Fig. 8: Copy number alterations and MYCN overexpression disrupt chromatin reconfiguration during trunk NC differentiation.

a ATAC-seq read coverage for WT cells at three example loci. The area reports the normalised read count aggregated per genomic bin (width = 500 bp). Multiple semi-transparent plots are overlaid for each replicate. Genes within each locus are shown on top with thin/thick lines indicating introns/exons. The arrows next to gene names indicate the direction of transcription. Selected peaks have been highlighted manually (dashed orange lines). b ATAC-seq read coverage of WT and mutant cells at D19 near the PHOX2B locus. Plots as in (a). c Principal component analysis of all ATAC-seq datasets, split by condition. Each data point represents one ATAC-seq sample with the shape indicating the stage at which the sample was collected. The geometric means of all data of the same stages are connected by arrows to visualise the stepwise chromatin changes. d Euler diagram visualising the overlap of differentially accessible regions in mutant hESC-derived trunk NC derivatives compared to WT (DEseq2¹⁴⁷; P_adj ≤ 0.005, |log₂FoldChange| ≥ log₂(1.5)). Numbers indicate the total number of regions per cell line aggregated over all stages. Source data are provided as a Source Data file. D0/3/9/14/19, day 0/3/9/14/19; WT, wild-type H7 hESCs.