Antibody Specificity: The success of ChIP depends heavily on the quality and specificity of the antibody used. Resolution: The resolution of ChIP is typically limited to several hundred base pairs, which may not be sufficient to pinpoint the exact binding site. Crosslinking Efficiency: Incomplete crosslinking can result in the loss of protein-DNA interactions, while excessive crosslinking can make the chromatin difficult to shear. Data Interpretation: Interpreting ChIP data can be complex, especially when dealing with indirect or transient interactions.
