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Browse SoyPLEX Experiment Data

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Exploration of microarrays as tools to assess substantial equivalence of genetically modified soybeans
Martina,,Stromvik, McGill University, Quebec, Canada (martina.stromvik@mcgill.ca)
Experiment design (25 hybridizations)
cultivar
•2601R •Bayfield •Mandarin •PS46R •S03W4

This experiment has been imported by PLEXdb from NCBI GEO (GSE9374)

Series_summary:
According to the Canadian Food Inspection Agency...[complete overview]

Experiment     Expression     Hybridizations & Samples     Quality Control     Compare Treatments     Downloads    

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Experiment Name: Exploration of microarrays as tools to assess substantial equivalence of genetically modified soybeans
Accession No: GM16
Microarray: Soybean
Visibility: public
Experiment Type:
Experiment Factor(s):
cultivar
•2601R   •Bayfield   •Mandarin   •PS46R   •S03W4
Quality Control: biological replicates
Treatment summary:
 cultivar  # replicates
 2601R  5
 Bayfield  5
 Mandarin  5
 PS46R  5
 S03W4  5
Total hybridizations: 25
Description: This experiment has been imported by PLEXdb from NCBI GEO (GSE9374)

Series_summary:
According to the Canadian Food Inspection Agency and Health Canada, genetically modified crops are considered safe if they are substantially equivalent to a conventional crop in regards to agronomic, physiological and compositional characteristics. A recurring issue in safety assessment of genetically modified crops is the paucity of analytical methods to detect unintended or unexpected outcomes of genetic modification. Traditional targeted compound comparative analyses are limited in scope and capacity to detect unintended changes in chemical composition. This study explored the potential of using microarray technology to assess the substantial equivalence of gene expression profiles between genetically modified and conventional soybean cultivars. Different pre processing methods were applied to the raw expression data from the arrays, and clustering methods were used to try and differentiate the genetically modified cultivars from the conventional cultivars. Results showed that more variation existed between different strains of conventional cultivars than between conventional and genetically modified cultivars.
For more information, please see: Cheng, K.C., Beaulieu, J., Iquira, E., Belzile, F.J., Fortin, M.G. and Strömvik, M.V. (2008). “Effect of transgenes on global gene expression in soybean is within the natural range of variation of their conventional counterparts.” Journal of Agricultural and Food Chemistry (in press)
Keywords: Expression comparison between genetically modified cultivars

Series_overall_design:
Five samples (biological replicates) of total RNA from each of the five different soybean varieties were selected for hybridization to Affymetrix Soybean GeneChips, for a total of 25 chips (following total RNA integrity assessment). Spike controls B2, bio-B, bio-C, bio-D and Cre-x were added to each hybridization cocktail. Arrays were washed and stained in an Affymetrix Fluidics Station prior to scanning on the Affymetrix GeneChip Scanner 3000. Image acquisition and processing was done with the Affymetrix Microarray Analysis Suite 5.0.
Publication: 'Effect of transgenes on global gene expression in soybean is within the natural range of variation of conventional cultivars', Cheng KC, Beaulieu J, Iquira E, Belzile FJ et al
J Agric Food Chem 2008 May 14;56(9):3057-6
pubmed: 18433101
Created: 2009-06-04 13:14:51
Last Update: 2009-06-04 13:36:54
GEO Accession GSE9374
Submitter: PLEXdb Curator
Name: Martina,,Stromvik
Institution: McGill University, Quebec, Canada
Head of Laboratory: --
email(s):
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