Fig. 3

Nucleosome organization information from targeted EM-seq of cfDNA. A Fragment length distribution of sequenced cfDNA fragments. A peak value at 167 bp (black dashed line) is consistent with the association with nucleosomes. B The distribution of dinucleotide fraction across 147 bp fragments and the flanking genomic regions. C Genome browser tracks showing sequencing signals of targeted EM-seq of healthy cfDNA (cfDNA targeted EM-seq) and nucleosome calls generated by ENCODE project with accession number ENCSR000CXP (Lymphoblastoid cell MNase-seq). DANPOS2, occupancy values reported by DANPOS2. Raw coverage, occupancy values estimated by read coverage. D-E Aggregate lines showing nucleosome occupancy profiles across TSSs (D) and polyadenylation sites (E) of target genes. PAS, polyadenylation sites. NDR, nucleosome depleted regions. Relative nucleosome occupancy represents nucleosome occupancy normalized by the average value of the plotted regions. Results in this figure are based on merged targeted EM-seq data of 60 healthy controls from cohort 1