Extended Data Fig. 8: ATAC-seq quality control.

a, Agilent TapeStation profiles obtained by chromatin tagmentation of human islets and EndoC-βH1 samples showing the laddering pattern of ATAC-seq libraries. The band sizes correspond to the expected nucleosomal pattern. *Notice that samples HI-19 CTRL and CYT were used as examples to illustrate the expected fragment distribution pattern in ATAC-seq experiments in Raurell-Vila et al.⁵². b, Summary of per-replicate sequencing metrics, showing total library sizes, percentage of aligned reads, percentage of mitochondrial aligned reads, normalized strand cross-correlation coefficient (NSC, values significantly lower than 1.1 (<1.05) tend to have low signal to noise or few peaks) and relative strand cross-correlation coefficient (RSC, values significantly lower than 1 (<0.8) tend to have low signal to noise). c, TSS enrichment over a 4 kb window centered on genes TSS compared to a set of genes randomized along the genome, showing the expected pattern of open chromatin centered on the TSS. d, Percentage of total reads found at called open chromatin peaks classified as distal (>2 kb from TSS) or promoters (≤2 kb from TSS) compared to a randomized set of peaks. e, UCSC views at islet-specific loci (NKX6.1, PDX1 and NEUROD1) showing the high reproducibility of ATAC-seq profiles among independent replicates.