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This page will contain our information about our evaluation of new kits to replace the old Affymetrix standard labeling kit that will be retired in late 2009. We are currently evaluating two kits: the 3'IVT kit from Affymetrix and the Ovation kit from NuGEN.


Information from Affymetrix about the 3'IVT Kit

Affymetrix Method figure:

Affy's 3'IVT versus One-Cycle comparison

Information from NuGEN about the Ovation Kit


BioMicroCenter Evaluation

We have begun testing of the 3' IVT and NuGEN kit.

Fragment Distributions:


TEST Old Kit 3'IVT NuGen
Amount Loaded 5 ug 200ng 200ng
Background Array1: 65
Array2: 93
Array1: 58
Array2: 62
Array1: 29
Array2: 27
 %Present Array1: 38.5%
Array2: 41%
Array1: 41%
Array2: 40%
Array1: 60%
Array2: 58%


Sample prep kit appears to be the largest clustering factor. NuGen clusters away from the other two.

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