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Old 02-21-2014, 02:28 AM   #1
Location: Germany

Join Date: Dec 2010
Posts: 80
Default Primerdimer/Short Product Bias on the MiSeq

Primerdimers are more efficient in cluster formation than longer products.
Our data suggests that the extent of this preference can be influenced by sample preparation after (!) cleanup. Anyone has a guess or even knowledge what step / how one could influence the ratio of primerdimer clusters versus normal size products?
Denaturing conditions?
Handling times?
HT1 buffer?

Background: We experienced that the rate of primerdimer rate is changing over time. In particular we have one example of 8 pools of samples that were cleaned up together but put on different runs. They show a marked difference in primerdimer rate that can not be explained by the nature of the samples.
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