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Old 05-05-2011, 07:00 AM   #1
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Default Fragment Size shift on Egel bye using the new TruSeq protocol ?

I am using the TruSeq protocols for RNA and DNA and I follow exactly the protocol, except Iím using an Egel (Egel: Invitrogen ĎSize Selectí 2%, Ladder: Invitrogen 100bp, 20ng/ul) before PCR instead of an Agarose Gel.
If I take my fragment size I want to use e.g. 600bp for my PCR and I run a Bioanalyzer after I see fragments around 500bp. So I have always to repeat my PCR's taking fragments around 700bp or higher to get fragments around 600bp.
This phenomenon I can see for DNA and RNA.

Anybody knows this problem?
Should I use a different Ladder?
Is the new adapter changing the migrating in the Egel?

thanks a lot for your help!
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Old 05-05-2011, 09:03 AM   #2
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I replied on your other thread.
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Old 05-05-2011, 01:37 PM   #3
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Yes, please do not duplicate post.
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