Supplementary Figure 11: ATAC-seq quality metrics.

a, Fragment length distribution of ATAC-seq reads from all size-selected libraries. Most of the reads fall into the NFR ( < 100 bp) and a clear mono-nucleosomal peak can be seen in all libraries. b, Fraction of reads per sample that fall into the NFR ( < 100 bp). All libraries show a similar high amount of NFR c, Distribution of peak width between conditions called on NFR reads with the parameters defined in Supplementary Methods. d, Principal component analysis based on DA peaks shows a clear separation between the ASD and control group; ASD: n = 8, control: n = 5. e, Enrichment (log2 FoldChange) for DA peaks that fall into gene-distal regions of the identified TMs. f, Fraction of TM hub genes (kME > 0.8) with DA peaks in gene-distal regions. g, Coverage maps of normalized ATAC-seq signals from ASD and control NSCs around the promoter region of NCDN, a TM1-associated gene, on chromosome 1. Individual sample coverages (ASD: n = 8, control: n = 5) are displayed and annotations below are based on previously annotated chromatin states (see Supplementary Methods).