Fig. 4: DSRCT CSC chromatin accessibility alterations.

A Pearson correlation between ATAC-seq biological replicates (S = sphere, A = adherent). B Volcano plot of differentially accessible chromatin regions in sphere versus adherent BER-DSRCT cells (red = sphere-enriched peaks, blue = adherent-enriched peaks). C Feature distribution of ATAC-seq peaks (all = all peaks, stable = peaks with FDR > 0.05, DE = peaks with FDR < 0.05, AAPs = peaks with FDR < 0.05 & sphere/adherent fold < 0, SAPs = peaks with FDR < 0.05 & sphere/adherent fold > 0). D Log2FC (sphere/adherent) RNA expression of closest gene to each ATAC-seq peak for adherent peaks (AAPs), sphere peaks (SAPs), and stable peaks (FDR > 0.05) (****p < 0.0001, student t test). E GSEA of BER-DSRCT sphere/adherent RNA expression data on the sets of the top 250 SAPs and top 250 AAPs. F GO-BP pathways enriched for SAPs and AAPs. G BER-DSRCT adherent (blue) and sphere (red) ATAC-seq tracks for SOX2, SOX13, CSF1, and TJP1. H ChIP-qPCR of differentially accessible regions in DSRCT cells grown in adherent (A) or sphere (S) culture and immunoprecipitated with anti-H3K27ac antibody or control IgG (n = 3, *p < 0.05, **p < 0.01).