Fig. 3

Identification and characterization of paternal-X expression in Eed ^+/+, Eed ^fl/fl, and Eed ^–/– TSCs. a Summary of allele-specific RNA-seq analysis of X-linked genes. b, c Euler diagrams assessing expression from the paternal X chromosome totaling ≥ 10% of total expression in three WT Eed ^+/+ TSC lines and one WT Eed ^fl/fl TSC line (b) and in three Eed ^–/– TSC lines (c). d Comparison of percent paternal-X expression in Eed ^–/– TSC lines compared with WT TSC lines. Percent paternal-X expression for individual Eed ^–/– TSC lines was compared with the average percent paternal-X expression in WT TSC lines (left). e Identification of genes with statistically significant difference in percent paternal-X expression in Eed ^–/– TSCs compared with WT TSCs. Percent paternal-X expression in the four WT TSC lines and three Eed ^–/– TSC lines was compared by T-test for the 77 genes that display a consistent increase in paternal-X expression in Eed ^–/– TSC lines. Of these, 74 genes are statistically significantly increased in paternal-X expression in Eed ^–/– TSC lines, following Benjamini–Hochberg correction of the p values for multiple testing (FDR = 0.1)