Protocol to apply spike-in ChIP-seq to capture massive histone acetylation in human cells

Inhibition of histone deacetylases causes rapid and robust acetylation of histones. In this case, histone acetylation is likely increased on nearly every nucleosome, and the per-cell DNA/chromatin yield in chromatin immunoprecipitation (ChIP) experiments is significantly increased. Spike-in controls are essential for normalizing ChIP sequencing (ChIP-seq) data to capture this massive effect. Here, we report a detailed protocol of H3K27-ac ChIP-seq in human cells with chromatin from an ancestral species as a spike-in control. For complete details on the use and execution of this protocol, please refer to Wu et al. (2021).