Fig. 1: Allele-specific changes in gene expression after Msl2 deletion.
a, Schematic of polymorphic male and female WT and Msl2-KO hybrid ES cell lines and ES-cell-derived clonal NPCs. The diagram was created using BioRender. A1, allele 1; A2, allele 2. b, Comparison of standard and allele-specific differential expression (DE) analysis between Msl2 KO and WT in male CaBl and BlCa and female CaBl and 9sCa NPCs. The blue dots indicate significantly differentially expressed genes from the standard analysis (q < 0.01). The red dots represent significantly differentially expressed genes from the allele-specific analysis (P < 0.05). c, Categorization of differentially expressed genes in WT (grey) and Msl2-KO (KO1/2 clones, pink) NPCs (left). Expression levels of allele 1 and allele 2 from allele-specific DE analysis are shown for male CaBl and female 9sCa WT and Msl2-KO1/2 NPCs (right). Significance was determined using two-sided nonparametric Wilcoxon rank-sum tests; *P < 0.05, **P < 0.01, ***P < 0.001; not significant (NS), P > 0.05. Exact P values are summarized in the Source Data. Sample sizes for statistical tests (from top to bottom): n = 177, 171, 67, 92, 1,068 and 300 (left) and n = 180, 130, 85, 87, 940 and 300 (right). Details on the box plots are provided in the Methods. d, Allelic differential expression changes (log2[FC] (Msl2 KO/WT)) in male CaBl and BlCa and female CaBl and 9sCa NPCs.
