Fig. 6
From: Multidimensional fragmentomic profiling of cell-free DNA released from patient-derived organoids
Reconstruction of circular DNA from cfDNA WGS data. A Cumulative proportions of circular DNA lengths in the plasma and organoid samples. B, C Length distribution analysis of circular DNA shorter than 1 kb in the plasma sample (B) and the organoid samples (C). D Circular DNA motifs around junction breaks according to cell states and circular DNA sizes in an LNO sample. Similar results were obtained for other replicates (data not shown). Junction breaks are indicated by gray dashed lines and triangle symbols. E The proportion of junction breaks in RepeatMasker-defined repeat classes for the organoid samples. Blue horizontal bars represent the proportions of RepeatMasker-defined repeats in the human genome. Red error bars represent the standard error of the mean. F Comparison of the number of circular DNA (counts per million mapped reads) for each sample type. Statistical analyses were performed using the R package rstatix, with Welch’s t test or a pairwise t test with Bonferroni correction (ns: not significant; p < 0.05 and *p < 0.01)