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Table 1 Summary of library preparation protocols used in analysis

From: Evaluation of whole-genome DNA methylation sequencing library preparation protocols

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
  1. 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