I am having a problem with my ChIPs....the inputs I run out on agarose gels all have bright bands running at <50bp. There is also significantly less DNA (by spectrophotometric measurements) than normal. Thinking it might be snRNA contamination, I tried treating the inputs with RNaseA to see if the band would disappear, but to no avail. I don't think it's a problem with over-shearing, because of the cell type (RAW chromatin just will not shear to that size) and because others in my lab seem to be doing fine using the same protocol and more sensitive cells. What could these bands be? Any ideas?
Thanks in advance,