Mighty Mouse is correct in terms of pol2 enriching to regions where the mechanisms are still unclear, like ncRNA. you may also consider titrating the antibody although your data looks great. alternatively, 2hrs incubation could be cut back to 1hr. :-)
my understanding is that protein A beads are generally better suited for rabbit polyclonal antibodies. i've seen the mouse monoclonals enrich better with protein G. Years ago i would use protien a/g sepharose beads but lately i'm using the MAGnify kit from invitrogen that uses a mix of protein a/g magnetic beads
My original choice was abcam's ab8580, but this is out of stock and their staff say they have no idea when new batches will be available. Upstate/Millipore's 07-473 is also now out of stock, and I'm waiting on their customer services to let me know if more will be available.
These two antibodies are by far the most popular I've seen in ChIP experiments. I will be using ChIP DNA for next gen sequencing so it's absolutely critical the antibody works well. Does anyone have a suggestion for an alternative, that has been used in a high profile publication, or you have personal experience with?
Invitrogen and Cell signalling have this antibody as well but don't know any publications.