis vinifera
Experiment type Expression profiling by array
Summary This SuperSeries is composed of the SubSeries listed below.

The interplay between environmental and genetic factors conditions the fruit ripening program in plants. Transcriptome analysis of grapevine fruits can help understanding these interactions to consciously cope with conditions leading to detrimental effects for viticultural purposes. However, considering the grapevine characteristic ripening asynchrony, which can be intensified by contrasting conditions, accurate grape sampling may be essential for molecular comparisons. In this study, berry density sorting according to floatability in NaCl solutions was assessed as a grape ripening staging strategy. Total sugar content was more correlated with berry density than with other non-invasive ripening parameters. The transcriptome was compared between three density classes collected near commercial maturity using grapevine whole-genome NimbleGen microarrays. Expression profiles clearly related with ripening progression were detected in a density series simultaneously collected from a vineyard of Albariño. By contrast, considerable differences were detected when the same density series was sampled on two different dates from the same vineyard of Tempranillo. Functional analysis indicated that environmental differences between both sampling moments determined most of these expression differences. Ripening degree-dependent responses to the environment were also detected. Finally, the effect of the sorting procedures on the grape transcriptome showed negligible when it was directly tested. Altogether, these findings evidence the convenience of homogenizing the developmental stage and the sampling time conditions for transcriptome comparisons. Berry density sorting proved useful to this end, although this method could be limited when the berry sugar concentration is not determined by the ripening developmental program.
 
Overall design Refer to individual Series
 
Citation Carbonell-Bejerano P., Rodriguez V., Hernaiz S., Royo C., Dal Santo S., Pezzotti M., Martinez-Zapater J.M., 2016. Reducing sampling bias in molecular studies of grapevine fruit ripening: transcriptomic assessment of the density sorting method. Theoretical and Experimental Plant Physiology 28, 109-129. doi: http://dx.doi.org/10.1007/s40626-016-0059-5
Submission date Dec 14, 2015
Last update date May 24, 2016
Contact name Pablo Carbonell-Bejerano
E-mail(s) pablo.carbonell@icvv.es
Organization name CSIC
Department Instituto de las Ciencias de la Vid y del Vino
Street address Madre de Dios, 51
City Logrono
State/province La Rioja
ZIP/Postal code 26006
Country Spain
 
Platforms (1)
GPL17894 NimbleGen 090918 Vitus vinifera exp HX12 [090918_Vitus_exp; GENE_CALL_ID version]
Samples (43)
GSM1971640 Albariño_pericarp_under-ripe_berry_class_no-watering_north_orientation_rep1
GSM1971641 Albariño_pericarp_under-ripe_berry_class_no-watering_south_orientation_rep1
GSM1971642 Albariño_pericarp_under-ripe_berry_class_no-watering_north_orientation_rep2
This SuperSeries is composed of the following SubSeries:
GSE75998 Transcriptome differences among Albariño densimetrically-sorted berries
GSE75999 Response of Tempranillo grapes to immersion in a concentrated NaCl solution
Relations
BioProject PRJNA305927

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
GSE76000_RAW.tar 104.2 Mb (http)(custom) TAR (of PAIR)

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