Comparison of target labeling methods for use with Affymetrix GeneChips.
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.


CONCLUSIONS
These 3 one-cycle labeling kits produce comparable hybridization results. This provides users with several kit options and flexibility when using the Affymetrix system.
Lonergan
William
W
Chronic Viral Diseases Branch, Division of Viral and Rickettsial Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA. wlonergan@cdc.gov <wlonergan@cdc.gov>
Whistler
Toni
T
Vernon
Suzanne D
SD
D005069:Evaluation Studies as Topic; D020869:Gene Expression Profiling / Q000379:methods*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D018075:RNA, Complementary / Q000378:metabolism*; D011933:Reagent Kits, Diagnostic; D012680:Sensitivity and Specificity; D013194:Staining and Labeling / Q000379:methods*
D018075:RNA, Complementary; D011933:Reagent Kits, Diagnostic