Methodology article

Comparison of target labeling methods for use with Affymetrix GeneChips

William Lonergan , Toni Whistler and Suzanne D Vernon

Chronic Viral Diseases Branch, Division of Viral and Rickettsial Diseases, Centers for Disease Control and Prevention, 1600 Clifton Rd, MS-G41, Atlanta, GA, 30329, USA

author email corresponding author email

BMC Biotechnology 2007, 7:24doi:10.1186/1472-6750-7-24

Published:	18 May 2007

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.