Table 1.

Summary of library preparation protocols used in analysis

Short Name	Kapa	NEB	PBAT	Swift	Low NEB	Low Swift
Company Name	Roche Sequencing	New England Biolabs	N/A	Swift Biosciences	New England Biolabs	Swift Biosciences
Kit / Protocol Name	KAPA Hyper Prep	NEBNext Enzymatic Methyl-seq	Miura F., Ito T. (2018)	Accel-NGS Methyl-Seq	NEBNext Enzymatic Methyl-seq	Accel-NGS Methyl-Seq
Kit or Protocol?	Kit	Kit	Protocol	Kit	Kit	Kit
Strands aligned to	OT/OB	OT/OB	CTOT/CTOB	OT/OB	OT/OB	OT/OB
WGBS or EM-seq?	WGBS	EM-seq	WGBS	WGBS	EM-seq	WGBS
DNA Input [ng]	300	200	100	100	10	10
# Samples	2 (A/B)	2 (A/B)	2 (A/B)	2 (A/B)	2 (A/B)	2 (A/B)
# Tech. Reps.	2 (1/2)	2 (1/2)	1 (1)	2 (1/2)	2 (1/2)	2 (1/2)
Sheared?	Yes	Yes	No	Yes	Yes	Yes
Conversion Kit	EZ DNA Methylation-Gold kit	N/A	EZ DNA Methylation-Gold kit	EZ DNA Methylation-Gold kit	N/A	EZ DNA Methylation-Gold kit
# Amplification Rounds	10	4	0	4	8	8
DNA Controls	lambda phage / pUC19	lambda phage / pUC19	lambda phage / pUC19	lambda phage / pUC19	lambda phage / pUC19	lambda phage / pUC19
Sequencer Used	Illumina NovaSeq6000	Illumina NovaSeq6000	Illumina NovaSeq6000	Illumina NovaSeq6000	Illumina NovaSeq6000	Illumina NovaSeq6000
Approx. Processing Time [hrs]	7	9	14-16	7	9	7

Throughout the text, the “Short Name” entry is used to describe which protocol is being discussed, rather than the full name. Sample and technical replicate names are included in parentheses. The lambda phage control is unmethylated, while the pUC19 control is methylated. These were added to the high molecular weight genomic DNA sample at a rate of 0.01% and 0.0005%, respectively. The OT and OB strands are the original top and original bottom strands, while the CTOT and CTOB are the complements of the original top and original bottom strands, respectively. These strands can also be referred to as the bisulfite Watson (OT), bisulfite Crick (OB), bisulfite Watson reverse (CTOT), and bisulfite Crick reverse (CTOB) strands