I'm having similar problems - my chromatin only gets sheared to about 2kb even at 10 minutes using the settings suggested. I'm using a lot fewer cells - about 100k of FACS sorted tissue. The crosslinking is 1% formaldehyde for 10 min followed by glycine quench and 2 rinses.
I was worried about incomplete cell lysis so I'm very interested to hear how you did it with these two buffers. Can you share more details on that?
I was worried about incomplete cell lysis so I'm very interested to hear how you did it with these two buffers. Can you share more details on that?
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