CHIP-seq experiment undergoes multiple steps. First involves cross-linking the protein and keeping them attached to the DNA during the experiment. Cross-linking is literally is similar to gluing proteins to DNA by a simple organic compound called formaldehyde (CH2O). Formaldehyde will freeze the dynamics of protein-DNA interaction and it will give a snapchat of what is going on inside the nucleus in the moment when it was added to the cells.

Fig. 4: Construction of cross-linking experiment. Tissues was collected , which composed of cells (piage oval ), inside nucleus (red circle) and have lots of chromatin (red rope). chromatin is a DNA (red line) and transcription factor (green circle). DNA and protein are cross -linked by formaldehyde (small X).