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Protocol for using heterologous spike-ins to normalize for technical variation in chromatin immunoprecipitation.

STAR protocols (2021-07-01)
Franziska Greulich, Aikaterini Mechtidou, Teresa Horn, Nina Henriette Uhlenhaut
ABSTRACT

Quantifying differential genome occupancy by chromatin immunoprecipitation (ChIP) remains challenging due to variation in chromatin fragmentation, immunoprecipitation efficiencies, and intertube variability. In this protocol, we add heterologous spike-ins from Drosophila chromatin as an internal control to the mice chromatin before immunoprecipitation to normalize for technical variation in ChIP-qPCR or ChIP-seq. The choice of spike-in depends on the evolutionary conservation of the protein of interest and the antibody used. For complete details on the use and execution of this protocol, please refer to Greulich et al. (2021).

MATERIALS
Product Number
Brand
Product Description

Sigma-Aldrich
Glycine, ReagentPlus®, ≥99% (HPLC)
Sigma-Aldrich
Water, BioPerformance Certified