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Old 09-05-2018, 01:25 AM   #1
sim.j.baum
Junior Member
 
Location: Hamburg

Join Date: Oct 2013
Posts: 1
Default hiChIP library prep library size distribution ok?

Dear all,
I have performed a library prep of hiChIP samples according to the Mumbach paper (Mumbach et al. 2017). As the tagmentation and Tn5 amount is critical I am little bit unsure if I over-tagmented. The fragment size after the shearing was between 200 - 3kb. After tagmentation and PCR of the lib. are the profiles looking like this on a hiSens. BioAnalyzer (please see attachment).


The first peak is approx. 270 and second is 700bp.

What do you think about the size distribution? Why are there two peaks (nucleosomes are digested/ prot.K digestion after ChIP)?

Also, would you clean up the primers which are in the second sample?

I hope for some feedback,
Best wishes,
Simon
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