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Old 07-19-2013, 06:20 PM   #1
MonaE
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Default Gel run before AMPure

I am using targeted sequencing designed by Qiagen. I would like to perform a gel run for my samples before measuring them by Qubid and AMPure step. The reason I want to do that is because if I depended ONLY on Qubid I will have a measurement for everything in my sample, while when I run a gel I can see my targeted amplicons based on their size in the gel. Does any one agree with me? if disagree can you tell me why and correct me if I am wrong?
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Old 07-19-2013, 09:05 PM   #2
Heisman
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With a normal ampure cleanup you can get rid of primers. Depending on exactly what you are doing you can do some size selection as well. Typically people will use a bioanalyzer or a tapestation as a final step to QC their library and to quantify it. If you do a gel extraction first you can lose a lot of material and possibly sacrifice the complexity of your library.
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Old 07-20-2013, 01:45 AM   #3
MonaE
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Thank you for your replay. I want to use the gel just to check the (efficiency) of my PCR that is all. I will not cut it or size select. This is becasue when I measure with quibid I get reading that is much higher than after AMPure which is a very tuff experiance for my sample as they end up with much lower reading after the AMPure. So I do not know if this low reading becasue my PCR was not working well from the begining or a result of the AMPure step.
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Old 07-20-2013, 06:35 AM   #4
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Ah, if you're just troubleshooting then go for it. Then you can determine if the problem is the PCR or the Ampure cleanup.
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