Fig. 3

Allele-specific gene expression changes after Kdm6a KO in male BC and CB clones. A, B Heatmaps of allelic gene expression normalized to the mean of each gene across alleles show the extent of fold changes for maternal (purple) and paternal (dark blue) alleles of downregulated DEGs (DESeq2—≥ 1.5 fold change and FDR < 0.05) (A) and upregulated DEGs (B) in two male wt controls, three male BC KO clones Kdm6a^Δ/Y including two clones Kdm6a^Δ/E with an exon 2–4 deletion (Kdm6a^ΔE1 Kdm6a^ΔE3) and one clone with a promoter deletion (Kdm6a^ΔP4). The genotypes of the clones are color-coded at the top. X-linked gene expression from the paternal allele was masked as zero (white boxes). Z scores (color-coded) representing deviations from the mean for each row are shown for each group of genes. C, D Same analysis as in (A, B) for but for CB clones. See also Table 2 and Additional file 11: Table S11. Group A includes genes downregulated on the maternal allele, group B, on the paternal allele, and group C, on both alleles. Group D includes genes upregulated on the maternal allele, group E, on the paternal allele, and group F, on both alleles