ChIP Negative Control - Chromatin Immunoprecipitation (Jul/09/2005 )
When doing a transcription factor ChIP assay on a human cell line, I wanted to use an IgG for my negative control. Instead of ordering the ChIP-grade IgG, I just used the secondary antibody we have in the lab for Western Blotting. My PCR reaction produced a band for the IgG negative control (G-anti-rabbit) - could the HRP conjugate be facilitating non-specific immunoprecipitation or otherwise interfere with the protocol?
I think you should use the same antibody used in real samples for negative control. If you use a different antibody, how do you know the DNA pull down by the antibody in real samples is specific?