I am running a ChIP Assay using third instar drosophila larvae and am looking for a protocol with MNase digestion. Most protocols I have found have a DNA crosslinking step using formaldehyde. I understand I can adapt these protocols to fit mine, but would like a little more guidance.

If I am using a MNase digestion, can I use formaldehyde protocols and basically skip the cross-linking and reversal steps?

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