It's now two months that I've been stuck in the shearing part of the ChIP assay. I'm using cup horn settings but I always have lots unsheared DNA and a perfect smear around 400bp. I have gone from 1 min of sonication to over 40 min but I still do have that unsheared part. I have tried anything that the company suggested: polystyrene tubes, decreasing the sample volume, distance from the horn, etc. However, it is still a big mess. I'm really exhausted and don't know what to do. I would be very very very thankful if any of you have any suggestion.
Ps. I'm doing ChIP on MCF-7 cells
Best
Amir
