Extended Data Fig. 3: Characterization of XIST enrichment on the X chromosome in naïve and primed hESCs.
From: XIST dampens X chromosome activity in a SPEN-dependent manner during early human development
a, PCA plot displaying the first two principal components of the XIST RAPseq data in naïve (PXGL) and primed H9 hESCs. b, Heatmap showing the Pearson correlation between naïve and primed XIST RAPseq replicates on the X chromosome. c, XIST RAPseq profiles showing the log2 enrichment over the X chromosome in naïve compared to primed H9 hESCs. d, Scatter plots showing the linear regression line and Pearson correlation for the comparison of XIST coverage scores with gene, LINE, retrotransposon, and LTR densities in naïve and primed H9 hESCs. e, Expression levels of XIST from naïve: PXGL (n = 3) and NaiveCult (n = 3), and primed (n = 3) H9 RNA-seq data. Data are presented as mean values +/- SD of replicates. f, CUT&RUN H3K4me3 profiles across the XIST gene in naïve and primed H9. XIST spliced isoforms detected in naïve and primed H9 along with the A-F repeats are shown. Arbitrary name of each isoform (XIST1.1, XIST1.2, etc) is indicated on the left, together with their expression pattern (Primed and/or Naïve). 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.
