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
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
