Editing BioMicroCenter:3primeIVT

{{BioMicroCenter}}

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 [https://www.affymetrix.com/products_services/reagents/specific/3_ivtexpresskit.affx#1_1 3'IVT kit] from Affymetrix and the [http://www.nugeninc.com/nugen/index.cfm/products/amplification-systems/ovation-amp-v2/ Ovation kit] from NuGEN. 

== Information from Affymetrix about the 3'IVT Kit ==
Affymetrix Method figure: <br>
https://www.affymetrix.com/_media/images/figures/expresskit_labeling_assay_lg.gif

[http://www.affymetrix.com/support/technical/technotes/3_ivtexpresskit_technote.pdf Affy's 3'IVT versus One-Cycle comparison]

== Information from NuGEN about the Ovation Kit ==

Nugen1 Image
Nugen2 Image

== BioMicroCenter Evaluation ==

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

===Fragment Distributions:===

[[Image:BioMicroCenter_Old_v_IVT_1.jpg|400px]]

=== Results ===

{|border="1"
 ! TEST !! Old Kit !! 3'IVT !! NuGen
 |-
 | Amount Loaded
 | 5 ug
 | 200ng
 | 200ng
 |-
 | Background
 | Array1: 65 <br> Array2: 93
 | Array1: 58 <br> Array2: 62
 | Array1: 29 <br> Array2: 27
 |-
 | %Present
 | Array1: 38.5% <br> Array2: 41%
 | Array1: 41% <br> Array2: 40%
 | Array1: 60% <br> Array2: 58%
|}
=== Clustergram ===
Sample prep kit appears to be the largest clustering factor. NuGen clusters away from the other two.

[[Image:BioMicroCenter_Affy_Test_CW_1.png|400px]]