I am using the Life Technologies MAGnify ChIP kit with 2 X10^6 freshly isolated human neutrophils. About 50% of the time, I get a decent smear on my agarose gel at the right size, and 50% of the time the smear is very faint. I have optimized the shearing conditions to get a population of fragments of the desired size but am struggling to understand why the yield of DNA is so variable.
I cross-link for 10 minutes with 1% formadlehyde and am using the Covaris S2 for 12 minutes shear consistently with my cells.
Any guidance about what may affect the yield of DNA would be greatly appreciated.