Extended Data Fig. 6: Characterization of SPEN expression and KD.
From: XIST dampens X chromosome activity in a SPEN-dependent manner during early human development
a, Protein abundance level of SPEN from publicly available proteomics data62 in naïve (n = 3) and primed (eroded) (n = 3) H9 cells. Data are presented as mean values +/- SD of replicates. Wilcoxon p-value = ns≥0.05. b, Expression level in CPM of naïve and core pluripotency factors in control (siScr) and SPEN knockdown naïve H9 (n = 3). Data are presented as mean values +/- SD of replicates. c, Volcano plots representing the significance versus Log2 fold change for all differentially expressed genes (FDR < 0.05, log2FC > |1 | ) upon SPEN KD (n = 3). Upregulated and downregulated X-linked genes are highlighted. d, Venn diagram showing the intersection of differentially expressed genes between siSPEN1 and siSPEN2 datasets. e, Bar plot showing the number of differentially expressed genes on all chromosomes in siSPEN1 and siSPEN2 conditions compared to siScr. f, Percentage of biallelically expressed SNPs from chromosome 7 in siScr (n = 3) and siSPEN (n = 3) naïve H9, obtained from RNA-seq data. g, X/A ratio from RNA-seq data of siRNA SPEN KD in naïve H9 cells (n = 3). Data are presented as mean values +/- SD of replicates. Unless otherwise specified, p-values were calculated by two-sided unpaired t-test. Levels of significance: ns≥0.05; * < 0.05; ** < 0.01; *** < 0.001; **** < 0.0001.
