Sonication:Article Title: Lamins and lineage-relevant transcription factors coordinate gene expression in lineage development
Article Snippet: .. End repair of the sonicated DNA was performed by mixing 50 μL of sonicated Hi-C DNA with 10 μL of 10x phosphorylation reaction buffer (NEB, B0201S), 0.5 μL of T4 DNA polymerase (NEB, M0203S), 0.5 μL of T4 polynucleotide kinase (NEB, M0201S), 5 μL of 10 mM dNTP mix (Qiagen, 201912), 15 μL of 10 mM dATP (NEB, N0440S), 2 μL of 10x diluted Klenow fragment DNA polymerase I (NEB, M0210L), and 17 μL of distilled water. ..
Hi-C:Article Title: Lamins and lineage-relevant transcription factors coordinate gene expression in lineage development
Article Snippet: .. End repair of the sonicated DNA was performed by mixing 50 μL of sonicated Hi-C DNA with 10 μL of 10x phosphorylation reaction buffer (NEB, B0201S), 0.5 μL of T4 DNA polymerase (NEB, M0203S), 0.5 μL of T4 polynucleotide kinase (NEB, M0201S), 5 μL of 10 mM dNTP mix (Qiagen, 201912), 15 μL of 10 mM dATP (NEB, N0440S), 2 μL of 10x diluted Klenow fragment DNA polymerase I (NEB, M0210L), and 17 μL of distilled water. ..
Phospho-proteomics:Article Title: Lamins and lineage-relevant transcription factors coordinate gene expression in lineage development
Article Snippet: .. End repair of the sonicated DNA was performed by mixing 50 μL of sonicated Hi-C DNA with 10 μL of 10x phosphorylation reaction buffer (NEB, B0201S), 0.5 μL of T4 DNA polymerase (NEB, M0203S), 0.5 μL of T4 polynucleotide kinase (NEB, M0201S), 5 μL of 10 mM dNTP mix (Qiagen, 201912), 15 μL of 10 mM dATP (NEB, N0440S), 2 μL of 10x diluted Klenow fragment DNA polymerase I (NEB, M0210L), and 17 μL of distilled water. ..
Virus:Article Title: Improved Cas9-targeted nanopore sequencing facilitates ultra-deep analysis of genomic variation.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains Bacteroides fragilis Tisza et al.30 BFG461 Staphylococcus aureus Silva et al.31 JE2:1.7a Chemicals, peptides, and recombinant proteins LongAmp Taq Master Mix (2X) NEB M0323S AMPure XP beads Beckman Coulter A63881 EB Ultra-II End-prep Enzyme Mix NEB E7546S Long-Fragment Buffer (LFB) ONT Part of SQK-LSK114 Brain Heart Infusion Broth Sigma 53286 Yeast extract Oxoid LP0021 Porcine hemin Sigma 51280 Vitamin K1 Sigma V3501 Resazurin Sigma R7017 RNase A Qiagen 19101 Modified M63 medium Silva et al.31 N/A Delafloxacin Sigma SML1869 Lysozyme MP Biomedicals 100831 Lysostaphin Sigma L7386 Streptavidin magnetic beads NEB S1420S IDTE buffer, pH 7.5 IDT and Gilpatrick et al.1 11-01-02-02 S. pyogenes Cas9 tracrRNA IDT and Gilpatrick et al.1 1072532 Nuclease-free duplex buffer IDT and Gilpatrick et al.1 11-01-03-01 rCutSmart buffer (10X) NEB and Gilpatrick et al.1 B6004 S. pyogenes HiFi Cas9 Alt-R nuclease V3 IDT and Gilpatrick et al.1 1081060 Quick Calf Intestinal Phosphatase NEB and Gilpatrick et al.1 M0525 Taq polymerase NEB and Gilpatrick et al.1 M0273 dATP solution (100 mM) NEB and Gilpatrick et al.1 N0440S Quick T4 ligase NEB M2200 Ultrapure bovine serum albumin Invitrogen AM2616 R10.4.1 Flongle flow cell ONT FLO-FLG114 R10.4.1 MinION flow cell ONT FLO-MIN114 Ligation sequencing DNA V14 ONT SQK-LSK114 Maxwell® HT 96 gDNA Blood Isolation System Promega A2671 Nanobind CBB kit PacBio 102-301-900 Critical commercial assays Qubit dsDNA BR assay Invitrogen Q32853 Qubit dsDNA HS assay Invitrogen Q32854 TapeStation gDNA ScreenTapes Agilent 5067–5365 TapeStation gDNA Reagents Agilent 5067–5366 Deposited data Raw data This paper BioProject: PRJNA1209975 Data files This paper Zenodo: https://doi.org/10.5281/zenodo.14640512 Extensive user-friendly protocol This paper Protocols.io: https://doi.org/10.17504/ protocols.io.n92ldrq5ng5b/v1 (Continued on next page) e1 Cell Reports Methods 6, 101410, May 18, 2026 Report ll OPEN ACCESS .. Bacteroides fragilis BFG46130 was grown on a supplemented BHI (BHIS) agar plate [52 g.L− 1 Brain Heart Infusion Agar (Sigma 70138), 5 g.L− 1 yeast extract (Oxoid LP0021), 5 mg.L− 1 porcine hemin (Sigma 51280), 10 mg.L− 1 Vitamin K1 (Sigma V3501)] for 48 h at 36◦C in an anaerobic workstation (Anaerobe Systems AS-500; 90%-5%-5% N2-H2-CO2).
Recombinant:Article Title: Improved Cas9-targeted nanopore sequencing facilitates ultra-deep analysis of genomic variation.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains Bacteroides fragilis Tisza et al.30 BFG461 Staphylococcus aureus Silva et al.31 JE2:1.7a Chemicals, peptides, and recombinant proteins LongAmp Taq Master Mix (2X) NEB M0323S AMPure XP beads Beckman Coulter A63881 EB Ultra-II End-prep Enzyme Mix NEB E7546S Long-Fragment Buffer (LFB) ONT Part of SQK-LSK114 Brain Heart Infusion Broth Sigma 53286 Yeast extract Oxoid LP0021 Porcine hemin Sigma 51280 Vitamin K1 Sigma V3501 Resazurin Sigma R7017 RNase A Qiagen 19101 Modified M63 medium Silva et al.31 N/A Delafloxacin Sigma SML1869 Lysozyme MP Biomedicals 100831 Lysostaphin Sigma L7386 Streptavidin magnetic beads NEB S1420S IDTE buffer, pH 7.5 IDT and Gilpatrick et al.1 11-01-02-02 S. pyogenes Cas9 tracrRNA IDT and Gilpatrick et al.1 1072532 Nuclease-free duplex buffer IDT and Gilpatrick et al.1 11-01-03-01 rCutSmart buffer (10X) NEB and Gilpatrick et al.1 B6004 S. pyogenes HiFi Cas9 Alt-R nuclease V3 IDT and Gilpatrick et al.1 1081060 Quick Calf Intestinal Phosphatase NEB and Gilpatrick et al.1 M0525 Taq polymerase NEB and Gilpatrick et al.1 M0273 dATP solution (100 mM) NEB and Gilpatrick et al.1 N0440S Quick T4 ligase NEB M2200 Ultrapure bovine serum albumin Invitrogen AM2616 R10.4.1 Flongle flow cell ONT FLO-FLG114 R10.4.1 MinION flow cell ONT FLO-MIN114 Ligation sequencing DNA V14 ONT SQK-LSK114 Maxwell® HT 96 gDNA Blood Isolation System Promega A2671 Nanobind CBB kit PacBio 102-301-900 Critical commercial assays Qubit dsDNA BR assay Invitrogen Q32853 Qubit dsDNA HS assay Invitrogen Q32854 TapeStation gDNA ScreenTapes Agilent 5067–5365 TapeStation gDNA Reagents Agilent 5067–5366 Deposited data Raw data This paper BioProject: PRJNA1209975 Data files This paper Zenodo: https://doi.org/10.5281/zenodo.14640512 Extensive user-friendly protocol This paper Protocols.io: https://doi.org/10.17504/ protocols.io.n92ldrq5ng5b/v1 (Continued on next page) e1 Cell Reports Methods 6, 101410, May 18, 2026 Report ll OPEN ACCESS .. Bacteroides fragilis BFG46130 was grown on a supplemented BHI (BHIS) agar plate [52 g.L− 1 Brain Heart Infusion Agar (Sigma 70138), 5 g.L− 1 yeast extract (Oxoid LP0021), 5 mg.L− 1 porcine hemin (Sigma 51280), 10 mg.L− 1 Vitamin K1 (Sigma V3501)] for 48 h at 36◦C in an anaerobic workstation (Anaerobe Systems AS-500; 90%-5%-5% N2-H2-CO2).
Article Title: crRNA scaffold remodeling controls CRISPR–Cas12a activity for enhanced performance
Article Snippet: .. LbCas12a (Cpf1, 100 μM), NEBuffer r2.1 (1×; 50 mM NaCl, 10 mM Tris–HCl, 10 mM MgCl 2 , 100 μg/ml Recombinant Albumin; pH 7.9), the Large Fragment Bst DNA polymerase (8 000 U/ml), ThermoPol ® Reaction Buffer (1×; 20 mM Tris–HCl, 10 mM (NH 4 ) 2 SO 4 , 10 mM KCl, 2 mM MgSO 4 , 0.1% Triton ® X-100; pH 8.8), MgSO 4 solution (100 mM), dNTP mix, and individual dATP/dGTP/dTTP nucleotides were purchased from New England Biolabs (Beijing, China). .. The DNA isothermal rapid amplification kit was obtained from Amp Future Bio-Tech Co. (Changzhou, China).
Modification:Article Title: Improved Cas9-targeted nanopore sequencing facilitates ultra-deep analysis of genomic variation.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains Bacteroides fragilis Tisza et al.30 BFG461 Staphylococcus aureus Silva et al.31 JE2:1.7a Chemicals, peptides, and recombinant proteins LongAmp Taq Master Mix (2X) NEB M0323S AMPure XP beads Beckman Coulter A63881 EB Ultra-II End-prep Enzyme Mix NEB E7546S Long-Fragment Buffer (LFB) ONT Part of SQK-LSK114 Brain Heart Infusion Broth Sigma 53286 Yeast extract Oxoid LP0021 Porcine hemin Sigma 51280 Vitamin K1 Sigma V3501 Resazurin Sigma R7017 RNase A Qiagen 19101 Modified M63 medium Silva et al.31 N/A Delafloxacin Sigma SML1869 Lysozyme MP Biomedicals 100831 Lysostaphin Sigma L7386 Streptavidin magnetic beads NEB S1420S IDTE buffer, pH 7.5 IDT and Gilpatrick et al.1 11-01-02-02 S. pyogenes Cas9 tracrRNA IDT and Gilpatrick et al.1 1072532 Nuclease-free duplex buffer IDT and Gilpatrick et al.1 11-01-03-01 rCutSmart buffer (10X) NEB and Gilpatrick et al.1 B6004 S. pyogenes HiFi Cas9 Alt-R nuclease V3 IDT and Gilpatrick et al.1 1081060 Quick Calf Intestinal Phosphatase NEB and Gilpatrick et al.1 M0525 Taq polymerase NEB and Gilpatrick et al.1 M0273 dATP solution (100 mM) NEB and Gilpatrick et al.1 N0440S Quick T4 ligase NEB M2200 Ultrapure bovine serum albumin Invitrogen AM2616 R10.4.1 Flongle flow cell ONT FLO-FLG114 R10.4.1 MinION flow cell ONT FLO-MIN114 Ligation sequencing DNA V14 ONT SQK-LSK114 Maxwell® HT 96 gDNA Blood Isolation System Promega A2671 Nanobind CBB kit PacBio 102-301-900 Critical commercial assays Qubit dsDNA BR assay Invitrogen Q32853 Qubit dsDNA HS assay Invitrogen Q32854 TapeStation gDNA ScreenTapes Agilent 5067–5365 TapeStation gDNA Reagents Agilent 5067–5366 Deposited data Raw data This paper BioProject: PRJNA1209975 Data files This paper Zenodo: https://doi.org/10.5281/zenodo.14640512 Extensive user-friendly protocol This paper Protocols.io: https://doi.org/10.17504/ protocols.io.n92ldrq5ng5b/v1 (Continued on next page) e1 Cell Reports Methods 6, 101410, May 18, 2026 Report ll OPEN ACCESS .. Bacteroides fragilis BFG46130 was grown on a supplemented BHI (BHIS) agar plate [52 g.L− 1 Brain Heart Infusion Agar (Sigma 70138), 5 g.L− 1 yeast extract (Oxoid LP0021), 5 mg.L− 1 porcine hemin (Sigma 51280), 10 mg.L− 1 Vitamin K1 (Sigma V3501)] for 48 h at 36◦C in an anaerobic workstation (Anaerobe Systems AS-500; 90%-5%-5% N2-H2-CO2).
Magnetic Beads:Article Title: Improved Cas9-targeted nanopore sequencing facilitates ultra-deep analysis of genomic variation.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains Bacteroides fragilis Tisza et al.30 BFG461 Staphylococcus aureus Silva et al.31 JE2:1.7a Chemicals, peptides, and recombinant proteins LongAmp Taq Master Mix (2X) NEB M0323S AMPure XP beads Beckman Coulter A63881 EB Ultra-II End-prep Enzyme Mix NEB E7546S Long-Fragment Buffer (LFB) ONT Part of SQK-LSK114 Brain Heart Infusion Broth Sigma 53286 Yeast extract Oxoid LP0021 Porcine hemin Sigma 51280 Vitamin K1 Sigma V3501 Resazurin Sigma R7017 RNase A Qiagen 19101 Modified M63 medium Silva et al.31 N/A Delafloxacin Sigma SML1869 Lysozyme MP Biomedicals 100831 Lysostaphin Sigma L7386 Streptavidin magnetic beads NEB S1420S IDTE buffer, pH 7.5 IDT and Gilpatrick et al.1 11-01-02-02 S. pyogenes Cas9 tracrRNA IDT and Gilpatrick et al.1 1072532 Nuclease-free duplex buffer IDT and Gilpatrick et al.1 11-01-03-01 rCutSmart buffer (10X) NEB and Gilpatrick et al.1 B6004 S. pyogenes HiFi Cas9 Alt-R nuclease V3 IDT and Gilpatrick et al.1 1081060 Quick Calf Intestinal Phosphatase NEB and Gilpatrick et al.1 M0525 Taq polymerase NEB and Gilpatrick et al.1 M0273 dATP solution (100 mM) NEB and Gilpatrick et al.1 N0440S Quick T4 ligase NEB M2200 Ultrapure bovine serum albumin Invitrogen AM2616 R10.4.1 Flongle flow cell ONT FLO-FLG114 R10.4.1 MinION flow cell ONT FLO-MIN114 Ligation sequencing DNA V14 ONT SQK-LSK114 Maxwell® HT 96 gDNA Blood Isolation System Promega A2671 Nanobind CBB kit PacBio 102-301-900 Critical commercial assays Qubit dsDNA BR assay Invitrogen Q32853 Qubit dsDNA HS assay Invitrogen Q32854 TapeStation gDNA ScreenTapes Agilent 5067–5365 TapeStation gDNA Reagents Agilent 5067–5366 Deposited data Raw data This paper BioProject: PRJNA1209975 Data files This paper Zenodo: https://doi.org/10.5281/zenodo.14640512 Extensive user-friendly protocol This paper Protocols.io: https://doi.org/10.17504/ protocols.io.n92ldrq5ng5b/v1 (Continued on next page) e1 Cell Reports Methods 6, 101410, May 18, 2026 Report ll OPEN ACCESS .. Bacteroides fragilis BFG46130 was grown on a supplemented BHI (BHIS) agar plate [52 g.L− 1 Brain Heart Infusion Agar (Sigma 70138), 5 g.L− 1 yeast extract (Oxoid LP0021), 5 mg.L− 1 porcine hemin (Sigma 51280), 10 mg.L− 1 Vitamin K1 (Sigma V3501)] for 48 h at 36◦C in an anaerobic workstation (Anaerobe Systems AS-500; 90%-5%-5% N2-H2-CO2).
Ligation:Article Title: Improved Cas9-targeted nanopore sequencing facilitates ultra-deep analysis of genomic variation.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains Bacteroides fragilis Tisza et al.30 BFG461 Staphylococcus aureus Silva et al.31 JE2:1.7a Chemicals, peptides, and recombinant proteins LongAmp Taq Master Mix (2X) NEB M0323S AMPure XP beads Beckman Coulter A63881 EB Ultra-II End-prep Enzyme Mix NEB E7546S Long-Fragment Buffer (LFB) ONT Part of SQK-LSK114 Brain Heart Infusion Broth Sigma 53286 Yeast extract Oxoid LP0021 Porcine hemin Sigma 51280 Vitamin K1 Sigma V3501 Resazurin Sigma R7017 RNase A Qiagen 19101 Modified M63 medium Silva et al.31 N/A Delafloxacin Sigma SML1869 Lysozyme MP Biomedicals 100831 Lysostaphin Sigma L7386 Streptavidin magnetic beads NEB S1420S IDTE buffer, pH 7.5 IDT and Gilpatrick et al.1 11-01-02-02 S. pyogenes Cas9 tracrRNA IDT and Gilpatrick et al.1 1072532 Nuclease-free duplex buffer IDT and Gilpatrick et al.1 11-01-03-01 rCutSmart buffer (10X) NEB and Gilpatrick et al.1 B6004 S. pyogenes HiFi Cas9 Alt-R nuclease V3 IDT and Gilpatrick et al.1 1081060 Quick Calf Intestinal Phosphatase NEB and Gilpatrick et al.1 M0525 Taq polymerase NEB and Gilpatrick et al.1 M0273 dATP solution (100 mM) NEB and Gilpatrick et al.1 N0440S Quick T4 ligase NEB M2200 Ultrapure bovine serum albumin Invitrogen AM2616 R10.4.1 Flongle flow cell ONT FLO-FLG114 R10.4.1 MinION flow cell ONT FLO-MIN114 Ligation sequencing DNA V14 ONT SQK-LSK114 Maxwell® HT 96 gDNA Blood Isolation System Promega A2671 Nanobind CBB kit PacBio 102-301-900 Critical commercial assays Qubit dsDNA BR assay Invitrogen Q32853 Qubit dsDNA HS assay Invitrogen Q32854 TapeStation gDNA ScreenTapes Agilent 5067–5365 TapeStation gDNA Reagents Agilent 5067–5366 Deposited data Raw data This paper BioProject: PRJNA1209975 Data files This paper Zenodo: https://doi.org/10.5281/zenodo.14640512 Extensive user-friendly protocol This paper Protocols.io: https://doi.org/10.17504/ protocols.io.n92ldrq5ng5b/v1 (Continued on next page) e1 Cell Reports Methods 6, 101410, May 18, 2026 Report ll OPEN ACCESS .. Bacteroides fragilis BFG46130 was grown on a supplemented BHI (BHIS) agar plate [52 g.L− 1 Brain Heart Infusion Agar (Sigma 70138), 5 g.L− 1 yeast extract (Oxoid LP0021), 5 mg.L− 1 porcine hemin (Sigma 51280), 10 mg.L− 1 Vitamin K1 (Sigma V3501)] for 48 h at 36◦C in an anaerobic workstation (Anaerobe Systems AS-500; 90%-5%-5% N2-H2-CO2).
Sequencing:Article Title: Improved Cas9-targeted nanopore sequencing facilitates ultra-deep analysis of genomic variation.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains Bacteroides fragilis Tisza et al.30 BFG461 Staphylococcus aureus Silva et al.31 JE2:1.7a Chemicals, peptides, and recombinant proteins LongAmp Taq Master Mix (2X) NEB M0323S AMPure XP beads Beckman Coulter A63881 EB Ultra-II End-prep Enzyme Mix NEB E7546S Long-Fragment Buffer (LFB) ONT Part of SQK-LSK114 Brain Heart Infusion Broth Sigma 53286 Yeast extract Oxoid LP0021 Porcine hemin Sigma 51280 Vitamin K1 Sigma V3501 Resazurin Sigma R7017 RNase A Qiagen 19101 Modified M63 medium Silva et al.31 N/A Delafloxacin Sigma SML1869 Lysozyme MP Biomedicals 100831 Lysostaphin Sigma L7386 Streptavidin magnetic beads NEB S1420S IDTE buffer, pH 7.5 IDT and Gilpatrick et al.1 11-01-02-02 S. pyogenes Cas9 tracrRNA IDT and Gilpatrick et al.1 1072532 Nuclease-free duplex buffer IDT and Gilpatrick et al.1 11-01-03-01 rCutSmart buffer (10X) NEB and Gilpatrick et al.1 B6004 S. pyogenes HiFi Cas9 Alt-R nuclease V3 IDT and Gilpatrick et al.1 1081060 Quick Calf Intestinal Phosphatase NEB and Gilpatrick et al.1 M0525 Taq polymerase NEB and Gilpatrick et al.1 M0273 dATP solution (100 mM) NEB and Gilpatrick et al.1 N0440S Quick T4 ligase NEB M2200 Ultrapure bovine serum albumin Invitrogen AM2616 R10.4.1 Flongle flow cell ONT FLO-FLG114 R10.4.1 MinION flow cell ONT FLO-MIN114 Ligation sequencing DNA V14 ONT SQK-LSK114 Maxwell® HT 96 gDNA Blood Isolation System Promega A2671 Nanobind CBB kit PacBio 102-301-900 Critical commercial assays Qubit dsDNA BR assay Invitrogen Q32853 Qubit dsDNA HS assay Invitrogen Q32854 TapeStation gDNA ScreenTapes Agilent 5067–5365 TapeStation gDNA Reagents Agilent 5067–5366 Deposited data Raw data This paper BioProject: PRJNA1209975 Data files This paper Zenodo: https://doi.org/10.5281/zenodo.14640512 Extensive user-friendly protocol This paper Protocols.io: https://doi.org/10.17504/ protocols.io.n92ldrq5ng5b/v1 (Continued on next page) e1 Cell Reports Methods 6, 101410, May 18, 2026 Report ll OPEN ACCESS .. Bacteroides fragilis BFG46130 was grown on a supplemented BHI (BHIS) agar plate [52 g.L− 1 Brain Heart Infusion Agar (Sigma 70138), 5 g.L− 1 yeast extract (Oxoid LP0021), 5 mg.L− 1 porcine hemin (Sigma 51280), 10 mg.L− 1 Vitamin K1 (Sigma V3501)] for 48 h at 36◦C in an anaerobic workstation (Anaerobe Systems AS-500; 90%-5%-5% N2-H2-CO2).
Isolation:Article Title: Improved Cas9-targeted nanopore sequencing facilitates ultra-deep analysis of genomic variation.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains Bacteroides fragilis Tisza et al.30 BFG461 Staphylococcus aureus Silva et al.31 JE2:1.7a Chemicals, peptides, and recombinant proteins LongAmp Taq Master Mix (2X) NEB M0323S AMPure XP beads Beckman Coulter A63881 EB Ultra-II End-prep Enzyme Mix NEB E7546S Long-Fragment Buffer (LFB) ONT Part of SQK-LSK114 Brain Heart Infusion Broth Sigma 53286 Yeast extract Oxoid LP0021 Porcine hemin Sigma 51280 Vitamin K1 Sigma V3501 Resazurin Sigma R7017 RNase A Qiagen 19101 Modified M63 medium Silva et al.31 N/A Delafloxacin Sigma SML1869 Lysozyme MP Biomedicals 100831 Lysostaphin Sigma L7386 Streptavidin magnetic beads NEB S1420S IDTE buffer, pH 7.5 IDT and Gilpatrick et al.1 11-01-02-02 S. pyogenes Cas9 tracrRNA IDT and Gilpatrick et al.1 1072532 Nuclease-free duplex buffer IDT and Gilpatrick et al.1 11-01-03-01 rCutSmart buffer (10X) NEB and Gilpatrick et al.1 B6004 S. pyogenes HiFi Cas9 Alt-R nuclease V3 IDT and Gilpatrick et al.1 1081060 Quick Calf Intestinal Phosphatase NEB and Gilpatrick et al.1 M0525 Taq polymerase NEB and Gilpatrick et al.1 M0273 dATP solution (100 mM) NEB and Gilpatrick et al.1 N0440S Quick T4 ligase NEB M2200 Ultrapure bovine serum albumin Invitrogen AM2616 R10.4.1 Flongle flow cell ONT FLO-FLG114 R10.4.1 MinION flow cell ONT FLO-MIN114 Ligation sequencing DNA V14 ONT SQK-LSK114 Maxwell® HT 96 gDNA Blood Isolation System Promega A2671 Nanobind CBB kit PacBio 102-301-900 Critical commercial assays Qubit dsDNA BR assay Invitrogen Q32853 Qubit dsDNA HS assay Invitrogen Q32854 TapeStation gDNA ScreenTapes Agilent 5067–5365 TapeStation gDNA Reagents Agilent 5067–5366 Deposited data Raw data This paper BioProject: PRJNA1209975 Data files This paper Zenodo: https://doi.org/10.5281/zenodo.14640512 Extensive user-friendly protocol This paper Protocols.io: https://doi.org/10.17504/ protocols.io.n92ldrq5ng5b/v1 (Continued on next page) e1 Cell Reports Methods 6, 101410, May 18, 2026 Report ll OPEN ACCESS .. Bacteroides fragilis BFG46130 was grown on a supplemented BHI (BHIS) agar plate [52 g.L− 1 Brain Heart Infusion Agar (Sigma 70138), 5 g.L− 1 yeast extract (Oxoid LP0021), 5 mg.L− 1 porcine hemin (Sigma 51280), 10 mg.L− 1 Vitamin K1 (Sigma V3501)] for 48 h at 36◦C in an anaerobic workstation (Anaerobe Systems AS-500; 90%-5%-5% N2-H2-CO2).
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