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ChIP-Seq (IP pulldown) Help!!

ChIP-Seq ChIP Immunoprecipitation

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#1 chip



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Posted 14 May 2012 - 06:02 AM


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.

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