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| Status |
Public on Apr 15, 2008 |
| Title |
Exploration of microarrays as tools to assess substantial equivalence of genetically modified soybeans |
| Organism |
Glycine max |
| Experiment type |
Expression profiling by array
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| 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.
Keywords: Expression comparison between genetically modified cultivars
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| 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.
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| Contributor(s) |
Cheng K, Stromvik M, Beaulieu J, Fortin M |
| Citation(s) |
18433101 |
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| Submission date |
Oct 18, 2007 |
| Last update date |
Nov 22, 2016 |
| Contact name |
Martina Stromvik |
| E-mail(s) |
martina.stromvik@mcgill.ca
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| Phone |
+1 (514) 398 8627
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| Fax |
+1 (514) 398 7897
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| URL |
http://www.mcgill.ca/plant/faculty/stromvik/
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| Organization name |
McGill University
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| Department |
Department of Plant Science
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| Lab |
Plant Bioinformatics
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| Street address |
21,111 Lakeshore Rd
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| City |
Ste-Anne-de-Bellevue |
| State/province |
Quebec |
| ZIP/Postal code |
H9X 3V9 |
| Country |
Canada |
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| Platforms (1) |
| GPL4592 |
[Soybean] Affymetrix Soybean Genome Array |
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| Samples (25)
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| Relations |
| BioProject |
PRJNA103081 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE9374_RAW.tar |
180.6 Mb |
(http)(custom) |
TAR (of CEL) |
| Processed data included within Sample table |
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