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Comparison of target labeling methods for use with Affymetrix GeneChips.
Lonergan W, Whistler T, Vernon SD
Comparison of target labeling methods for use with Affymetrix GeneChips.
BMC Biotechnology 2007;7:24.
The complete electronic version of this article is available at http://www.biomedcentral.com/1472-6750/7/24
Summary
A central component of our research strategy to identify biomarkers and the physiologic pathways of CFS involves measuring expression levels (activity) of genes (e.g., mRNA profiles). Gene expression profiling is a rapidly evolving technique and the Affymetrix GeneChip platform is one of the more powerful standards. RNA from study participants must be labeled (marked) before it can be used on this platform and there are a variety of commercial kits available. However, standardization and quality control are critical and we were aware of no previous peer reviewed comparison of the different kits. This manuscript describes our comparison of 3 of the more popular currently available commercial labeling kits.
Abstract
Background : Several different commercial one-cycle labeling kits are available for preparation of the target for use with the Affymetrix GeneChip platform. However, there have been no evaluations of these different kits to determine if comparable results were generated. We report on the cRNA target synthesis, labeling efficiency and hybridization results using the One-Cycle Target Labeling Assay™ (Affymetrix), the BioArray RNA Amplification and Labeling System™ (Enzo Life Sciences), and the Superscript RNA Amplification System (Invitrogen Life Technologies).
Results : The only notable difference between kits was in the yield of cRNA target synthesized during in vitro transcription, where the BioArray assay had to be repeated several times in order to have sufficient target. However, each kit resulted in comparable signal and detection calls when hybridized to the Affymetrix GeneChip.
Conclusion : These 3 one-cycle labeling kits produce comparable hybridization results. This provides users with several kit options and flexibility when using the Affymetrix system.
Page last modified on October 24, 2007
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