Protocol Online logo
Top : New Forum Archives (2009-): : ChIP and Next Generation Sequencing

No signal in qPCR from ChIP sample - (Oct/05/2014 )

I'm doing ChIP on dissected drosophila tissue (imaginal discs). I collected 400 pairs of discs and was able to get smeared chromatin. I tried to do ChIP-qPCR with an antibody that has been used in ChIP-seq in the same tissue, and only the first time I got it to work -nice enrichment only in the ChIP sample and low background in no antibody control. Now I think it was just beginner's luck. Ever since then, I could never get it worked again. The second time, I could still see enrichment in the ChIP sample, but the background was high. But from the third time on, I could not get any signal from ChIP sample at all... totally flat in qPCR result! But I could still get some amplification from no antibody control sample (~30 ct value).

 

Then I start to change to RNA polII antibody, thinking it should be easier. And for the most recent couple of trials, I could get enough ChIP-ed DNA, measured by Qubit, e.g. 2ng total using anti-PolII. But again, I couldn't amplify ANYTHING from ChIP sample, completely flat line. Input and no antibody control seemed to be normal. I tried to change to newly bought formaldehyde, and made fresh buffers. Now I don't know what else I could do.

 

Has anyone ever encountered this, i.e. no signal ONLY from ChIP sample in qPCR result?

 

Any suggestion would be helpful! Many thanks!

 

Tristan

-ndswxy-

Hi Tristan?

Have you checked your sonicated chromatin on the gel?

Have you tried increasing amount of the antibody or try another antibody from different company?

-trungbiotech-