We mapped ATAC-seq reads to hg19 human genome by Bowtie2 software (v2.2.9) with options “--local -D 15 -R 3 -N 1 -L 20 -i S,1,0.50 -k 1”. Reads with their mates were mapped in the same chromosome and their insert sizes were less than nucleosome size (=150bp) was retained for the identification of open chromatin regions. To identify Tn5 hypersensitive sites (THSs), peak calling was performed by findPeak in HOMER software (v4.9) with “-localSize 50000 -size 100 -minDist 50 -fragLength 0 -o auto”. ΔTHS score was calculated with all pairwise comparison of ESC, hCO and hMGEO by dnase_ddhs_scorer.py script with “-A” option in pyDNase library (v0.2.4) (Figure S2). ATAC-seq peaks with more than four ΔTHS score were defined as unique dOCRs to each stage. Wilcoxon rank-sum test was performed by comparing expression ratio (log2(ratio)) of target and non-target genes of dOCRs to evaluate enrichment of dOCRs. GO analysis was performed to genes, whose distance from dOCRs was less than 10kbp (Figure 4F).
