Extended Data Fig. 2: Differential gene expression analyses of WT and Msl2-KO ESC and NPCs.

(a) Standard differential expression (DE) (top) and allele-specific DE analysis (bottom) of Msl2-KO and WT in male CaBl/BlCa and female 9sCa ESCs. Blue dots represent significant DEgenes from standard analysis which compares total gene expression levels of  Msl2 KO to WT (KO/WT) (q-value < 0.01). Red dots represent significant DEgenes from allele-specific analysis which compares gene expression changes for allele 2 (A2) (KO/WT) to allele 1 (A1) (KO/WT) (p-value < 0.05, see Methods). Total number of DEgenes are indicated at the top. (b) Number of significantly up- (blue) and down-regulated (red) genes upon Msl2 KO obtained by standard DE analysis (q-value < 0.01). (c) Circos plots compare allelic downregulated genes in female 9sCa and male BlCa/CaBl ESCs (left) and male CaBl/BlCa and female CaBl/9sCa NPCs (right) on allele 1 (magenta) and allele 2 (cyan). Outer circle colours indicate the cell line (see a) and middle circle rulers indicate the number of significantly downregulated genes per cell line per allele (p-value < 0.01). Inner circle connections represent common genes between cell lines. Grey bars show overlapping downregulated genes between allele 1 and allele 2 for each cell line. (d) Allelic downregulated genes among female 9sCa and male CaBl/BlCa ESCs (top) and male CaBl/BlCa, female CaBl/9sCa NPCs (bottom). DEgenes for allele 1 (left) and allele 2 (right) are depicted. Significance was tested using Fisher’s exact test comparing NPCs to ESCs on individual alleles (see Methods). (e) Overlap of significantly downregulated genes obtained from standard (red), allele 1 (blue) and allele 2 (yellow) DE analysis for three ESCs (top) and four NPCs (bottom). (f) Gene ontology enrichment of allelic significantly downregulated genes identified in male CaBl/BlCa and female CaBl/9sCa NPCs (p-value < 0.01) (see c). Size of black dots indicates gene category ratio and colour range represents adjusted p-value (red to blue). (g) Gene ontology enrichment analysis of allelically significantly downregulated genes identified in female 9sCa and male CaBl/BlCa ESCs (p-value < 0.01). The ratio of genes in each category is indicated by the size of the dots and the adjusted p-value is highlighted by colour range (red to blue). (h) Number of significantly allele1- (blue) and allele2-biased (red) genes upon  Msl2 KO in female 9sCa, male CaBl/BlCa ESCs and female 9sCa/CaBl, male CaBl/BlCa NPCs obtained by allele-specific DE analysis (p-value < 0.05).