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    Bio-Rad precision plus pre stained markers biorad laboratories
    Precision Plus Pre Stained Markers Biorad Laboratories, supplied by Bio-Rad, used in various techniques. Bioz Stars score: 96/100, based on 1073 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/precision+plus+pre+stained+markers+biorad+laboratories/Precision+Plus+Protein+All+Blue+Prestained+Protein+Standards/pmc09638028__mmc3-581-133-137
    Average 96 stars, based on 1073 article reviews
    precision plus pre stained markers biorad laboratories - by Bioz Stars, 2026-09
    96/100 stars

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    Ubiquitin Proteomics:

    Article Title: DDI2 Is a Ubiquitin-Directed Endoprotease Responsible for Cleavage of Transcription Factor NRF1.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-Ubiquitin mouse mAb (P4D1) ENZO Life Sciences Cat# BML-PW0930; RRID: AB_10998070 Anti-Ubiquitin mouse mAb (P4G7) ENZO Life Sciences Cat# ENZ-ABS142; RRID: AB_2331077 Anti-TCF11/NRF1 rabbit mAb (D5B10) Cell signaling technology Europe BV Cat# 8052S; RRID: AB_11178947 Anti-mouse secondary (HRP) Santa Cruz Cat# sc-516102; RRID: AB_2687626 Anti-rabbit secondary (HRP) Jackson ImmunoResearch Cat# 711-035-152; RRID: AB_10015282 Anti-mouse secondary (HRP) VWR Cat# NA9310; RRID: AB_772193 Anti-Sumo 2 + Sumo 3 rabbit polyclonal Abcam Cat# ab3742; RRID; AB_304041 Anti-Sumo 1 (Y299) rabbit mAb Abcam Cat# ab32058; RRID: AB_778173 Anti-DDI2 rabbit polyclonal Bethyl Laboratories Cat# A304-629A Anti-Myc mouse monoclonal (9E10) Crick laboratories Evan et al. (1985) Bacterial and Virus Strains NEB 5-alpha Competent E. coli (High Efficiency) New England Biolabs Cat# C2987H BL21-CodonPlus (DE3)-RIL Competent Cells Agilent technologies LDA UK LTD Cat# 230245 XL10-Gold ultracompetent cells Agilent technologies LDA UK LTD Cat# 200315 BL21-CodonPlus (DE3)-RIL Competent Cells Agilent technologies LDA UK LTD Cat# 230245 Chemicals, Peptides, and Recombinant Proteins PS-341 (Bortezomib) Enzo Life Sciences Cat# BV-1846-1 Recombinant Human USP2 Catalytic Domain, CF BIO-TECHNE Cat# E-504-050 Recombinant Human USP2 Catalytic Domain, CF His tagged CALTAG Medsystems LTD Cat# AG-40T-0539-C050 Human Rad23 from E. coli MYBIOSOURCE INC Cat# MBS717584 N-Ethylmaleimide (NEM) Sigma-Aldrich Cat# 04260 Ampicillin Cambridge Bioscience limited Cat# 2484 MG-132 Sigma-Aldrich Cat# M7449 L Glutamine Fisher Scientific UK LTD Cat# 15410314 Medium, Basal; GIBCO; DMEM (for SILAC) Fisher Scientific UK LTD Cat# 12817552 Sodium Pyruvate, GIBCO Fisher Scientific UK LTD Cat# 12539059 L-Poline for SILAC Life Technologies LTD Cat# 8840 Dimethyl Sulfoxide (DMSO) Sigma-Aldrich Cat# D2650 Cycloheximide 2BSCIENTIFIC Cat# C084-10x1ml Blasticidin Thermo-Fisher (GIBCO) Cat# R21001 Polyornithine Sigma-Aldrich Cat# P4957 EPNP (1,2-Epoxy-3-(4-nitrophenoxy)propane: sc. .. 1,2-Epoxy-3-(4-nitrophenoxy)propane) Santa Cruz Cat# sc-258906 Tetra Ubiquitin K48 linked Boston Biochem Cat# UC-210B Tetra Ubiquitin K29 linked Boston Biochem Cat# UC-83 Tetra Ubiquitin K63 linked Boston Biochem Cat# UC-310B Tetra Ubiquitin K33 linked Boston Biochem Cat# UC-103 Octa Ubiquitin K63 linked Boston Biochem Cat# UC-318B Poly-ubiquitin (Ub2-16) K48 linked ENZO Life Sciences Cat# BML-UW0670 Critical Commercial Assays XT-sample buffer BioRad Laboratories Cat# 1610791 Precision PLUS pre-stained markers BioRad Laboratories Cat# 1610393 (Continued on next page) Molecular Cell 79, 1–10.e1–e7, July 16, 2020 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Fetal Bovine Serum Dialysed Labtech international limited Cat# FB-1001D DMEM/F12 Sigma-Aldrich Cat# D6421 FBS (Australian Origin) Thermo-Fisher (GIBCO) Cat# 10099-141 GlutaMAX Thermo-Fisher (GIBCO) Cat# 35050-038 Lipofectamine 2000 Thermo-Fisher Scientific Cat# 1668019 Lipofectamine 3000 Thermo-Fisher Scientific Cat# L3000015 QIAamp DNA Mini Kit QIAGEN Cat# 51306 Q5 High-Fidelity 2X Master Mix New England BioLabs Cat# M0492 4-15% TGX gels BioRad Laboratories Cat# 5671084 NuPAGE 10% Bis-Tris protein gels Life Technologies LTD Cat# NP03031BOX Criterion XT Tris-Acetate Gel 3-8% BioRad laboratories Cat# 3450130 Criterion XT Bis-Tris 4-12% BioRad Laboratories Cat# 3450124; Cat# 3450125 Nitrocellulose membrane 0.45 uM GE Healthcare Life Sciences Cat# 10600002 Nitrocellulose membrane 0.2 uM GE Healthcare Life Sciences Cat# 10600019 Hyperfilm ECL VWR international Cat# 29-9068-37 SuperSignal West Pico PLUS ECl reagent Thermo Scientific Cat# 34580 DMEM media Thermo Scientific Cat# 41966029 RPMI-1640 media Sigma-Aldrich Cat# R8758 Radiance ECL HRP substrate Azure Biosystems Cat# AC2101 Radiance plus femtogram HRP substrate Azure Biosystems Cat# AC2103 Ni-NTA Superflow QIAGEN LTD Cat# 30410 Glutathione Sepharose 4B Sigma-Aldrich Cat# GE17-0756-01 ANTI-FLAG M2 Affinity Gel Sigma-Aldrich Cat# A2220 InstantBlue Expedeon Cat# ISB1L HiTrap Q FF Fisher scientific UK LTD Cat# 10607275 HiLoad 16/60 superdex 200 GE health care Cat# 28-9893-35 XT MOPS running Buffer BIO-RAD Laboratories Cat# 1610788 XT Tricine running Buffer BIO-RAD Laboratories Cat# 1610790 XT MES running buffer BIO-RAD Laboratories Cat# 1610789 Deposited Data Proteomics (Mass Spec DDI2 interaction) This study PRIDE: PXD018215 Proteomics (Mass Spec DDI2 interaction and UbiSite) This study PRIDE: PXD019152 Source data (Western blots, etc.)

    Article Title: DDI2 Is a Ubiquitin-Directed Endoprotease Responsible for Cleavage of Transcription Factor NRF1
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-Ubiquitin mouse mAb (P4D1) ENZO Life Sciences Cat# BML-PW0930; RRID: AB_10998070 Anti-Ubiquitin mouse mAb (P4G7) ENZO Life Sciences Cat# ENZ-ABS142; RRID: AB_2331077 Anti-TCF11/NRF1 rabbit mAb (D5B10) Cell signaling technology Europe BV Cat# 8052S; RRID: AB_11178947 Anti-mouse secondary (HRP) Santa Cruz Cat# sc-516102; RRID: AB_2687626 Anti-rabbit secondary (HRP) Jackson ImmunoResearch Cat# 711-035-152; RRID: AB_10015282 Anti-mouse secondary (HRP) VWR Cat# NA9310; RRID: AB_772193 Anti-Sumo 2 + Sumo 3 rabbit polyclonal Abcam Cat# ab3742; RRID; AB_304041 Anti-Sumo 1 (Y299) rabbit mAb Abcam Cat# ab32058; RRID: AB_778173 Anti-DDI2 rabbit polyclonal Bethyl Laboratories Cat# A304-629A Anti-Myc mouse monoclonal (9E10) Crick laboratories Evan et al. (1985) Bacterial and Virus Strains NEB 5-alpha Competent E. coli (High Efficiency) New England Biolabs Cat# C2987H BL21-CodonPlus (DE3)-RIL Competent Cells Agilent technologies LDA UK LTD Cat# 230245 XL10-Gold ultracompetent cells Agilent technologies LDA UK LTD Cat# 200315 BL21-CodonPlus (DE3)-RIL Competent Cells Agilent technologies LDA UK LTD Cat# 230245 Chemicals, Peptides, and Recombinant Proteins PS-341 (Bortezomib) Enzo Life Sciences Cat# BV-1846-1 Recombinant Human USP2 Catalytic Domain, CF BIO-TECHNE Cat# E-504-050 Recombinant Human USP2 Catalytic Domain, CF His tagged CALTAG Medsystems LTD Cat# AG-40T-0539-C050 Human Rad23 from E. coli MYBIOSOURCE INC Cat# MBS717584 N-Ethylmaleimide (NEM) Sigma-Aldrich Cat# 04260 Ampicillin Cambridge Bioscience limited Cat# 2484 MG-132 Sigma-Aldrich Cat# M7449 L Glutamine Fisher Scientific UK LTD Cat# 15410314 Medium, Basal; GIBCO; DMEM (for SILAC) Fisher Scientific UK LTD Cat# 12817552 Sodium Pyruvate, GIBCO Fisher Scientific UK LTD Cat# 12539059 L-Poline for SILAC Life Technologies LTD Cat# 8840 Dimethyl Sulfoxide (DMSO) Sigma-Aldrich Cat# D2650 Cycloheximide 2BSCIENTIFIC Cat# C084-10x1ml Blasticidin Thermo-Fisher (GIBCO) Cat# R21001 Polyornithine Sigma-Aldrich Cat# P4957 EPNP (1,2-Epoxy-3-(4-nitrophenoxy)propane: sc. .. 1,2-Epoxy-3-(4-nitrophenoxy)propane) Santa Cruz Cat# sc-258906 Tetra Ubiquitin K48 linked Boston Biochem Cat# UC-210B Tetra Ubiquitin K29 linked Boston Biochem Cat# UC-83 Tetra Ubiquitin K63 linked Boston Biochem Cat# UC-310B Tetra Ubiquitin K33 linked Boston Biochem Cat# UC-103 Octa Ubiquitin K63 linked Boston Biochem Cat# UC-318B Poly-ubiquitin (Ub2-16) K48 linked ENZO Life Sciences Cat# BML-UW0670 Critical Commercial Assays XT-sample buffer BioRad Laboratories Cat# 1610791 Precision PLUS pre-stained markers BioRad Laboratories Cat# 1610393 (Continued on next page) e1 Molecular Cell 79, 332–341.e1–e7, July 16, 2020 .. REAGENT or RESOURCE SOURCE IDENTIFIER Fetal Bovine Serum Dialysed Labtech international limited Cat# FB-1001D DMEM/F12 Sigma-Aldrich Cat# D6421 FBS (Australian Origin) Thermo-Fisher (GIBCO) Cat# 10099-141 GlutaMAX Thermo-Fisher (GIBCO) Cat# 35050-038 Lipofectamine 2000 Thermo-Fisher Scientific Cat# 1668019 Lipofectamine 3000 Thermo-Fisher Scientific Cat# L3000015 QIAamp DNA Mini Kit QIAGEN Cat# 51306 Q5 High-Fidelity 2X Master Mix New England BioLabs Cat# M0492 4-15% TGX gels BioRad Laboratories Cat# 5671084 NuPAGE 10% Bis-Tris protein gels Life Technologies LTD Cat# NP03031BOX Criterion XT Tris-Acetate Gel 3-8% BioRad laboratories Cat# 3450130 Criterion XT Bis-Tris 4-12% BioRad Laboratories Cat# 3450124; Cat# 3450125 Nitrocellulose membrane 0.45 uM GE Healthcare Life Sciences Cat# 10600002 Nitrocellulose membrane 0.2 uM GE Healthcare Life Sciences Cat# 10600019 Hyperfilm ECL VWR international Cat# 29-9068-37 SuperSignal West Pico PLUS ECl reagent Thermo Scientific Cat# 34580 DMEM media Thermo Scientific Cat# 41966029 RPMI-1640 media Sigma-Aldrich Cat# R8758 Radiance ECL HRP substrate Azure Biosystems Cat# AC2101 Radiance plus femtogram HRP substrate Azure Biosystems Cat# AC2103 Ni-NTA Superflow QIAGEN LTD Cat# 30410 Glutathione Sepharose 4B Sigma-Aldrich Cat# GE17-0756-01 ANTI-FLAG M2 Affinity Gel Sigma-Aldrich Cat# A2220 InstantBlue Expedeon Cat# ISB1L HiTrap Q FF Fisher scientific UK LTD Cat# 10607275 HiLoad 16/60 superdex 200 GE health care Cat# 28-9893-35 XT MOPS running Buffer BIO-RAD Laboratories Cat# 1610788 XT Tricine running Buffer BIO-RAD Laboratories Cat# 1610790 XT MES running buffer BIO-RAD Laboratories Cat# 1610789 Deposited Data Proteomics (Mass Spec DDI2 interaction) This study PRIDE: PXD018215 Proteomics (Mass Spec DDI2 interaction and UbiSite) This study PRIDE: PXD019152 Source data (Western blots, etc.)

    Membrane:

    Article Title: Yeast Smy2 and its human homologs GIGYF1 and -2 regulate Cdc48/VCP function during transcription stress
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse monoclonal anti-Rpb1 Abcam Cat#ab5408; RRID: AB_304868 Mouse monoclonal anti-ubiquitin (P4D1) ENZO Life Sciences Cat#BML-PW0930; RRID: AB_10998070 Mouse monoclonal anti-ubiquitin (P4G7) ENZO Life Sciences Cat#ENZ-ABS142; RRID: AB_2331077 Mouse monoclonal anti-HA Santa Cruz Cat#1424; RRID: AB_301017 Mouse monoclonal anti-GST Abcam Cat#sc-516102; RRID: AB_2687626 Rabbit polyclonal anti-FLAG Sigma Cat#F7425; RRID: AB_439687 Mouse monoclonal anti-MYC (9E10) Crick Laboratories Evan et al. (1985) Rabbit polyclonal anti-Def1 (388–738) Crick Laboratories Wilson et al., 2013a, 2013b Mouse monoclonal anti-tubulin Sigma Cat#T5168, RRID: AB_477579 Rabbit monoclonal anti-proteasome 20S C2/HC2 Abcam Cat#ab109530; RRID: AB_10860339 Rabbit polyclonal anti-histone H3 Abcam Cat#ab18521; RRID:AB_732917 Rabbit polyclonal anti-GIGYF2 Bethyl Cat#A303-731A; RRID: AB_11204927 Rabbit polyclonal anti-GIGYF2 Proteintech Cat#24790-1-AP; RRID: AB_2879727 Rabbit polyclonal anti-GIGYF1 Bethyl Cat#A304-132A; RRID: AB_2621381 Rabbit polyclonal anti-UFD1L Proteintech Cat#10615-1; RRID: AB_2213944 Rabbit monoclonal anti-VCP Abcam Cat#ab109240; RRID: AB_10862588 Mouse monoclonal anti-VCP Abcam Cat#ab11433; RRID: AB_298039 Anti-rabbit secondary (HRP) Jackson ImmunoResearch Cat# 711-035-152; RRID: AB_10015282 Anti-mouse secondary (HRP) Jackson ImmunoResearch Cat# 715-035-151 RRID: AB_2340771 Anti-mouse secondary (HRP) Santa Cruz Cat# sc-516102; RRID: AB_2687626 Bacterial and virus strains NEB 5-alpha Competent E. coli (High Efficiency) New England Biolabs Cat#C2987H BL21-CodonPlus (DE3)-RIL Competent Cells Agilent technologies LDA UK LTD Cat#230245 Chemicals, peptides, and recombinant proteins lipofectamine 3000 Life Technologies Cat#L3000015 NMS873 Tebu-Bio Ltd. Cat#282T1853 CB-5083 Cayman Chemicals Cat#CAY19311 Dimethyl Sulfoxide (DMSO) Sigma-Aldrich Cat#D2650 N-Ethylmaleimide (NEM) Sigma-Aldrich Cat#04260 Ampicillin Cambridge Bioscience limited Cat#2484 MG-132 Sigma-Aldrich Cat#M7449 6-azauracil Sigma-Aldrich Cat#A1757 5-fluoroorotic acid Melford Laboratories Cat#F5001-5G Dsk2 beads Home-made; see Tufegdzic Vidakovic et al., 2019 N/A Hygromycin B Enzo Life Sciences ALX-380-306-G001 Critical commercial assays Duolink Kit in situ Red starter kit mouse/ rabbit Sigma-Aldrich Cat#DUO92101 Caspase-Glo 3/7 assay reagent Promega Corporation Cat#G8090 NucView 488 Caspase-3 Assay Kit Biotium Cat#BT30029-T (Continued on next page) e1 Cell Reports 41, 111536, October 25, 2022 .. REAGENT or RESOURCE SOURCE IDENTIFIER XT-sample buffer BioRad Laboratories Cat#1610791 4-15% TGX gels BioRad Laboratories Cat#5671084 NuPAGE 10% Bis-Tris protein gels Life Technologies LTD Cat#NP03031BOX Criterion XT Tris-Acetate Gel 3–8% BioRad laboratories Cat#3450130 Criterion XT Bis-Tris 4-12% BioRad Laboratories Cat#3450125 Nitrocellulose membrane 0.45 uM GE Healthcare Life Sciences Cat#10600002 Nitrocellulose membrane 0.2 uM GE Healthcare Life Sciences Cat#10600019 Hyperfilm ECL VWR international Cat#29-9068-37 SuperSignal West Pico PLUS ECL reagent Thermo Scientific Cat#34580 DMEM media Thermo Scientific Cat#41966029 XT Tricine running Buffer BIO-RAD Laboratories Cat#1610790 Basemuncher EXPEDEON LTD Cat#BM0100 Glutathione Sepharose 4B Sigma-Aldrich Cat#GE17-0756-01 ANTI-FLAG M2 Affinity Gel Sigma-Aldrich Cat#A2220 Protein G agarose beads Sigma-Aldrich Cat#11719416001 Complete EDTA-free protease inhibitor cocktail Sigma-Aldrich Cat#05056489001 PhosSTOP Sigma-Aldrich Cat#04906837001 SilverQuest Silver Staining Kit Thermo Fisher Cat#LC6070 Ponceau S Sigma-Aldrich Cat# P7170 Bio-Rad protein assay reagent Bio-Rad Cat#5000006 Precision PLUS pre-stained markers BioRad Laboratories Cat1610393 Experimental models: Cell lines Human lung fibroblast cell line MRC5VA Francis Crick Institute cell depository N/A Human lung fibroblast cell line MRC5VA GIGYF1 and 2 KO Francis Crick Institute cell depository N/A Experimental models: Organisms/Strains S.cerevisiae (strain W303 MATa ura3, leu2-3, 112, his3-11,15 trp1-1, ade2-1, can1-100) Gift from R. Rothstein N/A S.cerevisiae (strain W303 MATa ura3, leu2-3, 112, his3-11,15 trp1-1, ade2-1, can1-100) Gift from R. Rothstein N/A S.cerevisiae W303 MATa def1::TRP Woudstra et al., 2002 N/A S.cerevisiae W303 MATa rad16::LEU Woudstra et al., 2002 N/A S.cerevisiae W303 MATa def1::TRP rad16::LEU Woudstra et al., 2002 N/A S.cerevisiae W303 MATa rpo21::ADE2 (pJS121; RPO21 k330r TRP CEN) Somesh et al. (2007) N/A S.cerevisiae W303 MATa rpo21::ADE2 (pJS121; RPO21 k330r TRP CEN) def1::URA This manuscript N/A S.cerevisiae W303 MATa myc9TEV2-His6-Smy2 This manuscript N/A S.cerevisiae W303 MATa galactoseFLAG-Smy2 This manuscript N/A S.cerevisiae W303 MATa myc9-TEV2His6-Smy2 Cdc48-HA This manuscript N/A S.cerevisiae W303 cdc48-3 Cheng and Chen (2010) N/A S.cerevisiae W303 cdc48-3 Smy2::TRP This manuscript N/A (Continued on next page) Cell Reports 41, 111536, October 25, 2022 e2 Article ll OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER S.cerevisiae W303 Pre1-myc9 This manuscript N/A S.cerevisiae W303 Pre1-myc9 Smy2::HIS This manuscript N/A S.cerevisiae W303 Smy2::HIS This manuscript N/A S.cerevisiae W303 Smy2::LEU This manuscript N/A S.cerevisiae W303 Smy2::TRP This manuscript N/A S.cerevisiae W303 CDC48-FLAG3 This manuscript N/A S.cerevisiae W303 CDC48-FLAG3 Smy2::LEU This manuscript N/A S.cerevisiae Y7731 MATa cdc48-9::KanR ura3D0 leu2D0 his3D met15D cdc48-9 Magtanong et al., 2011 N/A S.cerevisiae Y7829 cdc48-2 MATa cdc482::KanR ura3D0 leu2D0 his3D met15D Magtanong et al., 2011 N/A S.cerevisiae (strain BY4742, MATa, his3D1, leu2D0, lys2D0, ura3D0) Open Biosystems N/A S.cerevisiae BY4742 ubx1D::KanMX Open Biosystems N/A S.cerevisiae BY4742 ubx2D::KanMX Open Biosystems N/A S.cerevisiae BY4742 ubx3D::KanMX Open Biosystems N/A S.cerevisiae BY4742 ubx4D::KanMX Open Biosystems N/A S.cerevisiae BY4742 ubx5D::KanMX Open Biosystems N/A S.cerevisiae BY4742 ubx6D::KanMX Open Biosystems N/A S.cerevisiae BY4742 ubx7D::KanMX Open Biosystems N/A S.cerevisiae BY4742 smy2D::KanMX Open Biosystems N/A S.cerevisiae BY4742 ubx1D::KanMX smy2::HIS This manuscript N/A Oligonucleotides All oligonucleotides are listed in Table S2 N/A N/A Recombinant DNA pSpCas9(BB)-2A-GFP (PX458) Addgene Cat#48138 pDEF1 2 micron URA This manuscript N/A pSMY2 2 micron URA This manuscript N/A pSmy2 CEN LEU This manuscript N/A pSMY2 2 micron LEU This manuscript N/A pSMY2 Y234A 2 micron LEU This manuscript N/A pGST 6p-1-GYF (205–261) This manuscript N/A pGST 6p-1-GAF (205–261) Y234A This manuscript N/A pGEX 6p-1 Sigma-Aldrich Cat#GE28-9546-48 pCDC48 CEN URA This manuscript N/A pGAL-FLAG3-Spt23-HA3 URA This manuscript N/A pRS426 URA 2 micron (Sikorski and Hieter, 1989) N/A pRS306 URA CEN (Sikorski and Hieter, 1989) N/A pRS305 LEU CEN (Sikorski and Hieter, 1989) N/A pRS425 LEU 2 micron (Sikorski and Hieter, 1989) N/A pGEX3-Dsk2 Anindya et al. (2007) N/A pGST-MD Wilson et al. (2012) N/A Software and algorithms TIDE Brinkman et al., (2014) http://tide.nki.nl/ Prism 9.2.0 GraphPad https://www.graphpad.com Perseus version 1.4.0.11 Tyanova et al. (2016) N/A FIJI ImageJ https://imagej.net/software/fiji/ (Continued on next page) e3 Cell Reports 41, 111536, October 25, 2022 Article ll OPEN ACCESS

    Protease Inhibitor:

    Article Title: Yeast Smy2 and its human homologs GIGYF1 and -2 regulate Cdc48/VCP function during transcription stress
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse monoclonal anti-Rpb1 Abcam Cat#ab5408; RRID: AB_304868 Mouse monoclonal anti-ubiquitin (P4D1) ENZO Life Sciences Cat#BML-PW0930; RRID: AB_10998070 Mouse monoclonal anti-ubiquitin (P4G7) ENZO Life Sciences Cat#ENZ-ABS142; RRID: AB_2331077 Mouse monoclonal anti-HA Santa Cruz Cat#1424; RRID: AB_301017 Mouse monoclonal anti-GST Abcam Cat#sc-516102; RRID: AB_2687626 Rabbit polyclonal anti-FLAG Sigma Cat#F7425; RRID: AB_439687 Mouse monoclonal anti-MYC (9E10) Crick Laboratories Evan et al. (1985) Rabbit polyclonal anti-Def1 (388–738) Crick Laboratories Wilson et al., 2013a, 2013b Mouse monoclonal anti-tubulin Sigma Cat#T5168, RRID: AB_477579 Rabbit monoclonal anti-proteasome 20S C2/HC2 Abcam Cat#ab109530; RRID: AB_10860339 Rabbit polyclonal anti-histone H3 Abcam Cat#ab18521; RRID:AB_732917 Rabbit polyclonal anti-GIGYF2 Bethyl Cat#A303-731A; RRID: AB_11204927 Rabbit polyclonal anti-GIGYF2 Proteintech Cat#24790-1-AP; RRID: AB_2879727 Rabbit polyclonal anti-GIGYF1 Bethyl Cat#A304-132A; RRID: AB_2621381 Rabbit polyclonal anti-UFD1L Proteintech Cat#10615-1; RRID: AB_2213944 Rabbit monoclonal anti-VCP Abcam Cat#ab109240; RRID: AB_10862588 Mouse monoclonal anti-VCP Abcam Cat#ab11433; RRID: AB_298039 Anti-rabbit secondary (HRP) Jackson ImmunoResearch Cat# 711-035-152; RRID: AB_10015282 Anti-mouse secondary (HRP) Jackson ImmunoResearch Cat# 715-035-151 RRID: AB_2340771 Anti-mouse secondary (HRP) Santa Cruz Cat# sc-516102; RRID: AB_2687626 Bacterial and virus strains NEB 5-alpha Competent E. coli (High Efficiency) New England Biolabs Cat#C2987H BL21-CodonPlus (DE3)-RIL Competent Cells Agilent technologies LDA UK LTD Cat#230245 Chemicals, peptides, and recombinant proteins lipofectamine 3000 Life Technologies Cat#L3000015 NMS873 Tebu-Bio Ltd. Cat#282T1853 CB-5083 Cayman Chemicals Cat#CAY19311 Dimethyl Sulfoxide (DMSO) Sigma-Aldrich Cat#D2650 N-Ethylmaleimide (NEM) Sigma-Aldrich Cat#04260 Ampicillin Cambridge Bioscience limited Cat#2484 MG-132 Sigma-Aldrich Cat#M7449 6-azauracil Sigma-Aldrich Cat#A1757 5-fluoroorotic acid Melford Laboratories Cat#F5001-5G Dsk2 beads Home-made; see Tufegdzic Vidakovic et al., 2019 N/A Hygromycin B Enzo Life Sciences ALX-380-306-G001 Critical commercial assays Duolink Kit in situ Red starter kit mouse/ rabbit Sigma-Aldrich Cat#DUO92101 Caspase-Glo 3/7 assay reagent Promega Corporation Cat#G8090 NucView 488 Caspase-3 Assay Kit Biotium Cat#BT30029-T (Continued on next page) e1 Cell Reports 41, 111536, October 25, 2022 .. REAGENT or RESOURCE SOURCE IDENTIFIER XT-sample buffer BioRad Laboratories Cat#1610791 4-15% TGX gels BioRad Laboratories Cat#5671084 NuPAGE 10% Bis-Tris protein gels Life Technologies LTD Cat#NP03031BOX Criterion XT Tris-Acetate Gel 3–8% BioRad laboratories Cat#3450130 Criterion XT Bis-Tris 4-12% BioRad Laboratories Cat#3450125 Nitrocellulose membrane 0.45 uM GE Healthcare Life Sciences Cat#10600002 Nitrocellulose membrane 0.2 uM GE Healthcare Life Sciences Cat#10600019 Hyperfilm ECL VWR international Cat#29-9068-37 SuperSignal West Pico PLUS ECL reagent Thermo Scientific Cat#34580 DMEM media Thermo Scientific Cat#41966029 XT Tricine running Buffer BIO-RAD Laboratories Cat#1610790 Basemuncher EXPEDEON LTD Cat#BM0100 Glutathione Sepharose 4B Sigma-Aldrich Cat#GE17-0756-01 ANTI-FLAG M2 Affinity Gel Sigma-Aldrich Cat#A2220 Protein G agarose beads Sigma-Aldrich Cat#11719416001 Complete EDTA-free protease inhibitor cocktail Sigma-Aldrich Cat#05056489001 PhosSTOP Sigma-Aldrich Cat#04906837001 SilverQuest Silver Staining Kit Thermo Fisher Cat#LC6070 Ponceau S Sigma-Aldrich Cat# P7170 Bio-Rad protein assay reagent Bio-Rad Cat#5000006 Precision PLUS pre-stained markers BioRad Laboratories Cat1610393 Experimental models: Cell lines Human lung fibroblast cell line MRC5VA Francis Crick Institute cell depository N/A Human lung fibroblast cell line MRC5VA GIGYF1 and 2 KO Francis Crick Institute cell depository N/A Experimental models: Organisms/Strains S.cerevisiae (strain W303 MATa ura3, leu2-3, 112, his3-11,15 trp1-1, ade2-1, can1-100) Gift from R. Rothstein N/A S.cerevisiae (strain W303 MATa ura3, leu2-3, 112, his3-11,15 trp1-1, ade2-1, can1-100) Gift from R. Rothstein N/A S.cerevisiae W303 MATa def1::TRP Woudstra et al., 2002 N/A S.cerevisiae W303 MATa rad16::LEU Woudstra et al., 2002 N/A S.cerevisiae W303 MATa def1::TRP rad16::LEU Woudstra et al., 2002 N/A S.cerevisiae W303 MATa rpo21::ADE2 (pJS121; RPO21 k330r TRP CEN) Somesh et al. (2007) N/A S.cerevisiae W303 MATa rpo21::ADE2 (pJS121; RPO21 k330r TRP CEN) def1::URA This manuscript N/A S.cerevisiae W303 MATa myc9TEV2-His6-Smy2 This manuscript N/A S.cerevisiae W303 MATa galactoseFLAG-Smy2 This manuscript N/A S.cerevisiae W303 MATa myc9-TEV2His6-Smy2 Cdc48-HA This manuscript N/A S.cerevisiae W303 cdc48-3 Cheng and Chen (2010) N/A S.cerevisiae W303 cdc48-3 Smy2::TRP This manuscript N/A (Continued on next page) Cell Reports 41, 111536, October 25, 2022 e2 Article ll OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER S.cerevisiae W303 Pre1-myc9 This manuscript N/A S.cerevisiae W303 Pre1-myc9 Smy2::HIS This manuscript N/A S.cerevisiae W303 Smy2::HIS This manuscript N/A S.cerevisiae W303 Smy2::LEU This manuscript N/A S.cerevisiae W303 Smy2::TRP This manuscript N/A S.cerevisiae W303 CDC48-FLAG3 This manuscript N/A S.cerevisiae W303 CDC48-FLAG3 Smy2::LEU This manuscript N/A S.cerevisiae Y7731 MATa cdc48-9::KanR ura3D0 leu2D0 his3D met15D cdc48-9 Magtanong et al., 2011 N/A S.cerevisiae Y7829 cdc48-2 MATa cdc482::KanR ura3D0 leu2D0 his3D met15D Magtanong et al., 2011 N/A S.cerevisiae (strain BY4742, MATa, his3D1, leu2D0, lys2D0, ura3D0) Open Biosystems N/A S.cerevisiae BY4742 ubx1D::KanMX Open Biosystems N/A S.cerevisiae BY4742 ubx2D::KanMX Open Biosystems N/A S.cerevisiae BY4742 ubx3D::KanMX Open Biosystems N/A S.cerevisiae BY4742 ubx4D::KanMX Open Biosystems N/A S.cerevisiae BY4742 ubx5D::KanMX Open Biosystems N/A S.cerevisiae BY4742 ubx6D::KanMX Open Biosystems N/A S.cerevisiae BY4742 ubx7D::KanMX Open Biosystems N/A S.cerevisiae BY4742 smy2D::KanMX Open Biosystems N/A S.cerevisiae BY4742 ubx1D::KanMX smy2::HIS This manuscript N/A Oligonucleotides All oligonucleotides are listed in Table S2 N/A N/A Recombinant DNA pSpCas9(BB)-2A-GFP (PX458) Addgene Cat#48138 pDEF1 2 micron URA This manuscript N/A pSMY2 2 micron URA This manuscript N/A pSmy2 CEN LEU This manuscript N/A pSMY2 2 micron LEU This manuscript N/A pSMY2 Y234A 2 micron LEU This manuscript N/A pGST 6p-1-GYF (205–261) This manuscript N/A pGST 6p-1-GAF (205–261) Y234A This manuscript N/A pGEX 6p-1 Sigma-Aldrich Cat#GE28-9546-48 pCDC48 CEN URA This manuscript N/A pGAL-FLAG3-Spt23-HA3 URA This manuscript N/A pRS426 URA 2 micron (Sikorski and Hieter, 1989) N/A pRS306 URA CEN (Sikorski and Hieter, 1989) N/A pRS305 LEU CEN (Sikorski and Hieter, 1989) N/A pRS425 LEU 2 micron (Sikorski and Hieter, 1989) N/A pGEX3-Dsk2 Anindya et al. (2007) N/A pGST-MD Wilson et al. (2012) N/A Software and algorithms TIDE Brinkman et al., (2014) http://tide.nki.nl/ Prism 9.2.0 GraphPad https://www.graphpad.com Perseus version 1.4.0.11 Tyanova et al. (2016) N/A FIJI ImageJ https://imagej.net/software/fiji/ (Continued on next page) e3 Cell Reports 41, 111536, October 25, 2022 Article ll OPEN ACCESS

    Silver Staining:

    Article Title: Yeast Smy2 and its human homologs GIGYF1 and -2 regulate Cdc48/VCP function during transcription stress
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse monoclonal anti-Rpb1 Abcam Cat#ab5408; RRID: AB_304868 Mouse monoclonal anti-ubiquitin (P4D1) ENZO Life Sciences Cat#BML-PW0930; RRID: AB_10998070 Mouse monoclonal anti-ubiquitin (P4G7) ENZO Life Sciences Cat#ENZ-ABS142; RRID: AB_2331077 Mouse monoclonal anti-HA Santa Cruz Cat#1424; RRID: AB_301017 Mouse monoclonal anti-GST Abcam Cat#sc-516102; RRID: AB_2687626 Rabbit polyclonal anti-FLAG Sigma Cat#F7425; RRID: AB_439687 Mouse monoclonal anti-MYC (9E10) Crick Laboratories Evan et al. (1985) Rabbit polyclonal anti-Def1 (388–738) Crick Laboratories Wilson et al., 2013a, 2013b Mouse monoclonal anti-tubulin Sigma Cat#T5168, RRID: AB_477579 Rabbit monoclonal anti-proteasome 20S C2/HC2 Abcam Cat#ab109530; RRID: AB_10860339 Rabbit polyclonal anti-histone H3 Abcam Cat#ab18521; RRID:AB_732917 Rabbit polyclonal anti-GIGYF2 Bethyl Cat#A303-731A; RRID: AB_11204927 Rabbit polyclonal anti-GIGYF2 Proteintech Cat#24790-1-AP; RRID: AB_2879727 Rabbit polyclonal anti-GIGYF1 Bethyl Cat#A304-132A; RRID: AB_2621381 Rabbit polyclonal anti-UFD1L Proteintech Cat#10615-1; RRID: AB_2213944 Rabbit monoclonal anti-VCP Abcam Cat#ab109240; RRID: AB_10862588 Mouse monoclonal anti-VCP Abcam Cat#ab11433; RRID: AB_298039 Anti-rabbit secondary (HRP) Jackson ImmunoResearch Cat# 711-035-152; RRID: AB_10015282 Anti-mouse secondary (HRP) Jackson ImmunoResearch Cat# 715-035-151 RRID: AB_2340771 Anti-mouse secondary (HRP) Santa Cruz Cat# sc-516102; RRID: AB_2687626 Bacterial and virus strains NEB 5-alpha Competent E. coli (High Efficiency) New England Biolabs Cat#C2987H BL21-CodonPlus (DE3)-RIL Competent Cells Agilent technologies LDA UK LTD Cat#230245 Chemicals, peptides, and recombinant proteins lipofectamine 3000 Life Technologies Cat#L3000015 NMS873 Tebu-Bio Ltd. Cat#282T1853 CB-5083 Cayman Chemicals Cat#CAY19311 Dimethyl Sulfoxide (DMSO) Sigma-Aldrich Cat#D2650 N-Ethylmaleimide (NEM) Sigma-Aldrich Cat#04260 Ampicillin Cambridge Bioscience limited Cat#2484 MG-132 Sigma-Aldrich Cat#M7449 6-azauracil Sigma-Aldrich Cat#A1757 5-fluoroorotic acid Melford Laboratories Cat#F5001-5G Dsk2 beads Home-made; see Tufegdzic Vidakovic et al., 2019 N/A Hygromycin B Enzo Life Sciences ALX-380-306-G001 Critical commercial assays Duolink Kit in situ Red starter kit mouse/ rabbit Sigma-Aldrich Cat#DUO92101 Caspase-Glo 3/7 assay reagent Promega Corporation Cat#G8090 NucView 488 Caspase-3 Assay Kit Biotium Cat#BT30029-T (Continued on next page) e1 Cell Reports 41, 111536, October 25, 2022 .. REAGENT or RESOURCE SOURCE IDENTIFIER XT-sample buffer BioRad Laboratories Cat#1610791 4-15% TGX gels BioRad Laboratories Cat#5671084 NuPAGE 10% Bis-Tris protein gels Life Technologies LTD Cat#NP03031BOX Criterion XT Tris-Acetate Gel 3–8% BioRad laboratories Cat#3450130 Criterion XT Bis-Tris 4-12% BioRad Laboratories Cat#3450125 Nitrocellulose membrane 0.45 uM GE Healthcare Life Sciences Cat#10600002 Nitrocellulose membrane 0.2 uM GE Healthcare Life Sciences Cat#10600019 Hyperfilm ECL VWR international Cat#29-9068-37 SuperSignal West Pico PLUS ECL reagent Thermo Scientific Cat#34580 DMEM media Thermo Scientific Cat#41966029 XT Tricine running Buffer BIO-RAD Laboratories Cat#1610790 Basemuncher EXPEDEON LTD Cat#BM0100 Glutathione Sepharose 4B Sigma-Aldrich Cat#GE17-0756-01 ANTI-FLAG M2 Affinity Gel Sigma-Aldrich Cat#A2220 Protein G agarose beads Sigma-Aldrich Cat#11719416001 Complete EDTA-free protease inhibitor cocktail Sigma-Aldrich Cat#05056489001 PhosSTOP Sigma-Aldrich Cat#04906837001 SilverQuest Silver Staining Kit Thermo Fisher Cat#LC6070 Ponceau S Sigma-Aldrich Cat# P7170 Bio-Rad protein assay reagent Bio-Rad Cat#5000006 Precision PLUS pre-stained markers BioRad Laboratories Cat1610393 Experimental models: Cell lines Human lung fibroblast cell line MRC5VA Francis Crick Institute cell depository N/A Human lung fibroblast cell line MRC5VA GIGYF1 and 2 KO Francis Crick Institute cell depository N/A Experimental models: Organisms/Strains S.cerevisiae (strain W303 MATa ura3, leu2-3, 112, his3-11,15 trp1-1, ade2-1, can1-100) Gift from R. Rothstein N/A S.cerevisiae (strain W303 MATa ura3, leu2-3, 112, his3-11,15 trp1-1, ade2-1, can1-100) Gift from R. Rothstein N/A S.cerevisiae W303 MATa def1::TRP Woudstra et al., 2002 N/A S.cerevisiae W303 MATa rad16::LEU Woudstra et al., 2002 N/A S.cerevisiae W303 MATa def1::TRP rad16::LEU Woudstra et al., 2002 N/A S.cerevisiae W303 MATa rpo21::ADE2 (pJS121; RPO21 k330r TRP CEN) Somesh et al. (2007) N/A S.cerevisiae W303 MATa rpo21::ADE2 (pJS121; RPO21 k330r TRP CEN) def1::URA This manuscript N/A S.cerevisiae W303 MATa myc9TEV2-His6-Smy2 This manuscript N/A S.cerevisiae W303 MATa galactoseFLAG-Smy2 This manuscript N/A S.cerevisiae W303 MATa myc9-TEV2His6-Smy2 Cdc48-HA This manuscript N/A S.cerevisiae W303 cdc48-3 Cheng and Chen (2010) N/A S.cerevisiae W303 cdc48-3 Smy2::TRP This manuscript N/A (Continued on next page) Cell Reports 41, 111536, October 25, 2022 e2 Article ll OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER S.cerevisiae W303 Pre1-myc9 This manuscript N/A S.cerevisiae W303 Pre1-myc9 Smy2::HIS This manuscript N/A S.cerevisiae W303 Smy2::HIS This manuscript N/A S.cerevisiae W303 Smy2::LEU This manuscript N/A S.cerevisiae W303 Smy2::TRP This manuscript N/A S.cerevisiae W303 CDC48-FLAG3 This manuscript N/A S.cerevisiae W303 CDC48-FLAG3 Smy2::LEU This manuscript N/A S.cerevisiae Y7731 MATa cdc48-9::KanR ura3D0 leu2D0 his3D met15D cdc48-9 Magtanong et al., 2011 N/A S.cerevisiae Y7829 cdc48-2 MATa cdc482::KanR ura3D0 leu2D0 his3D met15D Magtanong et al., 2011 N/A S.cerevisiae (strain BY4742, MATa, his3D1, leu2D0, lys2D0, ura3D0) Open Biosystems N/A S.cerevisiae BY4742 ubx1D::KanMX Open Biosystems N/A S.cerevisiae BY4742 ubx2D::KanMX Open Biosystems N/A S.cerevisiae BY4742 ubx3D::KanMX Open Biosystems N/A S.cerevisiae BY4742 ubx4D::KanMX Open Biosystems N/A S.cerevisiae BY4742 ubx5D::KanMX Open Biosystems N/A S.cerevisiae BY4742 ubx6D::KanMX Open Biosystems N/A S.cerevisiae BY4742 ubx7D::KanMX Open Biosystems N/A S.cerevisiae BY4742 smy2D::KanMX Open Biosystems N/A S.cerevisiae BY4742 ubx1D::KanMX smy2::HIS This manuscript N/A Oligonucleotides All oligonucleotides are listed in Table S2 N/A N/A Recombinant DNA pSpCas9(BB)-2A-GFP (PX458) Addgene Cat#48138 pDEF1 2 micron URA This manuscript N/A pSMY2 2 micron URA This manuscript N/A pSmy2 CEN LEU This manuscript N/A pSMY2 2 micron LEU This manuscript N/A pSMY2 Y234A 2 micron LEU This manuscript N/A pGST 6p-1-GYF (205–261) This manuscript N/A pGST 6p-1-GAF (205–261) Y234A This manuscript N/A pGEX 6p-1 Sigma-Aldrich Cat#GE28-9546-48 pCDC48 CEN URA This manuscript N/A pGAL-FLAG3-Spt23-HA3 URA This manuscript N/A pRS426 URA 2 micron (Sikorski and Hieter, 1989) N/A pRS306 URA CEN (Sikorski and Hieter, 1989) N/A pRS305 LEU CEN (Sikorski and Hieter, 1989) N/A pRS425 LEU 2 micron (Sikorski and Hieter, 1989) N/A pGEX3-Dsk2 Anindya et al. (2007) N/A pGST-MD Wilson et al. (2012) N/A Software and algorithms TIDE Brinkman et al., (2014) http://tide.nki.nl/ Prism 9.2.0 GraphPad https://www.graphpad.com Perseus version 1.4.0.11 Tyanova et al. (2016) N/A FIJI ImageJ https://imagej.net/software/fiji/ (Continued on next page) e3 Cell Reports 41, 111536, October 25, 2022 Article ll OPEN ACCESS



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