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    Name:
    T4 PDG T4 Endonuclease V
    Description:
    T4 PDG T4 Endonuclease V 2 000 units
    Catalog Number:
    m0308s
    Price:
    76
    Size:
    2 000 units
    Category:
    DNA Glycosylases
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    New England Biolabs ape1 new england biolabs
    T4 PDG T4 Endonuclease V
    T4 PDG T4 Endonuclease V 2 000 units
    https://www.bioz.com/result/ape1 new england biolabs/product/New England Biolabs
    Average 95 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    ape1 new england biolabs - by Bioz Stars, 2020-08
    95/100 stars

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    Polymerase Chain Reaction:

    Article Title: Genome-wide Nucleotide-Resolution Mapping of DNA Replication Patterns, Single-Strand Breaks, and Lesions by GLOE-Seq.
    Article Snippet: .. KEY RESOURCES TABLE REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse monoclonal anti-yeast Rad53 Susan Gasser; Hauer et al., 2017 N/A Rat monoclonal anti-tubulin, clone YL1/2 Sigma-Aldrich Cat# 92092402-1VL, RRID: CVCL_J781 Rabbit polyclonal anti-DNA Ligase 1 Elabscience Cat# E-AB-31210 Mouse monoclonal anti-Chk1, clone 2G1D5 Cell Signaling Technology Cat# 2360, RRID: AB_2080320 Rabbit polyclonal anti-phospho-Chk1 (Ser345) Cell Signaling Technology Cat# 2341, RRID: AB_330023 Goat anti-mouse immunoglobulins, HRP Dako Cat# P0447, RRID: AB_2617137 Goat anti-rabbit immunoglobulins, HRP Dako Cat# P0448, RRID: AB_2617138 Goat anti-rat immunoglobulins, HRP Dako Cat# P0450, RRID: AB_2630354 Goat anti-rat IgG Secondary Antibody, IRDye 800CW LI-COR Cat# 926-32219, RRID: AB_1850025 Chemicals, Peptides, and Recombinant Proteins Zymolyase 20T AMS Biotechnology Cat# 120491-1 T4 DNA ligase, 20,000,000 U/mL New England Biolabs Cat# B0202 Q5 High-Fidelity DNA polymerase New England Biolabs Cat# M0491 RNase A from bovine pancreas Sigma-Aldrich Cat# 10109169001 Proteinase K Roche Cat# 3115801001 Phenylmethanesulfonyl fluoride Sigma-Aldrich Cat# P7626 b-Agarase I, 1000 U/mL New England Biolabs Cat# M0392 Alpha-Factor peptide (WHWLQLKPGQPMY), > 95% ProteoGenix SAS Cat# GM-PT001 BsrDI New England Biolabs Cat# R0574 Nb.BsrDI New England Biolabs Cat# R0648 NotI New England Biolabs Cat# R0189 Nb.BtsI New England Biolabs Cat# R0707 Antarctic Phosphatase New England Biolabs Cat# M0289 T4 Endonuclease V (T4 PDG) New England Biolabs Cat# M0308 APE1 New England Biolabs Cat# M0282 hAAG New England Biolabs Cat# M0313 Lipofectamine RNAiMAX Transfection Reagent Thermo Fisher Scientific Cat# 13778150 Benzonase Sigma-Aldrich Cat# E1014-25KU PhosSTOP Phosphatase Inhibitor Sigma-Aldrich Cat# 04906837001 Opti-MEM Reduced Serum Medium Thermo Fisher Scientific Cat# 11058021 Critical Commercial Assays AMPure XP beads Beckman Coulter Cat# A63881 NEBNext Ultra II DNA Library Prep Kit for Illumina New England Biolabs Cat# E7645 Phusion Flash high-fidelity PCR master mix Thermo Fisher Scientific Cat# F-548 Dynabeads MyOne Streptavidin C1 Life Technologies Cat# 65001 High Sensitivity D1000 ScreenTape Agilent Technologies Cat# 5067-5584 High Sensitivity D1000 ScreenTape reagents Agilent Technologies Cat# 5067-5585 RNA ScreenTape Agilent Technologies Cat# 5067-5576 RNA ScreenTape sample buffer Agilent Technologies Cat# 5067-5577 RNA ScreenTape ladder Agilent Technologies Cat# 5067-5578 Qubit dsDNA HS Assay Kit Invitrogen Cat# Q32854 Agilent Bioanalyzer High Sensitivity DNA Kit Agilent Technologies Cat# 5067-4646 (Continued on next page) e1 Molecular Cell 78, 1–11.e1–e7, June 4, 2020 .. Continued REAGENT or RESOURCE SOURCE IDENTIFIER NextSeq 550 System High-Output Kit Illumina Cat# 20024906 NextSeq 550 System Mid-Output Kit Illumina Cat# 20024904 NuSieve GTG Agarose Lonza Cat# 859081 Yeast Genomic DNA Extraction Kit QIAGEN Cat# 10243 Bio-Rad Protein Assay Dye Reagent Bio-Rad Cat# 500-0006 NuPAGE LDS sample buffer Thermo Fisher Scientific Cat# NP0007 NuPAGE 4-12% Bis-Tris Protein Gels Thermo Fisher Scientific Cat# NP0322 Deposited Data Raw and analyzed data This paper GEO: GSE134225 Human reference genome UCSC GRCh37/hg19 UCSC Genome Browser ftp://hgdownload.soe.ucsc.edu/ goldenPath/hg19/chromosomes/ Yeast reference genome UCSC sacCer3 UCSC Genome Browser ftp://hgdownload.soe.ucsc.edu/ goldenPath/sacCer3/chromosomes/ 30 end maps of Nb.BtsI-digested DNA, WT and pol1-L868M, Fastq (Figure 2A, reanalyzed with GLOE-Pipe) Reijns et al., 2015 GEO: GSM1573437, GSM1573438 Motifs for Abf1, Reb1, Rap1 in yeast, GFF (Figure 4B) MacIsaac et al., 2006 https://downloads.yeastgenome.org/ published_datasets/MacIsaac_2006_ PMID_16522208/MacIsaac_high_ confidence_with_sequence.gff Nucleosome positions in yeast, BED (Figure 4B) Whitehouse et al., 2007 https://static-content.springer.com/ esm/art%3A10.1038%2Fnature06391/ MediaObjects/41586_2007_ BFnature06391_MOESM319_ESM.xls Okazaki fragment maps in Cdc9-depleted yeast, Fastq, rep 1 rep2 (Figure 4C, reanalyzed with GLOE-Pipe) Smith and Whitehouse, 2012 GEO: GSM835650, GSM835651 END-seq data in HCT116, Fastq (Figure 5, reanalyzed with GLOE-Pipe) Tubbs et al., 2018 GEO: GSM3227952 DNase I hypersensitivity data in HCT116, BigWig, rep1 rep2 (Figure 6B) ENCODE Project Consortium, 2012 GEO: GSM736493, GSM736600 OK-Seq and S50 data in HeLa and GM06990, rep1 rep2 (BedGraph, received from Chunlong Chen, chunlong.chen@curie.fr) (Figure 6B) Petryk et al., 2016 GEO SRA: SRP065949 (SRX1427549, SRX1427548, SRX1424659, SRX1424656) Experimental Models: Cell Lines HCT116 Cancer Research UK London Research Institute Cell Services N/A HCT116 LIG3 / :mL3 Oh et al., 2014 N/A Experimental Models: Organisms/Strains S. cerevisiae: strain W303 ATCC ATCC: 201238 S. cerevisiae: strain JKM179 Lee et al., 1998 N/A S. cerevisiae: strain DF5 ATCC ATCC: 200912 S. cerevisiae: strain DF5 apn1::KanMX apn2::KanMX This paper N/A S. cerevisiae: strain cdc9AID Kubota et al., 2013 N/A Oligonucleotides Primer #3898: CTACACGACGCTCTTCCGATCTNNN NN*N-NH2 (*phosphorothioate bond, IDT code *; NH2: 3 0-amino modification, IDT code /3AmMO/) Integrated DNA Technologies N/A Primer #3899: PO4-AGATCGGAAGAGCGTCGTGTAG GGAAAGAGTG TAGATCTCGTTTT-Bio (PO4: 50-phosphorylation, IDT code /5Phos/; T-Bio: 30-biotindT, IDT code /3BiodT/) Integrated DNA Technologies N/A (Continued on next page) Molecular Cell 78, 1–11.e1–e7, June 4, 2020 e2

    Transfection:

    Article Title: Genome-wide Nucleotide-Resolution Mapping of DNA Replication Patterns, Single-Strand Breaks, and Lesions by GLOE-Seq.
    Article Snippet: .. KEY RESOURCES TABLE REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse monoclonal anti-yeast Rad53 Susan Gasser; Hauer et al., 2017 N/A Rat monoclonal anti-tubulin, clone YL1/2 Sigma-Aldrich Cat# 92092402-1VL, RRID: CVCL_J781 Rabbit polyclonal anti-DNA Ligase 1 Elabscience Cat# E-AB-31210 Mouse monoclonal anti-Chk1, clone 2G1D5 Cell Signaling Technology Cat# 2360, RRID: AB_2080320 Rabbit polyclonal anti-phospho-Chk1 (Ser345) Cell Signaling Technology Cat# 2341, RRID: AB_330023 Goat anti-mouse immunoglobulins, HRP Dako Cat# P0447, RRID: AB_2617137 Goat anti-rabbit immunoglobulins, HRP Dako Cat# P0448, RRID: AB_2617138 Goat anti-rat immunoglobulins, HRP Dako Cat# P0450, RRID: AB_2630354 Goat anti-rat IgG Secondary Antibody, IRDye 800CW LI-COR Cat# 926-32219, RRID: AB_1850025 Chemicals, Peptides, and Recombinant Proteins Zymolyase 20T AMS Biotechnology Cat# 120491-1 T4 DNA ligase, 20,000,000 U/mL New England Biolabs Cat# B0202 Q5 High-Fidelity DNA polymerase New England Biolabs Cat# M0491 RNase A from bovine pancreas Sigma-Aldrich Cat# 10109169001 Proteinase K Roche Cat# 3115801001 Phenylmethanesulfonyl fluoride Sigma-Aldrich Cat# P7626 b-Agarase I, 1000 U/mL New England Biolabs Cat# M0392 Alpha-Factor peptide (WHWLQLKPGQPMY), > 95% ProteoGenix SAS Cat# GM-PT001 BsrDI New England Biolabs Cat# R0574 Nb.BsrDI New England Biolabs Cat# R0648 NotI New England Biolabs Cat# R0189 Nb.BtsI New England Biolabs Cat# R0707 Antarctic Phosphatase New England Biolabs Cat# M0289 T4 Endonuclease V (T4 PDG) New England Biolabs Cat# M0308 APE1 New England Biolabs Cat# M0282 hAAG New England Biolabs Cat# M0313 Lipofectamine RNAiMAX Transfection Reagent Thermo Fisher Scientific Cat# 13778150 Benzonase Sigma-Aldrich Cat# E1014-25KU PhosSTOP Phosphatase Inhibitor Sigma-Aldrich Cat# 04906837001 Opti-MEM Reduced Serum Medium Thermo Fisher Scientific Cat# 11058021 Critical Commercial Assays AMPure XP beads Beckman Coulter Cat# A63881 NEBNext Ultra II DNA Library Prep Kit for Illumina New England Biolabs Cat# E7645 Phusion Flash high-fidelity PCR master mix Thermo Fisher Scientific Cat# F-548 Dynabeads MyOne Streptavidin C1 Life Technologies Cat# 65001 High Sensitivity D1000 ScreenTape Agilent Technologies Cat# 5067-5584 High Sensitivity D1000 ScreenTape reagents Agilent Technologies Cat# 5067-5585 RNA ScreenTape Agilent Technologies Cat# 5067-5576 RNA ScreenTape sample buffer Agilent Technologies Cat# 5067-5577 RNA ScreenTape ladder Agilent Technologies Cat# 5067-5578 Qubit dsDNA HS Assay Kit Invitrogen Cat# Q32854 Agilent Bioanalyzer High Sensitivity DNA Kit Agilent Technologies Cat# 5067-4646 (Continued on next page) e1 Molecular Cell 78, 1–11.e1–e7, June 4, 2020 .. Continued REAGENT or RESOURCE SOURCE IDENTIFIER NextSeq 550 System High-Output Kit Illumina Cat# 20024906 NextSeq 550 System Mid-Output Kit Illumina Cat# 20024904 NuSieve GTG Agarose Lonza Cat# 859081 Yeast Genomic DNA Extraction Kit QIAGEN Cat# 10243 Bio-Rad Protein Assay Dye Reagent Bio-Rad Cat# 500-0006 NuPAGE LDS sample buffer Thermo Fisher Scientific Cat# NP0007 NuPAGE 4-12% Bis-Tris Protein Gels Thermo Fisher Scientific Cat# NP0322 Deposited Data Raw and analyzed data This paper GEO: GSE134225 Human reference genome UCSC GRCh37/hg19 UCSC Genome Browser ftp://hgdownload.soe.ucsc.edu/ goldenPath/hg19/chromosomes/ Yeast reference genome UCSC sacCer3 UCSC Genome Browser ftp://hgdownload.soe.ucsc.edu/ goldenPath/sacCer3/chromosomes/ 30 end maps of Nb.BtsI-digested DNA, WT and pol1-L868M, Fastq (Figure 2A, reanalyzed with GLOE-Pipe) Reijns et al., 2015 GEO: GSM1573437, GSM1573438 Motifs for Abf1, Reb1, Rap1 in yeast, GFF (Figure 4B) MacIsaac et al., 2006 https://downloads.yeastgenome.org/ published_datasets/MacIsaac_2006_ PMID_16522208/MacIsaac_high_ confidence_with_sequence.gff Nucleosome positions in yeast, BED (Figure 4B) Whitehouse et al., 2007 https://static-content.springer.com/ esm/art%3A10.1038%2Fnature06391/ MediaObjects/41586_2007_ BFnature06391_MOESM319_ESM.xls Okazaki fragment maps in Cdc9-depleted yeast, Fastq, rep 1 rep2 (Figure 4C, reanalyzed with GLOE-Pipe) Smith and Whitehouse, 2012 GEO: GSM835650, GSM835651 END-seq data in HCT116, Fastq (Figure 5, reanalyzed with GLOE-Pipe) Tubbs et al., 2018 GEO: GSM3227952 DNase I hypersensitivity data in HCT116, BigWig, rep1 rep2 (Figure 6B) ENCODE Project Consortium, 2012 GEO: GSM736493, GSM736600 OK-Seq and S50 data in HeLa and GM06990, rep1 rep2 (BedGraph, received from Chunlong Chen, chunlong.chen@curie.fr) (Figure 6B) Petryk et al., 2016 GEO SRA: SRP065949 (SRX1427549, SRX1427548, SRX1424659, SRX1424656) Experimental Models: Cell Lines HCT116 Cancer Research UK London Research Institute Cell Services N/A HCT116 LIG3 / :mL3 Oh et al., 2014 N/A Experimental Models: Organisms/Strains S. cerevisiae: strain W303 ATCC ATCC: 201238 S. cerevisiae: strain JKM179 Lee et al., 1998 N/A S. cerevisiae: strain DF5 ATCC ATCC: 200912 S. cerevisiae: strain DF5 apn1::KanMX apn2::KanMX This paper N/A S. cerevisiae: strain cdc9AID Kubota et al., 2013 N/A Oligonucleotides Primer #3898: CTACACGACGCTCTTCCGATCTNNN NN*N-NH2 (*phosphorothioate bond, IDT code *; NH2: 3 0-amino modification, IDT code /3AmMO/) Integrated DNA Technologies N/A Primer #3899: PO4-AGATCGGAAGAGCGTCGTGTAG GGAAAGAGTG TAGATCTCGTTTT-Bio (PO4: 50-phosphorylation, IDT code /5Phos/; T-Bio: 30-biotindT, IDT code /3BiodT/) Integrated DNA Technologies N/A (Continued on next page) Molecular Cell 78, 1–11.e1–e7, June 4, 2020 e2

    Recombinant:

    Article Title: Genome-wide Nucleotide-Resolution Mapping of DNA Replication Patterns, Single-Strand Breaks, and Lesions by GLOE-Seq.
    Article Snippet: .. KEY RESOURCES TABLE REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse monoclonal anti-yeast Rad53 Susan Gasser; Hauer et al., 2017 N/A Rat monoclonal anti-tubulin, clone YL1/2 Sigma-Aldrich Cat# 92092402-1VL, RRID: CVCL_J781 Rabbit polyclonal anti-DNA Ligase 1 Elabscience Cat# E-AB-31210 Mouse monoclonal anti-Chk1, clone 2G1D5 Cell Signaling Technology Cat# 2360, RRID: AB_2080320 Rabbit polyclonal anti-phospho-Chk1 (Ser345) Cell Signaling Technology Cat# 2341, RRID: AB_330023 Goat anti-mouse immunoglobulins, HRP Dako Cat# P0447, RRID: AB_2617137 Goat anti-rabbit immunoglobulins, HRP Dako Cat# P0448, RRID: AB_2617138 Goat anti-rat immunoglobulins, HRP Dako Cat# P0450, RRID: AB_2630354 Goat anti-rat IgG Secondary Antibody, IRDye 800CW LI-COR Cat# 926-32219, RRID: AB_1850025 Chemicals, Peptides, and Recombinant Proteins Zymolyase 20T AMS Biotechnology Cat# 120491-1 T4 DNA ligase, 20,000,000 U/mL New England Biolabs Cat# B0202 Q5 High-Fidelity DNA polymerase New England Biolabs Cat# M0491 RNase A from bovine pancreas Sigma-Aldrich Cat# 10109169001 Proteinase K Roche Cat# 3115801001 Phenylmethanesulfonyl fluoride Sigma-Aldrich Cat# P7626 b-Agarase I, 1000 U/mL New England Biolabs Cat# M0392 Alpha-Factor peptide (WHWLQLKPGQPMY), > 95% ProteoGenix SAS Cat# GM-PT001 BsrDI New England Biolabs Cat# R0574 Nb.BsrDI New England Biolabs Cat# R0648 NotI New England Biolabs Cat# R0189 Nb.BtsI New England Biolabs Cat# R0707 Antarctic Phosphatase New England Biolabs Cat# M0289 T4 Endonuclease V (T4 PDG) New England Biolabs Cat# M0308 APE1 New England Biolabs Cat# M0282 hAAG New England Biolabs Cat# M0313 Lipofectamine RNAiMAX Transfection Reagent Thermo Fisher Scientific Cat# 13778150 Benzonase Sigma-Aldrich Cat# E1014-25KU PhosSTOP Phosphatase Inhibitor Sigma-Aldrich Cat# 04906837001 Opti-MEM Reduced Serum Medium Thermo Fisher Scientific Cat# 11058021 Critical Commercial Assays AMPure XP beads Beckman Coulter Cat# A63881 NEBNext Ultra II DNA Library Prep Kit for Illumina New England Biolabs Cat# E7645 Phusion Flash high-fidelity PCR master mix Thermo Fisher Scientific Cat# F-548 Dynabeads MyOne Streptavidin C1 Life Technologies Cat# 65001 High Sensitivity D1000 ScreenTape Agilent Technologies Cat# 5067-5584 High Sensitivity D1000 ScreenTape reagents Agilent Technologies Cat# 5067-5585 RNA ScreenTape Agilent Technologies Cat# 5067-5576 RNA ScreenTape sample buffer Agilent Technologies Cat# 5067-5577 RNA ScreenTape ladder Agilent Technologies Cat# 5067-5578 Qubit dsDNA HS Assay Kit Invitrogen Cat# Q32854 Agilent Bioanalyzer High Sensitivity DNA Kit Agilent Technologies Cat# 5067-4646 (Continued on next page) e1 Molecular Cell 78, 1–11.e1–e7, June 4, 2020 .. Continued REAGENT or RESOURCE SOURCE IDENTIFIER NextSeq 550 System High-Output Kit Illumina Cat# 20024906 NextSeq 550 System Mid-Output Kit Illumina Cat# 20024904 NuSieve GTG Agarose Lonza Cat# 859081 Yeast Genomic DNA Extraction Kit QIAGEN Cat# 10243 Bio-Rad Protein Assay Dye Reagent Bio-Rad Cat# 500-0006 NuPAGE LDS sample buffer Thermo Fisher Scientific Cat# NP0007 NuPAGE 4-12% Bis-Tris Protein Gels Thermo Fisher Scientific Cat# NP0322 Deposited Data Raw and analyzed data This paper GEO: GSE134225 Human reference genome UCSC GRCh37/hg19 UCSC Genome Browser ftp://hgdownload.soe.ucsc.edu/ goldenPath/hg19/chromosomes/ Yeast reference genome UCSC sacCer3 UCSC Genome Browser ftp://hgdownload.soe.ucsc.edu/ goldenPath/sacCer3/chromosomes/ 30 end maps of Nb.BtsI-digested DNA, WT and pol1-L868M, Fastq (Figure 2A, reanalyzed with GLOE-Pipe) Reijns et al., 2015 GEO: GSM1573437, GSM1573438 Motifs for Abf1, Reb1, Rap1 in yeast, GFF (Figure 4B) MacIsaac et al., 2006 https://downloads.yeastgenome.org/ published_datasets/MacIsaac_2006_ PMID_16522208/MacIsaac_high_ confidence_with_sequence.gff Nucleosome positions in yeast, BED (Figure 4B) Whitehouse et al., 2007 https://static-content.springer.com/ esm/art%3A10.1038%2Fnature06391/ MediaObjects/41586_2007_ BFnature06391_MOESM319_ESM.xls Okazaki fragment maps in Cdc9-depleted yeast, Fastq, rep 1 rep2 (Figure 4C, reanalyzed with GLOE-Pipe) Smith and Whitehouse, 2012 GEO: GSM835650, GSM835651 END-seq data in HCT116, Fastq (Figure 5, reanalyzed with GLOE-Pipe) Tubbs et al., 2018 GEO: GSM3227952 DNase I hypersensitivity data in HCT116, BigWig, rep1 rep2 (Figure 6B) ENCODE Project Consortium, 2012 GEO: GSM736493, GSM736600 OK-Seq and S50 data in HeLa and GM06990, rep1 rep2 (BedGraph, received from Chunlong Chen, chunlong.chen@curie.fr) (Figure 6B) Petryk et al., 2016 GEO SRA: SRP065949 (SRX1427549, SRX1427548, SRX1424659, SRX1424656) Experimental Models: Cell Lines HCT116 Cancer Research UK London Research Institute Cell Services N/A HCT116 LIG3 / :mL3 Oh et al., 2014 N/A Experimental Models: Organisms/Strains S. cerevisiae: strain W303 ATCC ATCC: 201238 S. cerevisiae: strain JKM179 Lee et al., 1998 N/A S. cerevisiae: strain DF5 ATCC ATCC: 200912 S. cerevisiae: strain DF5 apn1::KanMX apn2::KanMX This paper N/A S. cerevisiae: strain cdc9AID Kubota et al., 2013 N/A Oligonucleotides Primer #3898: CTACACGACGCTCTTCCGATCTNNN NN*N-NH2 (*phosphorothioate bond, IDT code *; NH2: 3 0-amino modification, IDT code /3AmMO/) Integrated DNA Technologies N/A Primer #3899: PO4-AGATCGGAAGAGCGTCGTGTAG GGAAAGAGTG TAGATCTCGTTTT-Bio (PO4: 50-phosphorylation, IDT code /5Phos/; T-Bio: 30-biotindT, IDT code /3BiodT/) Integrated DNA Technologies N/A (Continued on next page) Molecular Cell 78, 1–11.e1–e7, June 4, 2020 e2

    Polyacrylamide Gel Electrophoresis:

    Article Title: Genome-wide Nucleotide-Resolution Mapping of DNA Replication Patterns, Single-Strand Breaks, and Lesions by GLOE-Seq.
    Article Snippet: .. KEY RESOURCES TABLE REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse monoclonal anti-yeast Rad53 Susan Gasser; Hauer et al., 2017 N/A Rat monoclonal anti-tubulin, clone YL1/2 Sigma-Aldrich Cat# 92092402-1VL, RRID: CVCL_J781 Rabbit polyclonal anti-DNA Ligase 1 Elabscience Cat# E-AB-31210 Mouse monoclonal anti-Chk1, clone 2G1D5 Cell Signaling Technology Cat# 2360, RRID: AB_2080320 Rabbit polyclonal anti-phospho-Chk1 (Ser345) Cell Signaling Technology Cat# 2341, RRID: AB_330023 Goat anti-mouse immunoglobulins, HRP Dako Cat# P0447, RRID: AB_2617137 Goat anti-rabbit immunoglobulins, HRP Dako Cat# P0448, RRID: AB_2617138 Goat anti-rat immunoglobulins, HRP Dako Cat# P0450, RRID: AB_2630354 Goat anti-rat IgG Secondary Antibody, IRDye 800CW LI-COR Cat# 926-32219, RRID: AB_1850025 Chemicals, Peptides, and Recombinant Proteins Zymolyase 20T AMS Biotechnology Cat# 120491-1 T4 DNA ligase, 20,000,000 U/mL New England Biolabs Cat# B0202 Q5 High-Fidelity DNA polymerase New England Biolabs Cat# M0491 RNase A from bovine pancreas Sigma-Aldrich Cat# 10109169001 Proteinase K Roche Cat# 3115801001 Phenylmethanesulfonyl fluoride Sigma-Aldrich Cat# P7626 b-Agarase I, 1000 U/mL New England Biolabs Cat# M0392 Alpha-Factor peptide (WHWLQLKPGQPMY), > 95% ProteoGenix SAS Cat# GM-PT001 BsrDI New England Biolabs Cat# R0574 Nb.BsrDI New England Biolabs Cat# R0648 NotI New England Biolabs Cat# R0189 Nb.BtsI New England Biolabs Cat# R0707 Antarctic Phosphatase New England Biolabs Cat# M0289 T4 Endonuclease V (T4 PDG) New England Biolabs Cat# M0308 APE1 New England Biolabs Cat# M0282 hAAG New England Biolabs Cat# M0313 Lipofectamine RNAiMAX Transfection Reagent Thermo Fisher Scientific Cat# 13778150 Benzonase Sigma-Aldrich Cat# E1014-25KU PhosSTOP Phosphatase Inhibitor Sigma-Aldrich Cat# 04906837001 Opti-MEM Reduced Serum Medium Thermo Fisher Scientific Cat# 11058021 Critical Commercial Assays AMPure XP beads Beckman Coulter Cat# A63881 NEBNext Ultra II DNA Library Prep Kit for Illumina New England Biolabs Cat# E7645 Phusion Flash high-fidelity PCR master mix Thermo Fisher Scientific Cat# F-548 Dynabeads MyOne Streptavidin C1 Life Technologies Cat# 65001 High Sensitivity D1000 ScreenTape Agilent Technologies Cat# 5067-5584 High Sensitivity D1000 ScreenTape reagents Agilent Technologies Cat# 5067-5585 RNA ScreenTape Agilent Technologies Cat# 5067-5576 RNA ScreenTape sample buffer Agilent Technologies Cat# 5067-5577 RNA ScreenTape ladder Agilent Technologies Cat# 5067-5578 Qubit dsDNA HS Assay Kit Invitrogen Cat# Q32854 Agilent Bioanalyzer High Sensitivity DNA Kit Agilent Technologies Cat# 5067-4646 (Continued on next page) e1 Molecular Cell 78, 1–11.e1–e7, June 4, 2020 .. Continued REAGENT or RESOURCE SOURCE IDENTIFIER NextSeq 550 System High-Output Kit Illumina Cat# 20024906 NextSeq 550 System Mid-Output Kit Illumina Cat# 20024904 NuSieve GTG Agarose Lonza Cat# 859081 Yeast Genomic DNA Extraction Kit QIAGEN Cat# 10243 Bio-Rad Protein Assay Dye Reagent Bio-Rad Cat# 500-0006 NuPAGE LDS sample buffer Thermo Fisher Scientific Cat# NP0007 NuPAGE 4-12% Bis-Tris Protein Gels Thermo Fisher Scientific Cat# NP0322 Deposited Data Raw and analyzed data This paper GEO: GSE134225 Human reference genome UCSC GRCh37/hg19 UCSC Genome Browser ftp://hgdownload.soe.ucsc.edu/ goldenPath/hg19/chromosomes/ Yeast reference genome UCSC sacCer3 UCSC Genome Browser ftp://hgdownload.soe.ucsc.edu/ goldenPath/sacCer3/chromosomes/ 30 end maps of Nb.BtsI-digested DNA, WT and pol1-L868M, Fastq (Figure 2A, reanalyzed with GLOE-Pipe) Reijns et al., 2015 GEO: GSM1573437, GSM1573438 Motifs for Abf1, Reb1, Rap1 in yeast, GFF (Figure 4B) MacIsaac et al., 2006 https://downloads.yeastgenome.org/ published_datasets/MacIsaac_2006_ PMID_16522208/MacIsaac_high_ confidence_with_sequence.gff Nucleosome positions in yeast, BED (Figure 4B) Whitehouse et al., 2007 https://static-content.springer.com/ esm/art%3A10.1038%2Fnature06391/ MediaObjects/41586_2007_ BFnature06391_MOESM319_ESM.xls Okazaki fragment maps in Cdc9-depleted yeast, Fastq, rep 1 rep2 (Figure 4C, reanalyzed with GLOE-Pipe) Smith and Whitehouse, 2012 GEO: GSM835650, GSM835651 END-seq data in HCT116, Fastq (Figure 5, reanalyzed with GLOE-Pipe) Tubbs et al., 2018 GEO: GSM3227952 DNase I hypersensitivity data in HCT116, BigWig, rep1 rep2 (Figure 6B) ENCODE Project Consortium, 2012 GEO: GSM736493, GSM736600 OK-Seq and S50 data in HeLa and GM06990, rep1 rep2 (BedGraph, received from Chunlong Chen, chunlong.chen@curie.fr) (Figure 6B) Petryk et al., 2016 GEO SRA: SRP065949 (SRX1427549, SRX1427548, SRX1424659, SRX1424656) Experimental Models: Cell Lines HCT116 Cancer Research UK London Research Institute Cell Services N/A HCT116 LIG3 / :mL3 Oh et al., 2014 N/A Experimental Models: Organisms/Strains S. cerevisiae: strain W303 ATCC ATCC: 201238 S. cerevisiae: strain JKM179 Lee et al., 1998 N/A S. cerevisiae: strain DF5 ATCC ATCC: 200912 S. cerevisiae: strain DF5 apn1::KanMX apn2::KanMX This paper N/A S. cerevisiae: strain cdc9AID Kubota et al., 2013 N/A Oligonucleotides Primer #3898: CTACACGACGCTCTTCCGATCTNNN NN*N-NH2 (*phosphorothioate bond, IDT code *; NH2: 3 0-amino modification, IDT code /3AmMO/) Integrated DNA Technologies N/A Primer #3899: PO4-AGATCGGAAGAGCGTCGTGTAG GGAAAGAGTG TAGATCTCGTTTT-Bio (PO4: 50-phosphorylation, IDT code /5Phos/; T-Bio: 30-biotindT, IDT code /3BiodT/) Integrated DNA Technologies N/A (Continued on next page) Molecular Cell 78, 1–11.e1–e7, June 4, 2020 e2

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    New England Biolabs ape1
    CUT domains stimulate <t>APE1</t> endonuclease activity in vitro. (A) Schematic of CUX1 recombinant proteins used in APE1 endonuclease assays. (B, C) APE1 endonuclease assays were carried out using purified APE1, in the presence of purified CUX1 recombinant proteins or controls (BSA or homeobox B3) at 50 nM or as indicated, and a radiolabeled probe containing an abasic site produced in 2 different ways: as a tetrahydrofuran (B) or through removal of a uracil residue by UDG (C). (D) Schematic of the APE1 assay that utilizes a molecular beacon probe containing a tetrahydrofuran site. The APE1 assay was carried out with purified APE1 in the presence of nothing, 50 nM BSA, or purified CUX1 recombinant proteins (C2C3HD, C1C2, and C3HD), as indicated.
    Ape1, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 52 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/ape1/product/New England Biolabs
    Average 99 stars, based on 52 article reviews
    Price from $9.99 to $1999.99
    ape1 - by Bioz Stars, 2020-08
    99/100 stars
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    CUT domains stimulate APE1 endonuclease activity in vitro. (A) Schematic of CUX1 recombinant proteins used in APE1 endonuclease assays. (B, C) APE1 endonuclease assays were carried out using purified APE1, in the presence of purified CUX1 recombinant proteins or controls (BSA or homeobox B3) at 50 nM or as indicated, and a radiolabeled probe containing an abasic site produced in 2 different ways: as a tetrahydrofuran (B) or through removal of a uracil residue by UDG (C). (D) Schematic of the APE1 assay that utilizes a molecular beacon probe containing a tetrahydrofuran site. The APE1 assay was carried out with purified APE1 in the presence of nothing, 50 nM BSA, or purified CUX1 recombinant proteins (C2C3HD, C1C2, and C3HD), as indicated.

    Journal: Neuro-Oncology

    Article Title: CUX1 stimulates APE1 enzymatic activity and increases the resistance of glioblastoma cells to the mono-alkylating agent temozolomide

    doi: 10.1093/neuonc/nox178

    Figure Lengend Snippet: CUT domains stimulate APE1 endonuclease activity in vitro. (A) Schematic of CUX1 recombinant proteins used in APE1 endonuclease assays. (B, C) APE1 endonuclease assays were carried out using purified APE1, in the presence of purified CUX1 recombinant proteins or controls (BSA or homeobox B3) at 50 nM or as indicated, and a radiolabeled probe containing an abasic site produced in 2 different ways: as a tetrahydrofuran (B) or through removal of a uracil residue by UDG (C). (D) Schematic of the APE1 assay that utilizes a molecular beacon probe containing a tetrahydrofuran site. The APE1 assay was carried out with purified APE1 in the presence of nothing, 50 nM BSA, or purified CUX1 recombinant proteins (C2C3HD, C1C2, and C3HD), as indicated.

    Article Snippet: Endonuclease reactions with bacterially purified proteins were conducted using 0.08 nM APE1 (New England Biolabs) and 50 nM bovine serum albumin (BSA) or the indicated proteins unless otherwise indicated and 1 pmol of 32 P-radiolabeled double-stranded oligonucleotides containing a tetrahydrofuran site or an abasic site generated by uracil-DNA glycosylase (UDG)/MPG and performed as described.

    Techniques: Activity Assay, In Vitro, Recombinant, Purification, Produced

    Dependence of initial velocity ( V ) on different concentrations of hairpin substrate. The 0.1 U/µL hAAG and 0.3 U/µL APE1 were used in this experiment. The time for hAAG-induced 2′-deoxyinosine excision reaction was 5 min. Error bars show the standard deviation of three experiments.

    Journal: Theranostics

    Article Title: Controllable Autocatalytic Cleavage-Mediated Fluorescence Recovery for Homogeneous Sensing of Alkyladenine DNA Glycosylase from Human Cancer Cells

    doi: 10.7150/thno.35393

    Figure Lengend Snippet: Dependence of initial velocity ( V ) on different concentrations of hairpin substrate. The 0.1 U/µL hAAG and 0.3 U/µL APE1 were used in this experiment. The time for hAAG-induced 2′-deoxyinosine excision reaction was 5 min. Error bars show the standard deviation of three experiments.

    Article Snippet: Inhibition assay Variable-concentration CdCl2 was incubated with 0.1 U/µL hAAG at 37 °C for 15 min. Then 2 µL of 10× ThermoPol reaction buffer, 0.3 U/µL APE1, 2 µL of 10× NEBuffer 4, and 100 nM HP1 were added into the reaction mixture, followed by incubation at 37 °C for 60 min. After the excision reaction, 5 μL of excision products was added into the amplification reaction system (250 nM HP2, 700 nM signal probes, 15 U of T7 exo, and 2 µL of 10× NEBuffer 4) for hAAG assay according to the procedures described above.

    Techniques: Standard Deviation

    (A) Nondenaturing PAGE analysis of the products of hAAG-catalyzed cleavage reaction under different reaction conditions. Lane M, the DNA ladder marker; lane 1, the synthesized cleavage product; lane 2, the synthesized trigger 1; lane 3, the synthesized HP1; lane 4, in the presence of APE1 + HP1; lane 5, in the presence of hAAG + APE1 + HP1. (B) Nondenaturing PAGE analysis of the products of T7 exo-assisted autocatalytic recycling cleavage reaction. Lane M, the DNA ladder marker; lane 1, in the absence of hAAG; lane 2, the synthesized trigger 2; lane 3, in the presence of hAAG. SYBR Gold is used as the fluorescent indicator. The 0.1 U/µL hAAG and 0.3 U/µL APE1 were used in this experiment.

    Journal: Theranostics

    Article Title: Controllable Autocatalytic Cleavage-Mediated Fluorescence Recovery for Homogeneous Sensing of Alkyladenine DNA Glycosylase from Human Cancer Cells

    doi: 10.7150/thno.35393

    Figure Lengend Snippet: (A) Nondenaturing PAGE analysis of the products of hAAG-catalyzed cleavage reaction under different reaction conditions. Lane M, the DNA ladder marker; lane 1, the synthesized cleavage product; lane 2, the synthesized trigger 1; lane 3, the synthesized HP1; lane 4, in the presence of APE1 + HP1; lane 5, in the presence of hAAG + APE1 + HP1. (B) Nondenaturing PAGE analysis of the products of T7 exo-assisted autocatalytic recycling cleavage reaction. Lane M, the DNA ladder marker; lane 1, in the absence of hAAG; lane 2, the synthesized trigger 2; lane 3, in the presence of hAAG. SYBR Gold is used as the fluorescent indicator. The 0.1 U/µL hAAG and 0.3 U/µL APE1 were used in this experiment.

    Article Snippet: Inhibition assay Variable-concentration CdCl2 was incubated with 0.1 U/µL hAAG at 37 °C for 15 min. Then 2 µL of 10× ThermoPol reaction buffer, 0.3 U/µL APE1, 2 µL of 10× NEBuffer 4, and 100 nM HP1 were added into the reaction mixture, followed by incubation at 37 °C for 60 min. After the excision reaction, 5 μL of excision products was added into the amplification reaction system (250 nM HP2, 700 nM signal probes, 15 U of T7 exo, and 2 µL of 10× NEBuffer 4) for hAAG assay according to the procedures described above.

    Techniques: Polyacrylamide Gel Electrophoresis, Marker, Synthesized

    Schematic illustration of the controllable autocatalytic cleavage-induced fluorescence recovery for hAAG assay. This strategy involves two consecutive steps: (1) the specific cleavage of HP1 at 2′-deoxyinosine site by hAAG and APE1, and (2) T7 exo-assisted autocatalytic recycling signal amplification.

    Journal: Theranostics

    Article Title: Controllable Autocatalytic Cleavage-Mediated Fluorescence Recovery for Homogeneous Sensing of Alkyladenine DNA Glycosylase from Human Cancer Cells

    doi: 10.7150/thno.35393

    Figure Lengend Snippet: Schematic illustration of the controllable autocatalytic cleavage-induced fluorescence recovery for hAAG assay. This strategy involves two consecutive steps: (1) the specific cleavage of HP1 at 2′-deoxyinosine site by hAAG and APE1, and (2) T7 exo-assisted autocatalytic recycling signal amplification.

    Article Snippet: Inhibition assay Variable-concentration CdCl2 was incubated with 0.1 U/µL hAAG at 37 °C for 15 min. Then 2 µL of 10× ThermoPol reaction buffer, 0.3 U/µL APE1, 2 µL of 10× NEBuffer 4, and 100 nM HP1 were added into the reaction mixture, followed by incubation at 37 °C for 60 min. After the excision reaction, 5 μL of excision products was added into the amplification reaction system (250 nM HP2, 700 nM signal probes, 15 U of T7 exo, and 2 µL of 10× NEBuffer 4) for hAAG assay according to the procedures described above.

    Techniques: Fluorescence, Amplification

    Dependence of the relative activity of hAAG on different concentrations of CdCl 2 . The 0.1 U/µL hAAG and 0.3 U/µL APE1 were used in this experiment. The error bars represent the standard deviations of the three experiments.

    Journal: Theranostics

    Article Title: Controllable Autocatalytic Cleavage-Mediated Fluorescence Recovery for Homogeneous Sensing of Alkyladenine DNA Glycosylase from Human Cancer Cells

    doi: 10.7150/thno.35393

    Figure Lengend Snippet: Dependence of the relative activity of hAAG on different concentrations of CdCl 2 . The 0.1 U/µL hAAG and 0.3 U/µL APE1 were used in this experiment. The error bars represent the standard deviations of the three experiments.

    Article Snippet: Inhibition assay Variable-concentration CdCl2 was incubated with 0.1 U/µL hAAG at 37 °C for 15 min. Then 2 µL of 10× ThermoPol reaction buffer, 0.3 U/µL APE1, 2 µL of 10× NEBuffer 4, and 100 nM HP1 were added into the reaction mixture, followed by incubation at 37 °C for 60 min. After the excision reaction, 5 μL of excision products was added into the amplification reaction system (250 nM HP2, 700 nM signal probes, 15 U of T7 exo, and 2 µL of 10× NEBuffer 4) for hAAG assay according to the procedures described above.

    Techniques: Activity Assay

    Mechanism of hAAG-catalyzed base-excision repair. The hAAG can remove the damaged 2′-deoxyinosine (red color) to produce an AP site. The AP site will subsequently be cleaved by APE1 to generate the 5′-dRP and 3′-OH termini.

    Journal: Theranostics

    Article Title: Controllable Autocatalytic Cleavage-Mediated Fluorescence Recovery for Homogeneous Sensing of Alkyladenine DNA Glycosylase from Human Cancer Cells

    doi: 10.7150/thno.35393

    Figure Lengend Snippet: Mechanism of hAAG-catalyzed base-excision repair. The hAAG can remove the damaged 2′-deoxyinosine (red color) to produce an AP site. The AP site will subsequently be cleaved by APE1 to generate the 5′-dRP and 3′-OH termini.

    Article Snippet: Inhibition assay Variable-concentration CdCl2 was incubated with 0.1 U/µL hAAG at 37 °C for 15 min. Then 2 µL of 10× ThermoPol reaction buffer, 0.3 U/µL APE1, 2 µL of 10× NEBuffer 4, and 100 nM HP1 were added into the reaction mixture, followed by incubation at 37 °C for 60 min. After the excision reaction, 5 μL of excision products was added into the amplification reaction system (250 nM HP2, 700 nM signal probes, 15 U of T7 exo, and 2 µL of 10× NEBuffer 4) for hAAG assay according to the procedures described above.

    Techniques:

    Data obtained under multiple-turnover conditions for determination of k 3 . Shown is a graph of concentration of product as a function of time for (A) Mixed-DUP, (B) Loop-DUP, (C) Stem-DUP, and (D) Stem-HP. Conditions were 50 nM DNA, 5 nM hOGG1 or 5 nM hOGG1/50 nM APE1 in 20 mM Tris-HCl, 70 mM NaCl, 2 mM MgCl 2 , 100 µg/mL BSA, pH 7.6.

    Journal: DNA repair

    Article Title: Incidence and persistence of 8-oxo-7,8-dihydroguanine within a hairpin intermediate exacerbates a toxic oxidation cycle associated with trinucleotide repeat expansion

    doi: 10.1016/j.dnarep.2011.06.003

    Figure Lengend Snippet: Data obtained under multiple-turnover conditions for determination of k 3 . Shown is a graph of concentration of product as a function of time for (A) Mixed-DUP, (B) Loop-DUP, (C) Stem-DUP, and (D) Stem-HP. Conditions were 50 nM DNA, 5 nM hOGG1 or 5 nM hOGG1/50 nM APE1 in 20 mM Tris-HCl, 70 mM NaCl, 2 mM MgCl 2 , 100 µg/mL BSA, pH 7.6.

    Article Snippet: APE1 has been shown to improve the efficiency of repair by stimulating the product release rate of OGG1 [ , , , ].

    Techniques: Concentration Assay