I would like to know some basic things about ChIP-seq (IP-pulldown) as this is first time I am doing this technique.
1) what would be the expected DNA concentration of individual IP after pull-down for ChIP-Seq? (Histones and non-histones e.g. RNA pol II/transcription factor)?
2) Is it a concern if DNA concentration of IP control and Ab-control is high, but PCR, Q-PCR is not giving any signal from these controls?
3) can we get ss-DNA also? This is because for a DNA under cont. transcription might shear as ss-DNA.
4) Is qubit assay enough to std. the DNA pull down until a proper concentration is achieved? or a PCR is a must thing to do irrespective of DNA concentration?
Thanks in advance!
Edited by chip, 14 May 2012 - 08:53 AM.