I'm comparing with SICER some chip seq experiments of mouse muscles subjected to a specific treatment vs non treated samples.
I'm monitoring ACH3 and H3K4ME3 histone modifications(so they are both activator at promoter level).
The strange thing is that most of the genes that are modulated according to their gene expression have at their promoter increased ACH3 islands and decreased H3K4ME3.
Do someone of you experienced a similar situation?
This could be a signal of something wrong in experiment setup?
thank you for every tip you could pprovide to me