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
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BioMicroCenter Evaluation
We have begun testing of the 3' IVT and NuGEN kit.
Fragment Distributions:
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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.
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