I was getting good results before, but all of a sudden when I repeated the procedure with the same cell line, same drug, and same drug concentrations, it went wrong. Please find attached before and after pictures.
What are you using to perform the fragmentation? Do you need it for chip? nucleosomes analysis? fish probes?
Just for checking apoptosis after drug treatment of cancer cell lines.
if you are using micrococcal nuclease or another endonuclease, the first thing that one could think observing the second picture is that the enzyme did not work: in the new picture there seem to be only high molecular weight DNA and small fragmented RNA. Next time you should have a control (DNA not digested) to see if there are differences between digested and not digested. Good luck
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