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

BMC Genomics

Table 2 Sequence Analysis Details for DNase-seq Samples

Avg. no. sequenced reads/sample	23.5 M
Avg. no. reads mapped/sample	19 M (80.8%)
Avg. no. reads mapped/sample after duplicate removal and equalization	14.7 M (62.5%)
Avg. no. peaks called/sample	256,007
Avg. fraction reads in peaks	0.55
No. peaks in RPS	157,108
Avg. size of peak in RPS	637 bp
Genome coverage of RPS	10.68%
No. differential peaks (p < 0.1)	1659
No. differential peaks within 10 kb of a gene	1287
No. differential peaks within 10 kb of a PMC DE gene	258; 5.31-fold enrichment (p < 2.2e-16)

One thousand six hundred fifty nine peaks with nominal p-values < 0.1 as calculated by DESeq2 [85] were determined to be enriched in the control embryos compared to PMC (−) embryos: these are DNase-seq differential peaks. Two hundred fifty eighty of these peaks were found to be within 10 kb of PMC DE genes

ISSN: 1471-2164