other:Article Title: An Improved Method for Measuring Chromatin-binding Dynamics Using Time-dependent Formaldehyde Crosslinking
Article Snippet: Amino acids: Adenine hemisulfate dihydrate (MP Biomedicals, catalog number: 02100195) L-Histidine hydrochloride monohydrate (Acros Organics, catalog number: 411731000) L-Lysine (Fisher Scientific, catalog number: BP386) L-Tyrosine (Acros Organics, catalog number: 140641000) L-Tryptophan (Fisher Scientific, catalog number: BP395) Uracil (Affymetrix, catalog number: 23020) L-Leucine (Acros Organics, catalog number: 125121000) L-Methionine (Fisher Scientific, catalog number: BP388) L-Arginine hydrochloride (Fisher Scientific, catalog number: BP372) L-Serine (Fisher Scientific, catalog number: BP393) Valine (Fisher Scientific, catalog number: BP397) L-Threonine (MP Biomedicals, catalog number: 02103053) L-Isoleucine (Fisher Scientific, catalog number: BP384) L-Phenylalanine (Fisher Scientific, catalog number: BP391) L-Cysteine hydrochloride monohydrate (Fisher Scientific, catalog number: BP376) L-Aspartic Acid (Acros Organics, catalog number: 105041000) L-Proline (Fisher Scientific, catalog number: BP392) Note: Commercially available yeast synthetic drop-out medium supplements (Sigma-Aldrich) can be used instead of a home-made dropout mix .
Article Title: An Improved Method for Measuring Chromatin-binding Dynamics Using Time-dependent Formaldehyde Crosslinking
Article Snippet: Amino acids: list-behavior=enumerated prefix-word= mark-type=lower-alpha max-label-size=0 Adenine hemisulfate dihydrate (MP Biomedicals, catalog number: 02100195) L-Histidine hydrochloride monohydrate (Acros Organics, catalog number: 411731000) L-Lysine (Fisher Scientific, catalog number: BP386) L-Tyrosine (Acros Organics, catalog number: 140641000) L-Tryptophan (Fisher Scientific, catalog number: BP395) Uracil (Affymetrix, catalog number: 23020) L-Leucine (Acros Organics, catalog number: 125121000) L-Methionine (Fisher Scientific, catalog number: BP388) L-Arginine hydrochloride (Fisher Scientific, catalog number: BP372) L-Serine (Fisher Scientific, catalog number: BP393) Valine (Fisher Scientific, catalog number: BP397) L-Threonine (MP Biomedicals, catalog number: 02103053) L-Isoleucine (Fisher Scientific, catalog number: BP384) L-Phenylalanine (Fisher Scientific, catalog number: BP391) L-Cysteine hydrochloride monohydrate (Fisher Scientific, catalog number: BP376) L-Aspartic Acid (Acros Organics, catalog number: 105041000) L-Proline (Fisher Scientific, catalog number: BP392) Note: Commercially available yeast synthetic drop-out medium supplements (Sigma-Aldrich) can be used instead of a home-made dropout mix .
Western Blot:Article Title: SUMO orchestrates multiple alternative DNA-protein crosslink repair pathways.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Secondary Goat Anti-Mouse Immunoglobulins/ HRP, 1:5000 Dako P0447; RRID:AB_2617137 Goat Anti-Rabbit Immunoglobulins/HRP, WB:1:5000 Dako P0448;: RRID:AB_2617138 Anti-HA (anti-HA.11 Epitope Tag Antibody clone 16B12), WB:1:2000‘ BioLegend 901502, lot B276381 or B242905; RRID:AB_2565006 Anti-Pgk1 antibody [22C5D8], WB:1:3000 Abcam ab113687, GR3195775-3; RRID:AB_10861977 Anti-Rad53 (monoclonal, K-medium), WB:1:100 Gift from Maksym Shyian (D. Shore laboratory) Mab clone EL7.E1 Anti-Flag M2, WB:1:5000 Sigma F3165, lot SLBQ7119V or SLCC4005: RRID:AB259529 Anti-Myc, WB: 1:5000 Abcam Ab32; lot GR310953-2 or GR3232358-2; RRID:AB_303599 Anti-Ubiquitin FK2 Calbiochem ST1200-100UG, lots 31671118, 3291266, 3443858; RRID:AB_2043482 Anti-SUMO (polyclonal), WB: 1:10000 Helle Ulrich laboratory: (Papouli et al., 2005) N/A Anti-PCNA (polyclonal), WB: 1:2500 Helle Ulrich laboratory: (Papouli et al., 2005) N/A Bacterial and virus strains E. coli DH5a N/A N/A Chemicals, peptides, and recombinant proteins D(+)-Glucose Carl Roth Art.-Nr. HN063 D(+)-Raffinose pentahydrate Carl Roth Art.-Nr. 5241.3 D(+)-Galactose USBiological G1030 Yeast Nitrogen Base Qbiogene 4027-532 Bacto Peptone BD Biosciences Ref. 211677 Yeast Extract BD Biosciences Ref. 212750 Ammonium Sulfate Carl Roth Art.-Nr. 3746.1 5-Fluoroorotic Acid Toronto Research Chemicals F595000 RNase A, PureLink, (20 mg/mL) Invitrogen 12091-021 DpnII NEB R0543L NlaIII NEB R0125L T4 Ligase Thermo Scientific EL0011 Linear Acrylamide Ambion AM9520 Taq polymerase NEB M0267L Salmon sperm ssDNA Sigma-Aldrich D1626 PEG4000 Carl Roth Art.-Nr. 0156.1 Zymolyase - 20T Amsbio 120491-1 Phusion High-Fidelity DNA Polymerase Thermo Scientific F530L Auxin (3-indoleacetic acid) Sigma-Aldrich I2886 Camptothecin (CPT) Lucerna-Chem Cat. 0215973225 WesternBright ECL HRP substrate Advansta K-12045 WesternBright Sirius HRP substrate Advansta K-12043 (Continued on next page) e1 Cell Reports 37, 110034, November 23, 2021 .. REAGENT or RESOURCE SOURCE IDENTIFIER cOmplete, Mini, EDTA-free Protease Inhibitor Cocktail Roche 4693159001 NEM (N-Ethylmaleimide) Sigma-Aldrich E1271 Dynabeads Protein G for Immunoprecipitation Invitrogen 10009D Dynabeads Pan Mouse IgG Invitrogen 11041 Alpha Factor PRIMM 201307-00007 Trypsin Promega V5113 Propidium Iodide Sigma P4170 Proteinase K Carl Roth 7528.3 Ni-NTA agarose QIAGEN 30210 Critical commercial assays The Bio-Rad protein assay Bio-Rad 500-0006 Phire Green Hot Start II PCR Master Mix Thermo Scientific F126L NEBuilder HiFi DNA Assembly Cloning Kit NEB E5520 NucleoSpin Gel and PCR Clean-up Macherey-Nagel Ref. 740609.250 MiSeq Reagent Kit v3 Illumina MS-102 SYBR Select Master Mix for CFX Applied biosystems 4472942 MinElute PCR Purification Kit QIAGEN 28006 Deposited data Sequencing data of the tdp1D wss1D siz2D transposon screen This Manuscript ENA: PRJEB47156 Sequencing data of ‘‘wss1D Tdp1-AID*-6HA TIR1 + auxin’’ transposon screen Serbyn et al. (2020), Mol.Cell ENA: PRJEB31382 The SUMO mass spectrometry proteomics data This Manuscript MassIVE: MSV000088129 Unprocessed imaging (immunoblots, spot assays, tetrad analyses) and FACS data This Manuscript Mendeley Data: https://data.mendeley. com/datasets/h7bxnynd7s/1 Experimental models: Organisms/strains S. cerevisiae: Strain background: W303 EUROSCARF BMA64 S. cerevisiae: Strain background: BY4741 EUROSCARF Y00000 Oligonucleotides See Table S3 for the list of oligonucleotides This Manuscript N/A Recombinant DNA See Table S3 for full list of plasmids This Manuscript N/A Software and algorithms Prism 9.1.2 GraphPad Software, Inc RRID:SCR_002798 RStudio Version 1.1.456 RStudio, Inc RRID:SCR_000432 Fiji ImageJ RRID:SCR_002285 SnapGene 3.2.1 GSL Biotech LLC RRID:SCR_015052 Kaluza Beckman Coulter RRID:SCR_016182 Other 0.5 mm Glass Beads BioSpec Products Cat. No 11079105 MagNA Lyser Instrument Roche 03358976001 Bioruptor Twin Diagenode UCD-400 Gallios 8 colors 2 Lasers flow cytometer Beckman Coulter B43619
Virus:Article Title: SUMO orchestrates multiple alternative DNA-protein crosslink repair pathways.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Secondary Goat Anti-Mouse Immunoglobulins/ HRP, 1:5000 Dako P0447; RRID:AB_2617137 Goat Anti-Rabbit Immunoglobulins/HRP, WB:1:5000 Dako P0448;: RRID:AB_2617138 Anti-HA (anti-HA.11 Epitope Tag Antibody clone 16B12), WB:1:2000‘ BioLegend 901502, lot B276381 or B242905; RRID:AB_2565006 Anti-Pgk1 antibody [22C5D8], WB:1:3000 Abcam ab113687, GR3195775-3; RRID:AB_10861977 Anti-Rad53 (monoclonal, K-medium), WB:1:100 Gift from Maksym Shyian (D. Shore laboratory) Mab clone EL7.E1 Anti-Flag M2, WB:1:5000 Sigma F3165, lot SLBQ7119V or SLCC4005: RRID:AB259529 Anti-Myc, WB: 1:5000 Abcam Ab32; lot GR310953-2 or GR3232358-2; RRID:AB_303599 Anti-Ubiquitin FK2 Calbiochem ST1200-100UG, lots 31671118, 3291266, 3443858; RRID:AB_2043482 Anti-SUMO (polyclonal), WB: 1:10000 Helle Ulrich laboratory: (Papouli et al., 2005) N/A Anti-PCNA (polyclonal), WB: 1:2500 Helle Ulrich laboratory: (Papouli et al., 2005) N/A Bacterial and virus strains E. coli DH5a N/A N/A Chemicals, peptides, and recombinant proteins D(+)-Glucose Carl Roth Art.-Nr. HN063 D(+)-Raffinose pentahydrate Carl Roth Art.-Nr. 5241.3 D(+)-Galactose USBiological G1030 Yeast Nitrogen Base Qbiogene 4027-532 Bacto Peptone BD Biosciences Ref. 211677 Yeast Extract BD Biosciences Ref. 212750 Ammonium Sulfate Carl Roth Art.-Nr. 3746.1 5-Fluoroorotic Acid Toronto Research Chemicals F595000 RNase A, PureLink, (20 mg/mL) Invitrogen 12091-021 DpnII NEB R0543L NlaIII NEB R0125L T4 Ligase Thermo Scientific EL0011 Linear Acrylamide Ambion AM9520 Taq polymerase NEB M0267L Salmon sperm ssDNA Sigma-Aldrich D1626 PEG4000 Carl Roth Art.-Nr. 0156.1 Zymolyase - 20T Amsbio 120491-1 Phusion High-Fidelity DNA Polymerase Thermo Scientific F530L Auxin (3-indoleacetic acid) Sigma-Aldrich I2886 Camptothecin (CPT) Lucerna-Chem Cat. 0215973225 WesternBright ECL HRP substrate Advansta K-12045 WesternBright Sirius HRP substrate Advansta K-12043 (Continued on next page) e1 Cell Reports 37, 110034, November 23, 2021 .. REAGENT or RESOURCE SOURCE IDENTIFIER cOmplete, Mini, EDTA-free Protease Inhibitor Cocktail Roche 4693159001 NEM (N-Ethylmaleimide) Sigma-Aldrich E1271 Dynabeads Protein G for Immunoprecipitation Invitrogen 10009D Dynabeads Pan Mouse IgG Invitrogen 11041 Alpha Factor PRIMM 201307-00007 Trypsin Promega V5113 Propidium Iodide Sigma P4170 Proteinase K Carl Roth 7528.3 Ni-NTA agarose QIAGEN 30210 Critical commercial assays The Bio-Rad protein assay Bio-Rad 500-0006 Phire Green Hot Start II PCR Master Mix Thermo Scientific F126L NEBuilder HiFi DNA Assembly Cloning Kit NEB E5520 NucleoSpin Gel and PCR Clean-up Macherey-Nagel Ref. 740609.250 MiSeq Reagent Kit v3 Illumina MS-102 SYBR Select Master Mix for CFX Applied biosystems 4472942 MinElute PCR Purification Kit QIAGEN 28006 Deposited data Sequencing data of the tdp1D wss1D siz2D transposon screen This Manuscript ENA: PRJEB47156 Sequencing data of ‘‘wss1D Tdp1-AID*-6HA TIR1 + auxin’’ transposon screen Serbyn et al. (2020), Mol.Cell ENA: PRJEB31382 The SUMO mass spectrometry proteomics data This Manuscript MassIVE: MSV000088129 Unprocessed imaging (immunoblots, spot assays, tetrad analyses) and FACS data This Manuscript Mendeley Data: https://data.mendeley. com/datasets/h7bxnynd7s/1 Experimental models: Organisms/strains S. cerevisiae: Strain background: W303 EUROSCARF BMA64 S. cerevisiae: Strain background: BY4741 EUROSCARF Y00000 Oligonucleotides See Table S3 for the list of oligonucleotides This Manuscript N/A Recombinant DNA See Table S3 for full list of plasmids This Manuscript N/A Software and algorithms Prism 9.1.2 GraphPad Software, Inc RRID:SCR_002798 RStudio Version 1.1.456 RStudio, Inc RRID:SCR_000432 Fiji ImageJ RRID:SCR_002285 SnapGene 3.2.1 GSL Biotech LLC RRID:SCR_015052 Kaluza Beckman Coulter RRID:SCR_016182 Other 0.5 mm Glass Beads BioSpec Products Cat. No 11079105 MagNA Lyser Instrument Roche 03358976001 Bioruptor Twin Diagenode UCD-400 Gallios 8 colors 2 Lasers flow cytometer Beckman Coulter B43619
Recombinant:Article Title: SUMO orchestrates multiple alternative DNA-protein crosslink repair pathways.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Secondary Goat Anti-Mouse Immunoglobulins/ HRP, 1:5000 Dako P0447; RRID:AB_2617137 Goat Anti-Rabbit Immunoglobulins/HRP, WB:1:5000 Dako P0448;: RRID:AB_2617138 Anti-HA (anti-HA.11 Epitope Tag Antibody clone 16B12), WB:1:2000‘ BioLegend 901502, lot B276381 or B242905; RRID:AB_2565006 Anti-Pgk1 antibody [22C5D8], WB:1:3000 Abcam ab113687, GR3195775-3; RRID:AB_10861977 Anti-Rad53 (monoclonal, K-medium), WB:1:100 Gift from Maksym Shyian (D. Shore laboratory) Mab clone EL7.E1 Anti-Flag M2, WB:1:5000 Sigma F3165, lot SLBQ7119V or SLCC4005: RRID:AB259529 Anti-Myc, WB: 1:5000 Abcam Ab32; lot GR310953-2 or GR3232358-2; RRID:AB_303599 Anti-Ubiquitin FK2 Calbiochem ST1200-100UG, lots 31671118, 3291266, 3443858; RRID:AB_2043482 Anti-SUMO (polyclonal), WB: 1:10000 Helle Ulrich laboratory: (Papouli et al., 2005) N/A Anti-PCNA (polyclonal), WB: 1:2500 Helle Ulrich laboratory: (Papouli et al., 2005) N/A Bacterial and virus strains E. coli DH5a N/A N/A Chemicals, peptides, and recombinant proteins D(+)-Glucose Carl Roth Art.-Nr. HN063 D(+)-Raffinose pentahydrate Carl Roth Art.-Nr. 5241.3 D(+)-Galactose USBiological G1030 Yeast Nitrogen Base Qbiogene 4027-532 Bacto Peptone BD Biosciences Ref. 211677 Yeast Extract BD Biosciences Ref. 212750 Ammonium Sulfate Carl Roth Art.-Nr. 3746.1 5-Fluoroorotic Acid Toronto Research Chemicals F595000 RNase A, PureLink, (20 mg/mL) Invitrogen 12091-021 DpnII NEB R0543L NlaIII NEB R0125L T4 Ligase Thermo Scientific EL0011 Linear Acrylamide Ambion AM9520 Taq polymerase NEB M0267L Salmon sperm ssDNA Sigma-Aldrich D1626 PEG4000 Carl Roth Art.-Nr. 0156.1 Zymolyase - 20T Amsbio 120491-1 Phusion High-Fidelity DNA Polymerase Thermo Scientific F530L Auxin (3-indoleacetic acid) Sigma-Aldrich I2886 Camptothecin (CPT) Lucerna-Chem Cat. 0215973225 WesternBright ECL HRP substrate Advansta K-12045 WesternBright Sirius HRP substrate Advansta K-12043 (Continued on next page) e1 Cell Reports 37, 110034, November 23, 2021 .. REAGENT or RESOURCE SOURCE IDENTIFIER cOmplete, Mini, EDTA-free Protease Inhibitor Cocktail Roche 4693159001 NEM (N-Ethylmaleimide) Sigma-Aldrich E1271 Dynabeads Protein G for Immunoprecipitation Invitrogen 10009D Dynabeads Pan Mouse IgG Invitrogen 11041 Alpha Factor PRIMM 201307-00007 Trypsin Promega V5113 Propidium Iodide Sigma P4170 Proteinase K Carl Roth 7528.3 Ni-NTA agarose QIAGEN 30210 Critical commercial assays The Bio-Rad protein assay Bio-Rad 500-0006 Phire Green Hot Start II PCR Master Mix Thermo Scientific F126L NEBuilder HiFi DNA Assembly Cloning Kit NEB E5520 NucleoSpin Gel and PCR Clean-up Macherey-Nagel Ref. 740609.250 MiSeq Reagent Kit v3 Illumina MS-102 SYBR Select Master Mix for CFX Applied biosystems 4472942 MinElute PCR Purification Kit QIAGEN 28006 Deposited data Sequencing data of the tdp1D wss1D siz2D transposon screen This Manuscript ENA: PRJEB47156 Sequencing data of ‘‘wss1D Tdp1-AID*-6HA TIR1 + auxin’’ transposon screen Serbyn et al. (2020), Mol.Cell ENA: PRJEB31382 The SUMO mass spectrometry proteomics data This Manuscript MassIVE: MSV000088129 Unprocessed imaging (immunoblots, spot assays, tetrad analyses) and FACS data This Manuscript Mendeley Data: https://data.mendeley. com/datasets/h7bxnynd7s/1 Experimental models: Organisms/strains S. cerevisiae: Strain background: W303 EUROSCARF BMA64 S. cerevisiae: Strain background: BY4741 EUROSCARF Y00000 Oligonucleotides See Table S3 for the list of oligonucleotides This Manuscript N/A Recombinant DNA See Table S3 for full list of plasmids This Manuscript N/A Software and algorithms Prism 9.1.2 GraphPad Software, Inc RRID:SCR_002798 RStudio Version 1.1.456 RStudio, Inc RRID:SCR_000432 Fiji ImageJ RRID:SCR_002285 SnapGene 3.2.1 GSL Biotech LLC RRID:SCR_015052 Kaluza Beckman Coulter RRID:SCR_016182 Other 0.5 mm Glass Beads BioSpec Products Cat. No 11079105 MagNA Lyser Instrument Roche 03358976001 Bioruptor Twin Diagenode UCD-400 Gallios 8 colors 2 Lasers flow cytometer Beckman Coulter B43619
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