Fig. 3

Footprints of DNA-binding proteins in cfDNA. A We classified fragments into two groups according to their length, with a cutoff of 118 bp. The shorter fragments were considered to be derived mainly from nucleosome-free regions (NFRs), whereas the longer fragments were considered to be derived mainly from nucleosome-bound regions (NBRs). B–D Bins per million mapped reads (BPM)-normalized depth around various protein binding regions, including transcription units, transcription start sites (TSSs) or end sites (TESs), transcription factor binding sites (TFBSs), and super enhancer regions, are shown for the plasma sample (B) and the proliferation (C) and apoptosis (D) for GNO samples. E Principal component analysis using the normalized depth of transcription units for all fragments, NFR fragments, or NBR fragments. The shape of each datapoint indicates the state (proliferation or apoptosis), and the color indicates the type of organoid (LNO, GNO, or GCO). The ellipses encompass samples of the same type and state