Sonication:

I'm currently optimizing the sonication conditions for shearing chromatin in HepG2 cells using the Bioruptor® Pico for downstream applications like ChIP-qPCR. While I've tried various settings, I'm struggling to achieve sufficient DNA concentration after DNA cleaning. Specifically, I'm not seeing a clear pellet after following the protocol of adding 20 µL of 3 M Sodium Acetate (pH 5.2) and 500 µL of 100% ethanol, then vortexing and incubating at -80°C for at least 1 hour (or -20°C overnight).

Could anyone share tips on improving DNA yield during this step? Also, how much DNA is typically needed to see clear bands after running on an agarose gel? Any advice on optimizing both the sonication and DNA precipitation steps would be greatly appreciated.

Nuclei Release:

For releasing nuclei from HepG2 cells, would it be better to use a Dounce homogenizer or a 30 1/2 inch syringe? What are the optimal settings or techniques for these tools to ensure efficient and gentle release of nuclei?