Second step is to lysate the cross-linked cells by using a lysis buffer which contain a compound called Triton X, a soap-similar compound that breaks down cells by breaking down its phospholipids of the cell membrane. The Triton-X will liberate chromatin from the cells and nuclei at this stage.

Then, sonication using ultrasound waves directed to the fee chromatin will result in breakdown of DNA to small fragments.

The end result of this step is small pieces of protein-bound DNA.

Fig. 5: Construction of Cell Lysis and DNA Fragmentation. lysis buffer was added to cross-linked cells, to get free chromatin. using sonication ,by ultrasound waves, resulted in fragmented DNA-bound protein.