Is there any difference in performing ChIP on suspension cells vs. adherent cells?
I'm currently using Activemotif ChIP-IT Express Enzymatic Kit
The only difference is in the processing of the cells. After crosslinking and quenching we need to pellet cells from suspension culture and wash at least 4 time with cold 1x PBS. This step is important to remove formaldehyde and glycine traces from cells. For adherent culture, cells were collected after removing formaldehyde and glycine from the cells. Rest of the ChIP protocol deals with cell pellet and hence remains same for both suspension as well as adherent cells.
I hope this will help you. Let me know if you have any other queries.
Another point is about chromatin shearing; usually, suspension cells are more difficult to shear.
Instead of doing an enzymatic shearing you could also try to sonicate the chromatin. For my cells (C2C12) this worked very well and you can be pretty sure that you break the nucleus.
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