Preparation of Cross-Linked Chromatin for ChIP

Abstract

After living cells have been treated with formaldehyde to lock proteins to their DNA substrates, the DNA–protein complexes must be extracted and fragmented as described here. For ChIP-chip, it is not essential that a majority of chromatin fragments are ∼500 bp; an average fragment size ranging 1–2 kb is sufficient. However, for ChIP-seq, the average chromatin fragment should be <500 bp.