Fig. 6

Windowed protection score with a 200-bp window size (WPS₂₀₀) at the TSS ± 2 kb of genes with high tissue expression in the bladder and kidney, but low expression (< 0.5 transcripts per million) in whole blood. The “high expression” groups for the kidney and bladder contained genes with expression levels between 4.5 and 928.0 transcripts per million and 7.8 and 731.3 transcripts per million, respectively. For genes with the highest bladder expression (a) and kidney expression (b), a clear nucleosome positioning signal in urine-derived cfDNA, but not in blood-derived cfDNA, is visible. For comparison, genes with the highest expression in whole blood (c) have a WPS₂₀₀ peak in both urine- and blood-derived cfDNA, as most of these genes are ubiquitously expressed. High-expression gene groups contain n = 1000 genes; zero expression gene groups contain n = 1458 genes for the bladder, n = 1429 for the kidney, and n = 2447 for the whole blood. d Overlap between genes with high kidney- and bladder-expression levels according to GTEx. About 38% of genes are shared between the two groups. e Overlap between genes with zero expression according to GTEx. About 36% of genes are shared between all groups. Fragments of 200–500 bp are studied in the merged datasets of the three healthy control individuals K16, K17, and K18. X-axes: offset from TSS in base pairs, Y-axes: normalized aggregate WPS₂₀₀