BioMicroCenter:3primeIVT

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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:
https://www.affymetrix.com/_media/images/figures/expresskit_labeling_assay_lg.gif

Affy's 3'IVT versus One-Cycle comparison

Information from NuGEN about the Ovation Kit

BioMicroCenter Nugen1.jpg BioMicroCenter Nugen2.jpg

BioMicroCenter Evaluation

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

Fragment Distributions:

BioMicroCenter Old v IVT 1.jpg

Results

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%

Clustergram

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

BioMicroCenter Affy Test CW 1.png