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nebnext enzymatic methyl seq conversion module  (New England Biolabs)


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    New England Biolabs nebnext enzymatic methyl seq conversion module
    Nebnext Enzymatic Methyl Seq Conversion Module, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 96/100, based on 183 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/modules/NEBNext+Enzymatic+Methyl-seq+Conversion+Module/pm42897348-329-8-8
    Average 96 stars, based on 183 article reviews
    nebnext enzymatic methyl seq conversion module - by Bioz Stars, 2026-11
    96/100 stars

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    Related Articles

    Purification:

    Article Title: Molecular predictors of minimal residual disease in newly diagnosed multiple myeloma treated with quadruplet therapy.
    Article Snippet: .. After purification, the libraries were converted with the NEBNext Enzymatic Methyl-seq Conversion Module according to the manufacturer’s recommendations; then, they were PCR-amplified and indexed. .. The libraries were sequenced on an Illumina NovaSeq X Plus sequencer as paired-end 2 × 150 bp reads, with an average depth of 13X.

    Article Title: The discovery of 5mC-selective deaminases and their application to ultra-sensitive direct sequencing of methylated sites at base resolution.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains XP12 ATCC 35934-B1 T4gt New England Biolabs N/A Unmethylated Lambda phage gDNA Promega Cat# D1521 5mCpG pUC19 plasmid DNA New England Biolabs Cat# E7122AAVIAL E.coli K-12 DHB4 gDNA New England Biolabs GenBank accession: CP014270.1 T7 Express Competent E.coli New England Biolabs Cat# C2566H 7 Express lysY/Iq Competent E. coli New England Biolabs Cat# C3013 dcm-6 cell gDNA New England Biolabs ER3662, CGSC Strain#: 6475 Δdcm cell gDNA New England Biolabs ER2861 Natrinema pallidum BOL6-1 gDNA This study GCF_005890195.1 Biological samples Human GM12878 gDNA Coriell Institute Cat# NA12878 Human brain gDNA biochain Cat# D1234035, LOT# C607510 Single donor human blood derived plasma Innovative Research Cat# IPLASK2E2ML HCT116 cell line ATCC Cat# CCL-247 DNMT1 and DNMT3b DKO HCT116 cell line John Hopkins Medicine N/A Chemicals, peptides, and recombinant proteins Acetic acid, LC-MS grade Sigma Cat# 49199-50ML-F Ammonium acetate, LC-MS grade Sigma Cat# 73594-100G-F Deoxynucleotide (dNTP) Solution Set New England Biolabs Cat# N0446S Methanol, LC-MS grade Sigma Cat#EM-MX0486-1 5-methyl-dCTP New England Biolabs Cat# N0356S Nuclease-free water New England Biolabs Cat# B1500L Quick CIP New England Biolabs Cat# M0525S Water, LC-MS grade VWR/BDH Cat# BDH23595.400 BugBuster Master Mix Millipore Cat #70584-M NEBExpress® E. coli Lysis Reagent New England Biolabs Cat# P8116 PEG8000 Sigma P5413 NaCl powder Sigma P9888 1M Tris-HCl, pH7.5, ultra pure grade AMRESCO E691 1M Tris-HCl, pH8.0, ultra pure grade AMRESCO E199 HpaII New England Biolabs Cat# R0171S HaeIII New England Biolabs Cat# R0108S AluI New England Biolabs Cat# R0137S AciI New England Biolabs Cat# R0551S BfaI New England Biolabs Cat# R0568S HhaI New England Biolabs Cat# R0139S HpyCH4IV New England Biolabs Cat# R0619S HpyCH4V New England Biolabs Cat# R0620S NlaIII New England Biolabs Cat# R0125S 10x rCutSmart Buffer New England Biolabs Cat# E6004 Proteinase K New England Biolabs Cat# P8107 AMPure XP beads Beckman Coulter Cat# A63880 NEBNext Ultra II Q5 Master Mix New England Biolabs Cat# E7645 (Continued on next page) Molecular Cell 86, 1–16.e1–e11, May 7, 2026 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Nucleoside digestion mix New England Biolabs Cat# M0649S 5-methyl-dCTP New England Biolabs Cat# N0356S rAlbumin New England Biolabs Cat# E9200 10x Deamination Buffer New England Biolabs Cat# E3356 T4 Phage β-glucosyltransferase (BGT) New England Biolabs Cat# M0357 1 M Bis-Tris, pH 6.07 Teknova B7305 Zinc chloride Sigma 208086 Imidazole Sigma I2399 NEBNext Sample Purification Beads New England Biolabs Cat# E7103 NEBNext Ultra II Q5U master mix New England Biolabs Cat# M0597 USER enzyme New England Biolabs Cat# M5505 Critical commercial assays NEBExpress® Ni-NTA Magnetic Beads New England Biolabs Cat# S1423 Monarch genomic DNA purification kit New England Biolabs Cat# T3010 Oligo clean and concentrator kit Zymo Cat# D4060 NEBNext Ultra II DNA library preparation kit New England Biolabs Cat# E7645 NEBNext Multiplex Oligos for Illumina New England Biolabs Cat# E6400 Monarch Plasmid Miniprep kit New England Biolabs Cat# T1110 Oligo cleanup and purification kit Norgen Biotek Cat# SKU34100 SMRT-bell Express Template Prep Kit PacBio Cat# 100-938-900 NEBNext Enzymatic Methyl-Seq Conversion Module New England Biolabs Cat# E7120 Deposited data Sequencing reads SRA PRJNA1200041 metaGPA1_B5 GenBank PV943624 metaGPA1_C4 GenBank PV943625 metaGPA1_D5 GenBank PV943626 metaGPA1_E10 GenBank PV943627 metaGPA1_E8 GenBank PV943628 metaGPA1_F4 GenBank PV943629 metaGPA2_H2 GenBank PV943630 metaGPA2_A10 GenBank PV943631 metaGPA2_A11 GenBank PV943632 metaGPA2_A8 GenBank PV943633 metaGPA2_C10 GenBank PV943634 metaGPA2_C5 GenBank PV943635 metaGPA2_E10 GenBank PV943636 metaGPA2_E12 GenBank PV943637 metaGPA2_F12 GenBank PV943638 metaGPA2_F7 GenBank PV943639 metaGPA2_G5 GenBank PV943640 metaGPA2_H10 GenBank PV943641 metaGPA2_H3 GenBank PV943642 metaGPA2_H4 GenBank PV943643 Oligonucleotides CE oligo L1 IDT /56-FAM/-ATACACCGATGCAGAA/iMe-dC/TCAT GGGCTTACGC (Continued on next page) e2 Molecular Cell 86, 1–16.e1–e11, May 7, 2026 ..

    Polymerase Chain Reaction:

    Article Title: Molecular predictors of minimal residual disease in newly diagnosed multiple myeloma treated with quadruplet therapy.
    Article Snippet: .. After purification, the libraries were converted with the NEBNext Enzymatic Methyl-seq Conversion Module according to the manufacturer’s recommendations; then, they were PCR-amplified and indexed. .. The libraries were sequenced on an Illumina NovaSeq X Plus sequencer as paired-end 2 × 150 bp reads, with an average depth of 13X.

    Bisulfite Methylation Profiling:

    Article Title: A comparative study of DNA conversion techniques: Assessing efficiency and sample suitability of enzymatic and bisulfite methods.
    Article Snippet: Bisulfite conversion, the conventional method for DNA methylation analysis, converts unmethylated cytosine to uracil while leaving methylated cytosine unchanged.. A recently developed enzymatic conversion method employing mild reaction conditions produces DNA sequences identical to those generated by bisulfite treatment.. In this method, methylated cytosine is oxidized to 5-carboxycytosine (5caC) by ten-eleven translocation dioxygenase 2 (TET2).

    Sample Purification:

    Article Title: The discovery of 5mC-selective deaminases and their application to ultra-sensitive direct sequencing of methylated sites at base resolution.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains XP12 ATCC 35934-B1 T4gt New England Biolabs N/A Unmethylated Lambda phage gDNA Promega Cat# D1521 5mCpG pUC19 plasmid DNA New England Biolabs Cat# E7122AAVIAL E.coli K-12 DHB4 gDNA New England Biolabs GenBank accession: CP014270.1 T7 Express Competent E.coli New England Biolabs Cat# C2566H 7 Express lysY/Iq Competent E. coli New England Biolabs Cat# C3013 dcm-6 cell gDNA New England Biolabs ER3662, CGSC Strain#: 6475 Δdcm cell gDNA New England Biolabs ER2861 Natrinema pallidum BOL6-1 gDNA This study GCF_005890195.1 Biological samples Human GM12878 gDNA Coriell Institute Cat# NA12878 Human brain gDNA biochain Cat# D1234035, LOT# C607510 Single donor human blood derived plasma Innovative Research Cat# IPLASK2E2ML HCT116 cell line ATCC Cat# CCL-247 DNMT1 and DNMT3b DKO HCT116 cell line John Hopkins Medicine N/A Chemicals, peptides, and recombinant proteins Acetic acid, LC-MS grade Sigma Cat# 49199-50ML-F Ammonium acetate, LC-MS grade Sigma Cat# 73594-100G-F Deoxynucleotide (dNTP) Solution Set New England Biolabs Cat# N0446S Methanol, LC-MS grade Sigma Cat#EM-MX0486-1 5-methyl-dCTP New England Biolabs Cat# N0356S Nuclease-free water New England Biolabs Cat# B1500L Quick CIP New England Biolabs Cat# M0525S Water, LC-MS grade VWR/BDH Cat# BDH23595.400 BugBuster Master Mix Millipore Cat #70584-M NEBExpress® E. coli Lysis Reagent New England Biolabs Cat# P8116 PEG8000 Sigma P5413 NaCl powder Sigma P9888 1M Tris-HCl, pH7.5, ultra pure grade AMRESCO E691 1M Tris-HCl, pH8.0, ultra pure grade AMRESCO E199 HpaII New England Biolabs Cat# R0171S HaeIII New England Biolabs Cat# R0108S AluI New England Biolabs Cat# R0137S AciI New England Biolabs Cat# R0551S BfaI New England Biolabs Cat# R0568S HhaI New England Biolabs Cat# R0139S HpyCH4IV New England Biolabs Cat# R0619S HpyCH4V New England Biolabs Cat# R0620S NlaIII New England Biolabs Cat# R0125S 10x rCutSmart Buffer New England Biolabs Cat# E6004 Proteinase K New England Biolabs Cat# P8107 AMPure XP beads Beckman Coulter Cat# A63880 NEBNext Ultra II Q5 Master Mix New England Biolabs Cat# E7645 (Continued on next page) Molecular Cell 86, 1–16.e1–e11, May 7, 2026 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Nucleoside digestion mix New England Biolabs Cat# M0649S 5-methyl-dCTP New England Biolabs Cat# N0356S rAlbumin New England Biolabs Cat# E9200 10x Deamination Buffer New England Biolabs Cat# E3356 T4 Phage β-glucosyltransferase (BGT) New England Biolabs Cat# M0357 1 M Bis-Tris, pH 6.07 Teknova B7305 Zinc chloride Sigma 208086 Imidazole Sigma I2399 NEBNext Sample Purification Beads New England Biolabs Cat# E7103 NEBNext Ultra II Q5U master mix New England Biolabs Cat# M0597 USER enzyme New England Biolabs Cat# M5505 Critical commercial assays NEBExpress® Ni-NTA Magnetic Beads New England Biolabs Cat# S1423 Monarch genomic DNA purification kit New England Biolabs Cat# T3010 Oligo clean and concentrator kit Zymo Cat# D4060 NEBNext Ultra II DNA library preparation kit New England Biolabs Cat# E7645 NEBNext Multiplex Oligos for Illumina New England Biolabs Cat# E6400 Monarch Plasmid Miniprep kit New England Biolabs Cat# T1110 Oligo cleanup and purification kit Norgen Biotek Cat# SKU34100 SMRT-bell Express Template Prep Kit PacBio Cat# 100-938-900 NEBNext Enzymatic Methyl-Seq Conversion Module New England Biolabs Cat# E7120 Deposited data Sequencing reads SRA PRJNA1200041 metaGPA1_B5 GenBank PV943624 metaGPA1_C4 GenBank PV943625 metaGPA1_D5 GenBank PV943626 metaGPA1_E10 GenBank PV943627 metaGPA1_E8 GenBank PV943628 metaGPA1_F4 GenBank PV943629 metaGPA2_H2 GenBank PV943630 metaGPA2_A10 GenBank PV943631 metaGPA2_A11 GenBank PV943632 metaGPA2_A8 GenBank PV943633 metaGPA2_C10 GenBank PV943634 metaGPA2_C5 GenBank PV943635 metaGPA2_E10 GenBank PV943636 metaGPA2_E12 GenBank PV943637 metaGPA2_F12 GenBank PV943638 metaGPA2_F7 GenBank PV943639 metaGPA2_G5 GenBank PV943640 metaGPA2_H10 GenBank PV943641 metaGPA2_H3 GenBank PV943642 metaGPA2_H4 GenBank PV943643 Oligonucleotides CE oligo L1 IDT /56-FAM/-ATACACCGATGCAGAA/iMe-dC/TCAT GGGCTTACGC (Continued on next page) e2 Molecular Cell 86, 1–16.e1–e11, May 7, 2026 ..

    Magnetic Beads:

    Article Title: The discovery of 5mC-selective deaminases and their application to ultra-sensitive direct sequencing of methylated sites at base resolution.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains XP12 ATCC 35934-B1 T4gt New England Biolabs N/A Unmethylated Lambda phage gDNA Promega Cat# D1521 5mCpG pUC19 plasmid DNA New England Biolabs Cat# E7122AAVIAL E.coli K-12 DHB4 gDNA New England Biolabs GenBank accession: CP014270.1 T7 Express Competent E.coli New England Biolabs Cat# C2566H 7 Express lysY/Iq Competent E. coli New England Biolabs Cat# C3013 dcm-6 cell gDNA New England Biolabs ER3662, CGSC Strain#: 6475 Δdcm cell gDNA New England Biolabs ER2861 Natrinema pallidum BOL6-1 gDNA This study GCF_005890195.1 Biological samples Human GM12878 gDNA Coriell Institute Cat# NA12878 Human brain gDNA biochain Cat# D1234035, LOT# C607510 Single donor human blood derived plasma Innovative Research Cat# IPLASK2E2ML HCT116 cell line ATCC Cat# CCL-247 DNMT1 and DNMT3b DKO HCT116 cell line John Hopkins Medicine N/A Chemicals, peptides, and recombinant proteins Acetic acid, LC-MS grade Sigma Cat# 49199-50ML-F Ammonium acetate, LC-MS grade Sigma Cat# 73594-100G-F Deoxynucleotide (dNTP) Solution Set New England Biolabs Cat# N0446S Methanol, LC-MS grade Sigma Cat#EM-MX0486-1 5-methyl-dCTP New England Biolabs Cat# N0356S Nuclease-free water New England Biolabs Cat# B1500L Quick CIP New England Biolabs Cat# M0525S Water, LC-MS grade VWR/BDH Cat# BDH23595.400 BugBuster Master Mix Millipore Cat #70584-M NEBExpress® E. coli Lysis Reagent New England Biolabs Cat# P8116 PEG8000 Sigma P5413 NaCl powder Sigma P9888 1M Tris-HCl, pH7.5, ultra pure grade AMRESCO E691 1M Tris-HCl, pH8.0, ultra pure grade AMRESCO E199 HpaII New England Biolabs Cat# R0171S HaeIII New England Biolabs Cat# R0108S AluI New England Biolabs Cat# R0137S AciI New England Biolabs Cat# R0551S BfaI New England Biolabs Cat# R0568S HhaI New England Biolabs Cat# R0139S HpyCH4IV New England Biolabs Cat# R0619S HpyCH4V New England Biolabs Cat# R0620S NlaIII New England Biolabs Cat# R0125S 10x rCutSmart Buffer New England Biolabs Cat# E6004 Proteinase K New England Biolabs Cat# P8107 AMPure XP beads Beckman Coulter Cat# A63880 NEBNext Ultra II Q5 Master Mix New England Biolabs Cat# E7645 (Continued on next page) Molecular Cell 86, 1–16.e1–e11, May 7, 2026 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Nucleoside digestion mix New England Biolabs Cat# M0649S 5-methyl-dCTP New England Biolabs Cat# N0356S rAlbumin New England Biolabs Cat# E9200 10x Deamination Buffer New England Biolabs Cat# E3356 T4 Phage β-glucosyltransferase (BGT) New England Biolabs Cat# M0357 1 M Bis-Tris, pH 6.07 Teknova B7305 Zinc chloride Sigma 208086 Imidazole Sigma I2399 NEBNext Sample Purification Beads New England Biolabs Cat# E7103 NEBNext Ultra II Q5U master mix New England Biolabs Cat# M0597 USER enzyme New England Biolabs Cat# M5505 Critical commercial assays NEBExpress® Ni-NTA Magnetic Beads New England Biolabs Cat# S1423 Monarch genomic DNA purification kit New England Biolabs Cat# T3010 Oligo clean and concentrator kit Zymo Cat# D4060 NEBNext Ultra II DNA library preparation kit New England Biolabs Cat# E7645 NEBNext Multiplex Oligos for Illumina New England Biolabs Cat# E6400 Monarch Plasmid Miniprep kit New England Biolabs Cat# T1110 Oligo cleanup and purification kit Norgen Biotek Cat# SKU34100 SMRT-bell Express Template Prep Kit PacBio Cat# 100-938-900 NEBNext Enzymatic Methyl-Seq Conversion Module New England Biolabs Cat# E7120 Deposited data Sequencing reads SRA PRJNA1200041 metaGPA1_B5 GenBank PV943624 metaGPA1_C4 GenBank PV943625 metaGPA1_D5 GenBank PV943626 metaGPA1_E10 GenBank PV943627 metaGPA1_E8 GenBank PV943628 metaGPA1_F4 GenBank PV943629 metaGPA2_H2 GenBank PV943630 metaGPA2_A10 GenBank PV943631 metaGPA2_A11 GenBank PV943632 metaGPA2_A8 GenBank PV943633 metaGPA2_C10 GenBank PV943634 metaGPA2_C5 GenBank PV943635 metaGPA2_E10 GenBank PV943636 metaGPA2_E12 GenBank PV943637 metaGPA2_F12 GenBank PV943638 metaGPA2_F7 GenBank PV943639 metaGPA2_G5 GenBank PV943640 metaGPA2_H10 GenBank PV943641 metaGPA2_H3 GenBank PV943642 metaGPA2_H4 GenBank PV943643 Oligonucleotides CE oligo L1 IDT /56-FAM/-ATACACCGATGCAGAA/iMe-dC/TCAT GGGCTTACGC (Continued on next page) e2 Molecular Cell 86, 1–16.e1–e11, May 7, 2026 ..

    DNA Purification:

    Article Title: The discovery of 5mC-selective deaminases and their application to ultra-sensitive direct sequencing of methylated sites at base resolution.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains XP12 ATCC 35934-B1 T4gt New England Biolabs N/A Unmethylated Lambda phage gDNA Promega Cat# D1521 5mCpG pUC19 plasmid DNA New England Biolabs Cat# E7122AAVIAL E.coli K-12 DHB4 gDNA New England Biolabs GenBank accession: CP014270.1 T7 Express Competent E.coli New England Biolabs Cat# C2566H 7 Express lysY/Iq Competent E. coli New England Biolabs Cat# C3013 dcm-6 cell gDNA New England Biolabs ER3662, CGSC Strain#: 6475 Δdcm cell gDNA New England Biolabs ER2861 Natrinema pallidum BOL6-1 gDNA This study GCF_005890195.1 Biological samples Human GM12878 gDNA Coriell Institute Cat# NA12878 Human brain gDNA biochain Cat# D1234035, LOT# C607510 Single donor human blood derived plasma Innovative Research Cat# IPLASK2E2ML HCT116 cell line ATCC Cat# CCL-247 DNMT1 and DNMT3b DKO HCT116 cell line John Hopkins Medicine N/A Chemicals, peptides, and recombinant proteins Acetic acid, LC-MS grade Sigma Cat# 49199-50ML-F Ammonium acetate, LC-MS grade Sigma Cat# 73594-100G-F Deoxynucleotide (dNTP) Solution Set New England Biolabs Cat# N0446S Methanol, LC-MS grade Sigma Cat#EM-MX0486-1 5-methyl-dCTP New England Biolabs Cat# N0356S Nuclease-free water New England Biolabs Cat# B1500L Quick CIP New England Biolabs Cat# M0525S Water, LC-MS grade VWR/BDH Cat# BDH23595.400 BugBuster Master Mix Millipore Cat #70584-M NEBExpress® E. coli Lysis Reagent New England Biolabs Cat# P8116 PEG8000 Sigma P5413 NaCl powder Sigma P9888 1M Tris-HCl, pH7.5, ultra pure grade AMRESCO E691 1M Tris-HCl, pH8.0, ultra pure grade AMRESCO E199 HpaII New England Biolabs Cat# R0171S HaeIII New England Biolabs Cat# R0108S AluI New England Biolabs Cat# R0137S AciI New England Biolabs Cat# R0551S BfaI New England Biolabs Cat# R0568S HhaI New England Biolabs Cat# R0139S HpyCH4IV New England Biolabs Cat# R0619S HpyCH4V New England Biolabs Cat# R0620S NlaIII New England Biolabs Cat# R0125S 10x rCutSmart Buffer New England Biolabs Cat# E6004 Proteinase K New England Biolabs Cat# P8107 AMPure XP beads Beckman Coulter Cat# A63880 NEBNext Ultra II Q5 Master Mix New England Biolabs Cat# E7645 (Continued on next page) Molecular Cell 86, 1–16.e1–e11, May 7, 2026 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Nucleoside digestion mix New England Biolabs Cat# M0649S 5-methyl-dCTP New England Biolabs Cat# N0356S rAlbumin New England Biolabs Cat# E9200 10x Deamination Buffer New England Biolabs Cat# E3356 T4 Phage β-glucosyltransferase (BGT) New England Biolabs Cat# M0357 1 M Bis-Tris, pH 6.07 Teknova B7305 Zinc chloride Sigma 208086 Imidazole Sigma I2399 NEBNext Sample Purification Beads New England Biolabs Cat# E7103 NEBNext Ultra II Q5U master mix New England Biolabs Cat# M0597 USER enzyme New England Biolabs Cat# M5505 Critical commercial assays NEBExpress® Ni-NTA Magnetic Beads New England Biolabs Cat# S1423 Monarch genomic DNA purification kit New England Biolabs Cat# T3010 Oligo clean and concentrator kit Zymo Cat# D4060 NEBNext Ultra II DNA library preparation kit New England Biolabs Cat# E7645 NEBNext Multiplex Oligos for Illumina New England Biolabs Cat# E6400 Monarch Plasmid Miniprep kit New England Biolabs Cat# T1110 Oligo cleanup and purification kit Norgen Biotek Cat# SKU34100 SMRT-bell Express Template Prep Kit PacBio Cat# 100-938-900 NEBNext Enzymatic Methyl-Seq Conversion Module New England Biolabs Cat# E7120 Deposited data Sequencing reads SRA PRJNA1200041 metaGPA1_B5 GenBank PV943624 metaGPA1_C4 GenBank PV943625 metaGPA1_D5 GenBank PV943626 metaGPA1_E10 GenBank PV943627 metaGPA1_E8 GenBank PV943628 metaGPA1_F4 GenBank PV943629 metaGPA2_H2 GenBank PV943630 metaGPA2_A10 GenBank PV943631 metaGPA2_A11 GenBank PV943632 metaGPA2_A8 GenBank PV943633 metaGPA2_C10 GenBank PV943634 metaGPA2_C5 GenBank PV943635 metaGPA2_E10 GenBank PV943636 metaGPA2_E12 GenBank PV943637 metaGPA2_F12 GenBank PV943638 metaGPA2_F7 GenBank PV943639 metaGPA2_G5 GenBank PV943640 metaGPA2_H10 GenBank PV943641 metaGPA2_H3 GenBank PV943642 metaGPA2_H4 GenBank PV943643 Oligonucleotides CE oligo L1 IDT /56-FAM/-ATACACCGATGCAGAA/iMe-dC/TCAT GGGCTTACGC (Continued on next page) e2 Molecular Cell 86, 1–16.e1–e11, May 7, 2026 ..

    DNA Library Preparation:

    Article Title: The discovery of 5mC-selective deaminases and their application to ultra-sensitive direct sequencing of methylated sites at base resolution.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains XP12 ATCC 35934-B1 T4gt New England Biolabs N/A Unmethylated Lambda phage gDNA Promega Cat# D1521 5mCpG pUC19 plasmid DNA New England Biolabs Cat# E7122AAVIAL E.coli K-12 DHB4 gDNA New England Biolabs GenBank accession: CP014270.1 T7 Express Competent E.coli New England Biolabs Cat# C2566H 7 Express lysY/Iq Competent E. coli New England Biolabs Cat# C3013 dcm-6 cell gDNA New England Biolabs ER3662, CGSC Strain#: 6475 Δdcm cell gDNA New England Biolabs ER2861 Natrinema pallidum BOL6-1 gDNA This study GCF_005890195.1 Biological samples Human GM12878 gDNA Coriell Institute Cat# NA12878 Human brain gDNA biochain Cat# D1234035, LOT# C607510 Single donor human blood derived plasma Innovative Research Cat# IPLASK2E2ML HCT116 cell line ATCC Cat# CCL-247 DNMT1 and DNMT3b DKO HCT116 cell line John Hopkins Medicine N/A Chemicals, peptides, and recombinant proteins Acetic acid, LC-MS grade Sigma Cat# 49199-50ML-F Ammonium acetate, LC-MS grade Sigma Cat# 73594-100G-F Deoxynucleotide (dNTP) Solution Set New England Biolabs Cat# N0446S Methanol, LC-MS grade Sigma Cat#EM-MX0486-1 5-methyl-dCTP New England Biolabs Cat# N0356S Nuclease-free water New England Biolabs Cat# B1500L Quick CIP New England Biolabs Cat# M0525S Water, LC-MS grade VWR/BDH Cat# BDH23595.400 BugBuster Master Mix Millipore Cat #70584-M NEBExpress® E. coli Lysis Reagent New England Biolabs Cat# P8116 PEG8000 Sigma P5413 NaCl powder Sigma P9888 1M Tris-HCl, pH7.5, ultra pure grade AMRESCO E691 1M Tris-HCl, pH8.0, ultra pure grade AMRESCO E199 HpaII New England Biolabs Cat# R0171S HaeIII New England Biolabs Cat# R0108S AluI New England Biolabs Cat# R0137S AciI New England Biolabs Cat# R0551S BfaI New England Biolabs Cat# R0568S HhaI New England Biolabs Cat# R0139S HpyCH4IV New England Biolabs Cat# R0619S HpyCH4V New England Biolabs Cat# R0620S NlaIII New England Biolabs Cat# R0125S 10x rCutSmart Buffer New England Biolabs Cat# E6004 Proteinase K New England Biolabs Cat# P8107 AMPure XP beads Beckman Coulter Cat# A63880 NEBNext Ultra II Q5 Master Mix New England Biolabs Cat# E7645 (Continued on next page) Molecular Cell 86, 1–16.e1–e11, May 7, 2026 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Nucleoside digestion mix New England Biolabs Cat# M0649S 5-methyl-dCTP New England Biolabs Cat# N0356S rAlbumin New England Biolabs Cat# E9200 10x Deamination Buffer New England Biolabs Cat# E3356 T4 Phage β-glucosyltransferase (BGT) New England Biolabs Cat# M0357 1 M Bis-Tris, pH 6.07 Teknova B7305 Zinc chloride Sigma 208086 Imidazole Sigma I2399 NEBNext Sample Purification Beads New England Biolabs Cat# E7103 NEBNext Ultra II Q5U master mix New England Biolabs Cat# M0597 USER enzyme New England Biolabs Cat# M5505 Critical commercial assays NEBExpress® Ni-NTA Magnetic Beads New England Biolabs Cat# S1423 Monarch genomic DNA purification kit New England Biolabs Cat# T3010 Oligo clean and concentrator kit Zymo Cat# D4060 NEBNext Ultra II DNA library preparation kit New England Biolabs Cat# E7645 NEBNext Multiplex Oligos for Illumina New England Biolabs Cat# E6400 Monarch Plasmid Miniprep kit New England Biolabs Cat# T1110 Oligo cleanup and purification kit Norgen Biotek Cat# SKU34100 SMRT-bell Express Template Prep Kit PacBio Cat# 100-938-900 NEBNext Enzymatic Methyl-Seq Conversion Module New England Biolabs Cat# E7120 Deposited data Sequencing reads SRA PRJNA1200041 metaGPA1_B5 GenBank PV943624 metaGPA1_C4 GenBank PV943625 metaGPA1_D5 GenBank PV943626 metaGPA1_E10 GenBank PV943627 metaGPA1_E8 GenBank PV943628 metaGPA1_F4 GenBank PV943629 metaGPA2_H2 GenBank PV943630 metaGPA2_A10 GenBank PV943631 metaGPA2_A11 GenBank PV943632 metaGPA2_A8 GenBank PV943633 metaGPA2_C10 GenBank PV943634 metaGPA2_C5 GenBank PV943635 metaGPA2_E10 GenBank PV943636 metaGPA2_E12 GenBank PV943637 metaGPA2_F12 GenBank PV943638 metaGPA2_F7 GenBank PV943639 metaGPA2_G5 GenBank PV943640 metaGPA2_H10 GenBank PV943641 metaGPA2_H3 GenBank PV943642 metaGPA2_H4 GenBank PV943643 Oligonucleotides CE oligo L1 IDT /56-FAM/-ATACACCGATGCAGAA/iMe-dC/TCAT GGGCTTACGC (Continued on next page) e2 Molecular Cell 86, 1–16.e1–e11, May 7, 2026 ..

    Multiplex Assay:

    Article Title: The discovery of 5mC-selective deaminases and their application to ultra-sensitive direct sequencing of methylated sites at base resolution.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains XP12 ATCC 35934-B1 T4gt New England Biolabs N/A Unmethylated Lambda phage gDNA Promega Cat# D1521 5mCpG pUC19 plasmid DNA New England Biolabs Cat# E7122AAVIAL E.coli K-12 DHB4 gDNA New England Biolabs GenBank accession: CP014270.1 T7 Express Competent E.coli New England Biolabs Cat# C2566H 7 Express lysY/Iq Competent E. coli New England Biolabs Cat# C3013 dcm-6 cell gDNA New England Biolabs ER3662, CGSC Strain#: 6475 Δdcm cell gDNA New England Biolabs ER2861 Natrinema pallidum BOL6-1 gDNA This study GCF_005890195.1 Biological samples Human GM12878 gDNA Coriell Institute Cat# NA12878 Human brain gDNA biochain Cat# D1234035, LOT# C607510 Single donor human blood derived plasma Innovative Research Cat# IPLASK2E2ML HCT116 cell line ATCC Cat# CCL-247 DNMT1 and DNMT3b DKO HCT116 cell line John Hopkins Medicine N/A Chemicals, peptides, and recombinant proteins Acetic acid, LC-MS grade Sigma Cat# 49199-50ML-F Ammonium acetate, LC-MS grade Sigma Cat# 73594-100G-F Deoxynucleotide (dNTP) Solution Set New England Biolabs Cat# N0446S Methanol, LC-MS grade Sigma Cat#EM-MX0486-1 5-methyl-dCTP New England Biolabs Cat# N0356S Nuclease-free water New England Biolabs Cat# B1500L Quick CIP New England Biolabs Cat# M0525S Water, LC-MS grade VWR/BDH Cat# BDH23595.400 BugBuster Master Mix Millipore Cat #70584-M NEBExpress® E. coli Lysis Reagent New England Biolabs Cat# P8116 PEG8000 Sigma P5413 NaCl powder Sigma P9888 1M Tris-HCl, pH7.5, ultra pure grade AMRESCO E691 1M Tris-HCl, pH8.0, ultra pure grade AMRESCO E199 HpaII New England Biolabs Cat# R0171S HaeIII New England Biolabs Cat# R0108S AluI New England Biolabs Cat# R0137S AciI New England Biolabs Cat# R0551S BfaI New England Biolabs Cat# R0568S HhaI New England Biolabs Cat# R0139S HpyCH4IV New England Biolabs Cat# R0619S HpyCH4V New England Biolabs Cat# R0620S NlaIII New England Biolabs Cat# R0125S 10x rCutSmart Buffer New England Biolabs Cat# E6004 Proteinase K New England Biolabs Cat# P8107 AMPure XP beads Beckman Coulter Cat# A63880 NEBNext Ultra II Q5 Master Mix New England Biolabs Cat# E7645 (Continued on next page) Molecular Cell 86, 1–16.e1–e11, May 7, 2026 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Nucleoside digestion mix New England Biolabs Cat# M0649S 5-methyl-dCTP New England Biolabs Cat# N0356S rAlbumin New England Biolabs Cat# E9200 10x Deamination Buffer New England Biolabs Cat# E3356 T4 Phage β-glucosyltransferase (BGT) New England Biolabs Cat# M0357 1 M Bis-Tris, pH 6.07 Teknova B7305 Zinc chloride Sigma 208086 Imidazole Sigma I2399 NEBNext Sample Purification Beads New England Biolabs Cat# E7103 NEBNext Ultra II Q5U master mix New England Biolabs Cat# M0597 USER enzyme New England Biolabs Cat# M5505 Critical commercial assays NEBExpress® Ni-NTA Magnetic Beads New England Biolabs Cat# S1423 Monarch genomic DNA purification kit New England Biolabs Cat# T3010 Oligo clean and concentrator kit Zymo Cat# D4060 NEBNext Ultra II DNA library preparation kit New England Biolabs Cat# E7645 NEBNext Multiplex Oligos for Illumina New England Biolabs Cat# E6400 Monarch Plasmid Miniprep kit New England Biolabs Cat# T1110 Oligo cleanup and purification kit Norgen Biotek Cat# SKU34100 SMRT-bell Express Template Prep Kit PacBio Cat# 100-938-900 NEBNext Enzymatic Methyl-Seq Conversion Module New England Biolabs Cat# E7120 Deposited data Sequencing reads SRA PRJNA1200041 metaGPA1_B5 GenBank PV943624 metaGPA1_C4 GenBank PV943625 metaGPA1_D5 GenBank PV943626 metaGPA1_E10 GenBank PV943627 metaGPA1_E8 GenBank PV943628 metaGPA1_F4 GenBank PV943629 metaGPA2_H2 GenBank PV943630 metaGPA2_A10 GenBank PV943631 metaGPA2_A11 GenBank PV943632 metaGPA2_A8 GenBank PV943633 metaGPA2_C10 GenBank PV943634 metaGPA2_C5 GenBank PV943635 metaGPA2_E10 GenBank PV943636 metaGPA2_E12 GenBank PV943637 metaGPA2_F12 GenBank PV943638 metaGPA2_F7 GenBank PV943639 metaGPA2_G5 GenBank PV943640 metaGPA2_H10 GenBank PV943641 metaGPA2_H3 GenBank PV943642 metaGPA2_H4 GenBank PV943643 Oligonucleotides CE oligo L1 IDT /56-FAM/-ATACACCGATGCAGAA/iMe-dC/TCAT GGGCTTACGC (Continued on next page) e2 Molecular Cell 86, 1–16.e1–e11, May 7, 2026 ..

    Plasmid Preparation:

    Article Title: The discovery of 5mC-selective deaminases and their application to ultra-sensitive direct sequencing of methylated sites at base resolution.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains XP12 ATCC 35934-B1 T4gt New England Biolabs N/A Unmethylated Lambda phage gDNA Promega Cat# D1521 5mCpG pUC19 plasmid DNA New England Biolabs Cat# E7122AAVIAL E.coli K-12 DHB4 gDNA New England Biolabs GenBank accession: CP014270.1 T7 Express Competent E.coli New England Biolabs Cat# C2566H 7 Express lysY/Iq Competent E. coli New England Biolabs Cat# C3013 dcm-6 cell gDNA New England Biolabs ER3662, CGSC Strain#: 6475 Δdcm cell gDNA New England Biolabs ER2861 Natrinema pallidum BOL6-1 gDNA This study GCF_005890195.1 Biological samples Human GM12878 gDNA Coriell Institute Cat# NA12878 Human brain gDNA biochain Cat# D1234035, LOT# C607510 Single donor human blood derived plasma Innovative Research Cat# IPLASK2E2ML HCT116 cell line ATCC Cat# CCL-247 DNMT1 and DNMT3b DKO HCT116 cell line John Hopkins Medicine N/A Chemicals, peptides, and recombinant proteins Acetic acid, LC-MS grade Sigma Cat# 49199-50ML-F Ammonium acetate, LC-MS grade Sigma Cat# 73594-100G-F Deoxynucleotide (dNTP) Solution Set New England Biolabs Cat# N0446S Methanol, LC-MS grade Sigma Cat#EM-MX0486-1 5-methyl-dCTP New England Biolabs Cat# N0356S Nuclease-free water New England Biolabs Cat# B1500L Quick CIP New England Biolabs Cat# M0525S Water, LC-MS grade VWR/BDH Cat# BDH23595.400 BugBuster Master Mix Millipore Cat #70584-M NEBExpress® E. coli Lysis Reagent New England Biolabs Cat# P8116 PEG8000 Sigma P5413 NaCl powder Sigma P9888 1M Tris-HCl, pH7.5, ultra pure grade AMRESCO E691 1M Tris-HCl, pH8.0, ultra pure grade AMRESCO E199 HpaII New England Biolabs Cat# R0171S HaeIII New England Biolabs Cat# R0108S AluI New England Biolabs Cat# R0137S AciI New England Biolabs Cat# R0551S BfaI New England Biolabs Cat# R0568S HhaI New England Biolabs Cat# R0139S HpyCH4IV New England Biolabs Cat# R0619S HpyCH4V New England Biolabs Cat# R0620S NlaIII New England Biolabs Cat# R0125S 10x rCutSmart Buffer New England Biolabs Cat# E6004 Proteinase K New England Biolabs Cat# P8107 AMPure XP beads Beckman Coulter Cat# A63880 NEBNext Ultra II Q5 Master Mix New England Biolabs Cat# E7645 (Continued on next page) Molecular Cell 86, 1–16.e1–e11, May 7, 2026 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Nucleoside digestion mix New England Biolabs Cat# M0649S 5-methyl-dCTP New England Biolabs Cat# N0356S rAlbumin New England Biolabs Cat# E9200 10x Deamination Buffer New England Biolabs Cat# E3356 T4 Phage β-glucosyltransferase (BGT) New England Biolabs Cat# M0357 1 M Bis-Tris, pH 6.07 Teknova B7305 Zinc chloride Sigma 208086 Imidazole Sigma I2399 NEBNext Sample Purification Beads New England Biolabs Cat# E7103 NEBNext Ultra II Q5U master mix New England Biolabs Cat# M0597 USER enzyme New England Biolabs Cat# M5505 Critical commercial assays NEBExpress® Ni-NTA Magnetic Beads New England Biolabs Cat# S1423 Monarch genomic DNA purification kit New England Biolabs Cat# T3010 Oligo clean and concentrator kit Zymo Cat# D4060 NEBNext Ultra II DNA library preparation kit New England Biolabs Cat# E7645 NEBNext Multiplex Oligos for Illumina New England Biolabs Cat# E6400 Monarch Plasmid Miniprep kit New England Biolabs Cat# T1110 Oligo cleanup and purification kit Norgen Biotek Cat# SKU34100 SMRT-bell Express Template Prep Kit PacBio Cat# 100-938-900 NEBNext Enzymatic Methyl-Seq Conversion Module New England Biolabs Cat# E7120 Deposited data Sequencing reads SRA PRJNA1200041 metaGPA1_B5 GenBank PV943624 metaGPA1_C4 GenBank PV943625 metaGPA1_D5 GenBank PV943626 metaGPA1_E10 GenBank PV943627 metaGPA1_E8 GenBank PV943628 metaGPA1_F4 GenBank PV943629 metaGPA2_H2 GenBank PV943630 metaGPA2_A10 GenBank PV943631 metaGPA2_A11 GenBank PV943632 metaGPA2_A8 GenBank PV943633 metaGPA2_C10 GenBank PV943634 metaGPA2_C5 GenBank PV943635 metaGPA2_E10 GenBank PV943636 metaGPA2_E12 GenBank PV943637 metaGPA2_F12 GenBank PV943638 metaGPA2_F7 GenBank PV943639 metaGPA2_G5 GenBank PV943640 metaGPA2_H10 GenBank PV943641 metaGPA2_H3 GenBank PV943642 metaGPA2_H4 GenBank PV943643 Oligonucleotides CE oligo L1 IDT /56-FAM/-ATACACCGATGCAGAA/iMe-dC/TCAT GGGCTTACGC (Continued on next page) e2 Molecular Cell 86, 1–16.e1–e11, May 7, 2026 ..

    Sequencing:

    Article Title: The discovery of 5mC-selective deaminases and their application to ultra-sensitive direct sequencing of methylated sites at base resolution.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains XP12 ATCC 35934-B1 T4gt New England Biolabs N/A Unmethylated Lambda phage gDNA Promega Cat# D1521 5mCpG pUC19 plasmid DNA New England Biolabs Cat# E7122AAVIAL E.coli K-12 DHB4 gDNA New England Biolabs GenBank accession: CP014270.1 T7 Express Competent E.coli New England Biolabs Cat# C2566H 7 Express lysY/Iq Competent E. coli New England Biolabs Cat# C3013 dcm-6 cell gDNA New England Biolabs ER3662, CGSC Strain#: 6475 Δdcm cell gDNA New England Biolabs ER2861 Natrinema pallidum BOL6-1 gDNA This study GCF_005890195.1 Biological samples Human GM12878 gDNA Coriell Institute Cat# NA12878 Human brain gDNA biochain Cat# D1234035, LOT# C607510 Single donor human blood derived plasma Innovative Research Cat# IPLASK2E2ML HCT116 cell line ATCC Cat# CCL-247 DNMT1 and DNMT3b DKO HCT116 cell line John Hopkins Medicine N/A Chemicals, peptides, and recombinant proteins Acetic acid, LC-MS grade Sigma Cat# 49199-50ML-F Ammonium acetate, LC-MS grade Sigma Cat# 73594-100G-F Deoxynucleotide (dNTP) Solution Set New England Biolabs Cat# N0446S Methanol, LC-MS grade Sigma Cat#EM-MX0486-1 5-methyl-dCTP New England Biolabs Cat# N0356S Nuclease-free water New England Biolabs Cat# B1500L Quick CIP New England Biolabs Cat# M0525S Water, LC-MS grade VWR/BDH Cat# BDH23595.400 BugBuster Master Mix Millipore Cat #70584-M NEBExpress® E. coli Lysis Reagent New England Biolabs Cat# P8116 PEG8000 Sigma P5413 NaCl powder Sigma P9888 1M Tris-HCl, pH7.5, ultra pure grade AMRESCO E691 1M Tris-HCl, pH8.0, ultra pure grade AMRESCO E199 HpaII New England Biolabs Cat# R0171S HaeIII New England Biolabs Cat# R0108S AluI New England Biolabs Cat# R0137S AciI New England Biolabs Cat# R0551S BfaI New England Biolabs Cat# R0568S HhaI New England Biolabs Cat# R0139S HpyCH4IV New England Biolabs Cat# R0619S HpyCH4V New England Biolabs Cat# R0620S NlaIII New England Biolabs Cat# R0125S 10x rCutSmart Buffer New England Biolabs Cat# E6004 Proteinase K New England Biolabs Cat# P8107 AMPure XP beads Beckman Coulter Cat# A63880 NEBNext Ultra II Q5 Master Mix New England Biolabs Cat# E7645 (Continued on next page) Molecular Cell 86, 1–16.e1–e11, May 7, 2026 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Nucleoside digestion mix New England Biolabs Cat# M0649S 5-methyl-dCTP New England Biolabs Cat# N0356S rAlbumin New England Biolabs Cat# E9200 10x Deamination Buffer New England Biolabs Cat# E3356 T4 Phage β-glucosyltransferase (BGT) New England Biolabs Cat# M0357 1 M Bis-Tris, pH 6.07 Teknova B7305 Zinc chloride Sigma 208086 Imidazole Sigma I2399 NEBNext Sample Purification Beads New England Biolabs Cat# E7103 NEBNext Ultra II Q5U master mix New England Biolabs Cat# M0597 USER enzyme New England Biolabs Cat# M5505 Critical commercial assays NEBExpress® Ni-NTA Magnetic Beads New England Biolabs Cat# S1423 Monarch genomic DNA purification kit New England Biolabs Cat# T3010 Oligo clean and concentrator kit Zymo Cat# D4060 NEBNext Ultra II DNA library preparation kit New England Biolabs Cat# E7645 NEBNext Multiplex Oligos for Illumina New England Biolabs Cat# E6400 Monarch Plasmid Miniprep kit New England Biolabs Cat# T1110 Oligo cleanup and purification kit Norgen Biotek Cat# SKU34100 SMRT-bell Express Template Prep Kit PacBio Cat# 100-938-900 NEBNext Enzymatic Methyl-Seq Conversion Module New England Biolabs Cat# E7120 Deposited data Sequencing reads SRA PRJNA1200041 metaGPA1_B5 GenBank PV943624 metaGPA1_C4 GenBank PV943625 metaGPA1_D5 GenBank PV943626 metaGPA1_E10 GenBank PV943627 metaGPA1_E8 GenBank PV943628 metaGPA1_F4 GenBank PV943629 metaGPA2_H2 GenBank PV943630 metaGPA2_A10 GenBank PV943631 metaGPA2_A11 GenBank PV943632 metaGPA2_A8 GenBank PV943633 metaGPA2_C10 GenBank PV943634 metaGPA2_C5 GenBank PV943635 metaGPA2_E10 GenBank PV943636 metaGPA2_E12 GenBank PV943637 metaGPA2_F12 GenBank PV943638 metaGPA2_F7 GenBank PV943639 metaGPA2_G5 GenBank PV943640 metaGPA2_H10 GenBank PV943641 metaGPA2_H3 GenBank PV943642 metaGPA2_H4 GenBank PV943643 Oligonucleotides CE oligo L1 IDT /56-FAM/-ATACACCGATGCAGAA/iMe-dC/TCAT GGGCTTACGC (Continued on next page) e2 Molecular Cell 86, 1–16.e1–e11, May 7, 2026 ..

    Article Title: Integrated targeted sequencing reveals unique tissue-of-origin and donor-derived cell-free DNA signatures in stable organ transplant recipients
    Article Snippet: .. For sequencing, up to 150 ng of sheared gDNA or up to 70 ng of cfDNA was converted using the NEBNext Enzymatic Methyl-seq Conversion Module (New England Biolabs, Ipswich, MA, USA) by oxidizing 5-mC to 5-hmC and subsequently deaminating unmethylated cytosines. .. The NGS Methylation Detection System (Twist Bioscience, South San Francisco, CA, USA) platform was used and 120 bp biotinylated probes were synthesized by Twist Bioscience.



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