Can you help me with this?
I am doing Chip using the EZ-Magna ChIP™ HiSens Chromatin Immunoprecipitation Kit from Millipore. I have done Chip on MeCP2(methylated binding protein) and it worked perfectly etc I had good enrichment from the positive control region versus the negative control regions and good enrichment against the IgG as well
The problem is when I moved on to do the RNA Pol II Ser2P Chip and I am using the antibody from abcam (ab5095) I always have enrichment in the intergenic regions which RNA Pol II-ser2P not supposed to bind to. This enrichment is even higher than my positive controls (gene bodies Gapdh and Actb)
Has anyone experienced the same thing?