Extended Data Fig. 3: Principal component analysis of epigenetic datasets.

a, PCA of parental ATAC-seq data colored by strain (top) and batch (bottom). b, PCA of parental H3K27Ac ChIP-seq data colored by strain (top) and batch (bottom). c, PCA of F1 hybrid ATAC-seq and ChIP-seq data with data colored by strain and read alignment method, read alignment methods include perfectly aligned reads (pink) and perfectly aligned reads overlying mutations that discriminate between BALB/cJ and C57BL/6J (maroon). d, PCA of parental LPS treated Kupffer cells with control Kupffer cells as comparison, colored by strain (top) and batch (bottom).