Supplementary Fig. 11: Differential analysis of single-cell ChIP-seq H3K27me3 profiles of mouse stromal cells from the HBCx-95 model.

(a) Left panel: differentially bound regions in cells from each cluster versus all remaining cells identified by two-sided Wilcoxon signedrank test. Genomic regions were considered enriched (red) or depleted (green) if the adjusted P values were lower than 0.01 and the absolute log2 fold change greater than 1. Middle and right panels: barplots displaying the -log10 of adjusted P values from pathway analysis (using MSigDB, adjusted P value < 0.1) for regions depleted in H3K27me3 specifically in Chrom_c2 and Chrom_c3. The top 10 significant gene sets are indicated on the barplots. (b) Left panel: snapshot of a differentially depleted locus for cells from Chrom_c2 (Col4a1) versus all other cells, with cumulative single-cell profiles for each cell type and cluster (n = 276, 184 and 307 single-cells for Chrom_c1, Chrom_c2 and Chrom_c3 respectively). Differentially bound regions identified by two-sided Wilcoxon signed-rank test is indicated in gray with the corresponding adjusted P value and log2 fold change, calculated in respect to Chrom_c2. The number and the proportion of cells with H3K27me3 enrichment within each cluster are indicated above tracks. Right panels: t-SNE representation of scChIP-seq and scRNA-seq datasets, dots are colored according to H3K27me3 enrichment and expression signals in each cell for Col4a1 locus.