Global analysis of primary mesenchyme cell cis-regulatory modules by chromatin accessibility profiling

BMC Genomics

Table 3 Correspondence Between ATAC-seq and DNase-seq Datasets

No. peaks in DNase-seq RPS	157,108
No. peaks in ATAC-seq RPS	295,441
No. of DNase-seq RPS peaks overlapping ATAC-seq RPS peaks	138,145 (88% of DNase-seq RPS)
No. of ATAC-seq RPS peaks overlapping DNase-seq RPS peaks	130,552 (44% of ATAC-seq RPS)
No. of DNase-seq differential peaks	1659 peaks
No. of ATAC-seq differential peaks	1582 peaks
No. of overlapping differential peaks	161 (p = 2.2e-16)
No. of overlapping differential peaks within 10 kb of PMC DE genes	73 (p < 5.5e-10; 2.38-fold avg. enrichment)

One hundred sixty one peaks are present in both the DNase-seq and ATAC-seq differential peak set, overlapping by at least 75% in one direction. Of these 161 overlapping peaks, 73 are within 10 kb of PMC DE genes

ISSN: 1471-2164