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

BMC Genomics

Table 1 Sequence Analysis Details for ATAC-seq Samples

Avg. no. sequence reads/sample	89 M
Avg. no. reads mapped/sample	69 M (77.5%)
Avg. no. reads/sample after duplicate removal and equalization	43 M (48.3%)
Avg. no. peaks called/sample	367,113
Avg. fraction reads in peaks	0.635
No. peaks in RPS	295,441
Avg. size of peak in RPS	597 bp
Genome coverage of RPS	18.84%
No. differential peaks (p < 0.2)	1582
No. differential peaks within 10 kb of genes	1063
No. differential peaks within 10 kb of PMC DE genes	275; 5.99-fold enrichment (p < 2.2e-16)

One thousand five hundred eighty two peaks with nominal p-values < 0.2 as calculated by DESeq2 [85] were determined to be enriched in the isolated PMCs compared to the other non-PMC cells: these are ATAC-seq differential peaks. Two hundred seventy five of the 1582 differential peaks were found to be within 10 kb of PMC DE genes, a highly significant enrichment

ISSN: 1471-2164