Very interesting thread !
Dario, I am also trying to optimized my lysis-sonication protocol and found out that lysis buffer volumen was crucial in my case. I would say you are not lysing properly the cells and therefore you get more DNA released increasing the sonication times. It seems you have more DNA on the wells that could be DNA just released from nuclei by sonication. Just an idea....
Good luck
Dario, I am also trying to optimized my lysis-sonication protocol and found out that lysis buffer volumen was crucial in my case. I would say you are not lysing properly the cells and therefore you get more DNA released increasing the sonication times. It seems you have more DNA on the wells that could be DNA just released from nuclei by sonication. Just an idea....
Good luck
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