Additional file 7 of KDM6A facilitates Xist upregulation at the onset of X inactivation

Additional file 7 Supplemental Figure S4. Confirmation of X-linked gene expression changes in E8-Kdm6aΔPΔP13 KO cells. (A) Allelic X-linked gene expression ratios (BL6:cast) in E8 wt and KO cells (E8-Kdm6aΔPΔP13) at D0, D2, and D4 of differentiation. Ratios between expressed X-linked genes (>1TPM) are shown. X expression ratios near 0.5 reflect the largely random nature of XCI in these cells. (B) Plots of expression changes from the BL6 and cast X chromosomes in E8 wt and KO cells (E8-Kdm6aΔPΔP13) at D4. The XIC is highlighted. Log2 TPM fold change (KO/wt) along the X chromosomes is shown. Genes with a decrease of expression in KO versus wt are in blue, and with an increase in red. (D) Venn diagram of the number of X-linked genes with upregulation following Kdm6a KO. The majority of genes are upregulated from the BL6 and cast X chromosomes. (D) Plots of expression changes (based on log2 TPM) for genes with increased expression from each X chromosome (BL6 purple and cast blue) between E8 wt and E8-Kdm6aΔPΔP13 KO cells at D4. The X-axis includes 254 X-linked genes. There is a slightly greater increase in expression from the BL6 X chromosome (purple).