Differential binding analysis (DBA) was performed across the entire mouse genome to estimate the level of technical noise to be expected for a given factor. Identified regions were annotated as promoter, intragenic, and intergenic using compEpiTools R-package (Kishore et al., 2015). (A) Only ten regions showed differences in H3K4me3 occupancy between female and male germline-derived Tc1 mice with a fold change greater than 2.5 (FDR < 0.1), all of which were low-intensity. (B) Across the entire mouse genome, 471 regions (~1% of the 47,000 total) enriched for H3K27ac showed differences between female and male germline-derived Tc1 mice with a fold change greater than 2.5. Most of these 471 regions showed higher signal intensity in male germline-derived offspring. (C) To estimate the expected background for ChIP assays, four biological replicates of H3K27ac in livers of BL6 wild-type mice were randomly assigned to two conditions to mirror the male-female germline experiment. Comparison of these two randomly assigned H3K27ac experiments identified 599 sites with a fold change greater than 2.5 (FDR <0.1) that were evenly distributed around the diagonal.