What should I do if I have barely enough cells to perform ChIP assays?

When working with limited cell or tissue samples for ChIP assays, one should make adjustments to the standard protocol to maximize results and minimize material loss. One modification involves using siliconized tubes during fixation to prevent the material from sticking to the tube walls, thus reducing material loss. Additionally, if sample amounts are extremely limited, the nuclear isolation step can be omitted to simplify the process. For immunoprecipitation, it's crucial to use a highly sensitive and specific antibody validated for ChIP-Seq assays to ensure reliable results. In ChIP-Seq assays with limited material, library preparation is critical. PCR duplicates can arise during amplification, which complicates data analysis. One can use NGS library preparation kits with adapters containing unique molecular identifiers. These identifiers enable the removal of PCR duplicates during bioinformatic analysis, ensuring accurate results.