I did ChIP in 293T before, and it works well. Recently I changed the LNCaP cells to do the ChIP. Everything is same, including the sonication condition(although I know the sonication conditions should differ in different cells, the electrophoresis result shows the fragments are between 200 and 1000bp). But when I do the PCR at last, I found there is a primer dimer under the target band(it didn't exist in 293T ChIP). So when I do the sybergreen Q-PCR, the standard curve is not right at all.
I wonder whether the chromatin of LNCaP is harder to do PCR than that of 293T, and should I design new pairs of primers? Or should I change the sonication condition?
ChIP works in 293T cells, but not in LNCaP cells
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