Protocol for the development and use of spike-in control for chromatin immunoprecipitation (ChIP) of chromatin-binding proteins

This paper describes a protocol for developing and using an exogenous spike-in control to improve chromatin immunoprecipitation (ChIP) sensitivity and generate high-confidence datasets. The authors use Saccharomyces cerevisiae chromatin as a spike-in control in ChIP experiments for two Schizosaccharomyces pombe heterochromatin-associated proteins, enabling normalization of ChIP signals based on immunoprecipitation efficiencies across samples. They outline steps for spike-in control preparation, validation, and data normalization, while the key limitation is that the approach is demonstrated in yeast systems (S. cerevisiae spike-in with S. pombe targets), rather than in human or disease-relevant tissues. The paper does not explicitly discuss endometriosis or adenomyosis; it was included in the corpus via a keyword match in the upstream search index.

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