Highly quantitative measurement of differential protein-genome binding with PerCell chromatin sequencing

Quantitative comparison of ChIP-seq profiling between experimental conditions or samples remains technically challenging for the epigenetics field. Here, we report a strategy combining the use of well-defined cellular spike-in ratios of orthologous species' chromatin and a bioinformatic analysis pipeline to facilitate highly quantitative comparisons of 2D chromatin sequencing across experimental conditions. We find that the PerCell methodology results in efficient and consistent levels of spike-in vs. experimental genomic reads. We demonstrate use of the method and pipeline to enable quantitative, internally normalized chromatin sequencing on zebrafish embryos and human cancer cells. Overall, we propose the PerCell method to enable cross-species comparative epigenomics and promote uniformity of data analyses and sharing across labs. Overall design: Chromatin immunoprecipitation DNA sequencing (ChIP-seq) for 1) H3K27ac histone modification in Rh4 rhabdomyosarcoma cells treated with DMSO, 0.5 µM A485, or 0.5 µM Entinostat; and 2) CTCF in Rh4 rhabdomyosarcoma cells with 100%, 75%, 50%, or 25% of spike-in mouse reads retained.