Table 1.

Feature comparison among cfMBD-seq, low input MBD-seq, and cfMeDIP-seq

		cfMBD-seq (N = 8)	Low input MBD-seq (N = 4)	cfMeDIP-seq (N = 24)
Experiment
	Filler DNA	Methylated DNA only	No filler	Mixture of methylated and unmethylated DNA
	DNA Denaturation	Not required	Not required	Required
	Capture protein	MeCP2	MBD2	Anti-5mc
	Capture time	5 hours (including 3 hours incubation)	5 hours (including 3 hours incubation)	23 hours (including 17 hours overnight incubation)
Quality Control
	Reads passed filter	83.15% [82.93%-83.68%]	85.40% [85.03%-85.70%]	74.90% [74.53%-75.45%]
	Duplicate rate	3.45% [3.40%-3.90%]	2.65% [2.60%-2.78%]	12.00% [9.00%-19.23%]
	Used reads	79.60% [79.15%-80.43%]	82.75% [82.25%-83.10%]	62.65% [55.60%-66.65%]
Methylation Enrichment
	Reads on CpG islands	60.13% [58.78%-60.81%]	19.95% [19.25%-20.11%]	38.16% [37.21%-41.28%]
	Reads on CpG islands/shores/shelves	94.81% [94.61%-94.98%]	85.70% [85.51%-85.76%]	90.90% [90.91%-91.55%]
	CpG density at peak	29.98 [29.54–30.33]	15.76 [15.41–15.88]	22.88 [22.37–23.50]
	Noise	0.12 [0.12–0.15]	0.13 [0.10–0.16]	0.02 [0.02–0.02]

Median along with [first quartile (Q1) – third quartile (Q3)] are shown. See supplementary table for detail including numbers of raw reads, duplicate reads, uniquely mapping reads, peak, and noise per sample.