Fig. 1

Global gene expression changes after Kdm6a KO in BC and CB clones. A Schematic illustrating the Kdm6a CRISPR deletions in BC and CB ES cells. Also included are clone identifiers (see Additional file 8). Exonic (E) deletion results in the loss of about 45 kb in length while the promoter (P) deletion results in a loss of about 4 kb in length. B, C Scatter plots of differential gene expression in three BC male Kdm6a^Δ/Y clones (Kdm6a^ΔE1, Kdm6a^ΔE3, and Kdm6a^ΔP4) versus two male BC wt clones (B), and three CB male Kdm6a ^Δ/Y clones (Kdm6a^ΔE2.5, Kdm6a^ΔE2.7, and Kdm6a^ΔP2.1) versus two CB male wt clones (C). Log₂ values of genes with > 1TPM in at least one replicate are shown. Downregulated DEGs are labeled in red, upregulated DEGs in green, and genes lacking differential expression in grey. DESeq2 was employed to identify differentially expressed genes (DEGs) in each cross using an FDR cutoff of < 0.05 and a ≥ 1.5 fold-change. D Venn diagrams of downregulated and upregulated genes as measured by a ≥ 1.25 fold change in log₂ TPM in male BC and CB Kdm6a^Δ/Y clones versus wt. E GO analysis of dysregulated genes with a ≥ 1.25 fold change in log₂ TPM found in common between the BC and CB crosses. Numbers in parentheses represent the fold enrichment over expected number of genes within a given biological process, while those not in parentheses represent the number of genes in each category. F Log₂ expression fold changes for genes dysregulated in male Kdm6a^Δ/Y clones derived from BC and CB crosses. The genes shown are associated with processes implicated in phenotypes seen in Kabuki syndrome (*p ≤ 0.05; **p ≤ 0.01; Has2 p = .05). See also Additional file 9