i am doing PolII Chip-seq in Saccharomyces cerevisiae and I have a big problem to get enough DNA after sonication.I am using the brandson sonifier. I tried several conditions, 3 cycles of 15 min (30 sec ON, 30 sec OFF). In agarose gel, I am able to see fragments ranging from 500 nt to 100 nt but when I cheked the amount of DNA by qubit, I got 14 ng./ul which means 22 ug of DNA in 500 ml of culture!!!!!
Any advices are welcome!!!