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    Structured Review

    Valiant Co Ltd acid
    Acid, supplied by Valiant Co Ltd, used in various techniques. Bioz Stars score: 93/100, based on 10 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/0210203705/Indole-3-acetic+acid/10__7554_slash_elife__77987-344-3-5
    Average 93 stars, based on 10 article reviews
    acid - by Bioz Stars, 2026-09
    93/100 stars

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    Related Articles

    Concentration Assay:

    Article Title: Investigating Bacillus amyloliquefaciens VFS2 for Vicia faba ‐ fusarium wilt biocontrol and plant growth promotion under osmotic stress
    Article Snippet: .. To calculate the concentration of IAA for each treatment, a standard curve ranging from 0 to 100 μg ml −1 of pure IAA (Indole‐3‐acetic acid, MP Biomedicals, inc.) was used. ..

    Article Title: CDT1 inhibits CMG helicase in early S phase to separate origin licensing from DNA synthesis.
    Article Snippet: Media was exchanged with growth media after 2 h, and cells were then immediately live-imaged. siRNA and plasmids were both complexed in Opti-MEM serum-free media (Gibco Cat# 31985070). .. Stock solutions of drugs were dissolved in DMSO (Sigma-Aldrich Cat# D2650) and used at the given working concentration unless otherwise stated: 2 mM hydroxyurea (HU, dissolved in water, Cayman Chemical Cat# 23725), 2 mM thymidine (dissolved in PBS at 100mM, Sigma-Aldrich Cat# T9250-1G), 2 mg/mL aphidicolin (Sigma-Aldrich Cat# 5047440001), 2 mMAZ-20 (ATRi, Cayman Chemical Cat# 17589), 1 mMMK-1775 (WEE1i, Cayman Chemical Cat# 21266), 1 mg/mL Doxycycline hyclate (Sigma-Aldrich Cat# D9891), 2 mM MLN-4924 (Abcam Cat# ab216470), 500 mM indole-3 acetic acid (auxin, MP Biomedicals Cat# 0210203705), 100 nM BMS650032 (Adooq Bioscience Cat# A112955), 500 mM L-mimosine (20x stock solution dissolved in DMEM/F12, Cayman Chemical Cat# 14337). ..

    Article Title: Investigating Bacillus amyloliquefaciens VFS2 for Vicia faba-fusarium wilt biocontrol and plant growth promotion under osmotic stress.
    Article Snippet: .. To calculate the concentration of IAA for each treatment, a standard curve ranging from 0 to 100 μg ml−1 of pure IAA (Indole-3-acetic acid, MP Biomedicals, inc.) was used. ..

    other:

    Article Title: Maize Seedling Growth and Hormone Response Assays Using the Rolled Towel Method.
    Article Snippet: 6-Benzylaminopurine (BAP), 10 mM 0.11 g BAP (Sigma Aldrich, B3408-100 MG) 1 ml 1 M NaOH Store at −20°C for up to 1 month in 1-ml aliquots Bleach solution, 6% 25 ml of standard household bleach 475 ml of MQ water Mix and store in 500-ml glass or plastic bottles such as Pyrex or Nalgene Store at room temperature for up to 6 months Brassinolide (BL), 1 M 10 mg brassinolide (Millipore Sigma, cat. no. B1439) 1 ml 95% ethanol Store at −20°C for up to 1 month in 1-ml aliquots Indole-3-acetic acid (IAA), 10 mM 35 mg indole-3-acetic acid (MP Biomedicals, cat. no. 102037) Draves et al. 11 of 16 Current Protocols nloaded from https://currentprotocols.onlinelibrary.w iley.com /doi/10.1002/cpz1.562 by C A PE S, W iley O nline L ibrary on [01/02/2024].

    Recombinant:

    Article Title: Protein UFMylation regulates early events during ribosomal DNA-damage response.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse monoclonal anti-Treacle (H-6) Santa Cruz Biotechnology sc-374536 RRID:AB_10987865 Rabbit polyclonal anti-TCOF1 Millipore Sigma HPA038237 RRID:AB_10670660 Mouse monoclonal anti-MRE11 (12D7) GeneTex GTX70212 RRID:AB_372398 Mouse monoclonal anti-NBS1 (1D7) GeneTex GTX70224 RRID:AB_372445 Mouse monoclonal anti-TOPBP1 (B-7) Santa Cruz Biotechnology sc-271043 RRID:AB_10610636 Rabbit monoclonal anti-GAPDH (D16H11) Cell Signaling #5174 RRID:AB_10622025 Rabbit monoclonal anti-HA tag (C29F4) Cell Signaling #3724 RRID:AB_1549585 Rabbit polyclonal anti-UFL1 Abclonal A20528 Rabbit polyclonal anti-UFL1 Millipore Sigma HPA030558 RRID:AB_10600663 Rabbit monoclonal anti-UFM1 Abclonal A20875 Rabbit polyclonal anti-DDRGK1 Proteintech 21445-1-AP RRID:AB_2827383 Rabbit polyclonal anti-DDRGK1 Novus Biologicals NBP2-87256; RRID: AB_3428641 Mouse monoclonal anti-H3 Elabscience E-AB-22003 Rabbit polyclonal anti-GFP Abcam Ab290 RRID:AB_2313768 Mouse monoclonal anti-GFP Roche 11814460001 RRID:AB_390913 Rabbit monoclonal anti-Phopsho-Histone H2A.X Ser139 (20E3) Cell Signaling #9718 RRID:AB_2118009 Rabbit polyclonal anti-53BP1 Cell Signaling #4937 RRID:AB_10694558 Rabbit polyclonal anti-BRCA1 Abclonal A0212; RRID: AB_2757026 Rabbit polyclonal anti-ATM (D2E2) Cell Signaling #2873 RRID:AB_2062659 Rabbit monoclonal anti-V5 tag (D3H8Q) Cell Signaling #13202 RRID:AB_2687461 Rabbit polyclonal anti-Actin Sigma A2066, RRID:AB_476693 Mouse monoclonal anti-SMC6 (A-3) Santa Cruz Biotechnology sc-365742 RRID:AB_10846328 Mouse monoclonal anti-SMC5 (B-11) Santa Cruz Biotechnology sc-393282 Mouse monoclonal anti-Phospho-ATM Ser1981 Invitrogen MA12020 RRID:AB_1086244 F(ab’)2-Goat anti-Rabbit IgG (H + L) Cross-Adsorbed secondary antibody, Alexa FluorTM 680 Invitrogen A21077 RRID:AB_1500771 IRDye 800CW Goat anti-Rabbit IgG secondary antibody Licor 926–32211 RRID:AB_621843 IRDye 680LT Goat anti-Mouse IgG secondary antibody Licor 926–68020 RRID:AB_10706161 (Continued on next page) Cell Reports 43, 114738, September 24, 2024 21 .. REAGENT or RESOURCE SOURCE IDENTIFIER AmershamTM CyDyeTM 800 Goat-Anti-Mouse secondary antibody Cytiva 29360789 Alexa Fluor 488 goat anti-rabbit secondary antibody Invitrogen 22845951 Alexa Fluor 594 goat anti-mouse secondary antibody Invitrogen 2301112 Alexa Fluor 488 goat anti-mouse secondary antibody Invitrogen 2551357 Alexa Fluor 594 goat anti-rabbit secondary antibody Invitrogen 2268327 Nanobody Anti-GFP Rothbauer et al.102 GBP Chemicals, peptides, and recombinant proteins TRIzol Invitrogen 15596026 Trypsin Protease Promega V511A cOmpleteTM EDTA-free Protease Inhibitor Cocktail Sigma 11873580001 Sodium Fluoride (NaF) Sigma 201154 Sodium pyrophosphate decahydrate (NaPyPh) Sigma 221368 b-Glycerophosphate disodium salt hydrate (BGP) Sigma G9422 Sodium Orthovanadate (NaO) New England Biolabs P0758L X-tremeGENETM HP DNA Transfection Reagent Sigma XTGHP-RO Paraformaldehyde Sigma 158127 Goat Serum Sigma G9023 RNaseA ThermoFisher Scientific EN0531 Propidium Iodide Sigma 537059 Benzonase Nuclease Sigma E1014 DynabeadsTM M-270 Epoxy ThermoFisher Scientific 14302D DyLight 800 NHS Ester ThermoFisher Scientific 46421 Triethanolamine Sigma T58300 Tricene MP Biomedicals 807416 Lithium dodecyl sulfate Sigma BP1309-25 Crystal Violet Sigma C581 Shield-1 MedChemExpress HY-112210 4-Hydroxytamoxifen MedChemExpress HY-16950 Dimethyl sulfoxide (DMSO) Sigma BP231 ProLongTM Gold Antifade Mountant with DNA Stain DAPI ThermoFisher Scientific P36931 HisPurTM Ni-NTA Magnetic Beads ThermoFisher Scientific 88831 Dithiothreitol (DTT) ThermoFisher Scientific BP172 Urea Sigma U5378 Polybrene Sigma TR-1003 Ammonium Bicarbonate Sigma A6141 Amersham Hybond-N+ Cytiva RPN303B Doxycycline hyclate Wisent 450-185 XG 3-Indoleacetic acid (IAA) MP Biomedicals ICN10203725 Critical commercial assays Wizard Genomic DNA Purification kit Promega A1120 Click-iTTM RNA Alexa FluorTM 594 Imaging Kit Invitrogen C10330 BioRad Lowry DC Assay BioRad 5000111 In-Fusion Snap Assembly Takara 638946 (Continued on next page) 22 Cell Reports 43, 114738, September 24, 2024 Article ll OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER Deposited data CRISPR-Cas9 rDNA dropout screen This study NCBI GEO: GSE253809 TCOF1-eGFP/eGFP-NLS affinity purification mass spectrometry and His10UFM1DSC affinity purification mass spectrometry This study PRIDE repository: PXD048568; project DOI: 10.6019/PXD048568 Experimental models: Cell lines hTERT-RPE1 ATCC N/A hTERT-RPE1 p53 / Cas9 Alexandre Orthwein N/A hTERT-RPE1 p53 / Cas9+ DD-HA-ER-I-PpoI This study N/A hTERT-RPE1 p53 / Cas9+ DD-HA-ER-I-PpoI + eGFP-NLS This study N/A hTERT-RPE1 p53 / Cas9+ DD-HA-ER-I-PpoI + TCOF1-eGFP This study N/A hTERT-RPE1 p53 / Cas9+ DD-HA-ER-I-PpoI + His10-UFM1DSC This study N/A hTERT-RPE1 p53 / Cas9+ DD-HA-ER-I-PpoI, UFL1 KO This study N/A hTERT-RPE1 p53 / Cas9+ DD-HA-ER-I-PpoI, DDRGK1 KO This study N/A U2OS + DD-HA-ER-I-PpoI This study N/A HCT116 SMC6-mAC (mAID-Clover) mCherry H3 Venegas et al.89 N/A Oligonucleotides Primers used for library preparation Hart et al.49 Table S4 sgRNAs Hart et al.49 Walczak et al.83 Platt et al.103 Table S4 Northern Blot Probes This study Table S4 Recombinant DNA Plasmid: pLX303-DD-HA-ER-I-PpoI (G418) This study N/A Plasmid: Lenti-Guide-GFP-T2A-His10-UFM1DSC This study N/A Plasmid: pRK10-His10-UFM1DSC This study N/A Plasmid: Lenti-Guide-Puro-UBA5 This study N/A Plasmid: Lenti-Guide-Puro-UFM1 This study N/A Plasmid: Lenti-Guide-Puro-DDRGK1 This study N/A Plasmid Lenti-Guide-Puro-UFSP2: This study N/A Plasmid: Lenti-Guide-Puro-UFC1#1 This study N/A Plasmid: Lenti-Guide-Puro-UFC1#2 This study N/A Plasmid: Lenti-Guide-GFP-UFL1#1 This study N/A Plasmid: Lenti-Guide-GFP-UFL1#2 This study N/A Plasmid: Lenti-Guide-Puro-UFL1#1 This study N/A Plasmid: Lenti-Guide-Puro-UFL1#2 This study N/A Plasmid: Lenti-Guide-Puro 50 ETS #1 This study N/A Plasmid: Lenti-Guide-Puro-LacZ This study N/A Plasmid: pSH-EF-IRES-eGFP-V5-NLS This study N/A Plasmid: pSH-EF-IRES-TCOF1-eGFP This study N/A Plasmid: Lenti-Guide-Puro FAM208A#1 This study N/A Plasmid: Lenti-Guide-Puro FAM208A#2 This study N/A Plasmid: Lenti-Guide-Puro SETDB1#1 This study N/A Plasmid: Lenti-Guide-Puro SETDB1#2 This study N/A Plasmid: Lenti-Guide-mCherry-AAVS1 Noordermeer et al.104 N/A Plasmid: pCas9-sgAAVS1-1 Li et al.105 N/A Plasmid: pCas9-sgAAVS1-2 Li et al.105 N/A Plasmid: pMD2.G Addgene 12259 Plasmid: psPAX2 Addgene 12260 (Continued on next page) Cell Reports 43, 114738, September 24, 2024 23 Article ll OPEN ACCESS

    Protease Inhibitor:

    Article Title: Protein UFMylation regulates early events during ribosomal DNA-damage response.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse monoclonal anti-Treacle (H-6) Santa Cruz Biotechnology sc-374536 RRID:AB_10987865 Rabbit polyclonal anti-TCOF1 Millipore Sigma HPA038237 RRID:AB_10670660 Mouse monoclonal anti-MRE11 (12D7) GeneTex GTX70212 RRID:AB_372398 Mouse monoclonal anti-NBS1 (1D7) GeneTex GTX70224 RRID:AB_372445 Mouse monoclonal anti-TOPBP1 (B-7) Santa Cruz Biotechnology sc-271043 RRID:AB_10610636 Rabbit monoclonal anti-GAPDH (D16H11) Cell Signaling #5174 RRID:AB_10622025 Rabbit monoclonal anti-HA tag (C29F4) Cell Signaling #3724 RRID:AB_1549585 Rabbit polyclonal anti-UFL1 Abclonal A20528 Rabbit polyclonal anti-UFL1 Millipore Sigma HPA030558 RRID:AB_10600663 Rabbit monoclonal anti-UFM1 Abclonal A20875 Rabbit polyclonal anti-DDRGK1 Proteintech 21445-1-AP RRID:AB_2827383 Rabbit polyclonal anti-DDRGK1 Novus Biologicals NBP2-87256; RRID: AB_3428641 Mouse monoclonal anti-H3 Elabscience E-AB-22003 Rabbit polyclonal anti-GFP Abcam Ab290 RRID:AB_2313768 Mouse monoclonal anti-GFP Roche 11814460001 RRID:AB_390913 Rabbit monoclonal anti-Phopsho-Histone H2A.X Ser139 (20E3) Cell Signaling #9718 RRID:AB_2118009 Rabbit polyclonal anti-53BP1 Cell Signaling #4937 RRID:AB_10694558 Rabbit polyclonal anti-BRCA1 Abclonal A0212; RRID: AB_2757026 Rabbit polyclonal anti-ATM (D2E2) Cell Signaling #2873 RRID:AB_2062659 Rabbit monoclonal anti-V5 tag (D3H8Q) Cell Signaling #13202 RRID:AB_2687461 Rabbit polyclonal anti-Actin Sigma A2066, RRID:AB_476693 Mouse monoclonal anti-SMC6 (A-3) Santa Cruz Biotechnology sc-365742 RRID:AB_10846328 Mouse monoclonal anti-SMC5 (B-11) Santa Cruz Biotechnology sc-393282 Mouse monoclonal anti-Phospho-ATM Ser1981 Invitrogen MA12020 RRID:AB_1086244 F(ab’)2-Goat anti-Rabbit IgG (H + L) Cross-Adsorbed secondary antibody, Alexa FluorTM 680 Invitrogen A21077 RRID:AB_1500771 IRDye 800CW Goat anti-Rabbit IgG secondary antibody Licor 926–32211 RRID:AB_621843 IRDye 680LT Goat anti-Mouse IgG secondary antibody Licor 926–68020 RRID:AB_10706161 (Continued on next page) Cell Reports 43, 114738, September 24, 2024 21 .. REAGENT or RESOURCE SOURCE IDENTIFIER AmershamTM CyDyeTM 800 Goat-Anti-Mouse secondary antibody Cytiva 29360789 Alexa Fluor 488 goat anti-rabbit secondary antibody Invitrogen 22845951 Alexa Fluor 594 goat anti-mouse secondary antibody Invitrogen 2301112 Alexa Fluor 488 goat anti-mouse secondary antibody Invitrogen 2551357 Alexa Fluor 594 goat anti-rabbit secondary antibody Invitrogen 2268327 Nanobody Anti-GFP Rothbauer et al.102 GBP Chemicals, peptides, and recombinant proteins TRIzol Invitrogen 15596026 Trypsin Protease Promega V511A cOmpleteTM EDTA-free Protease Inhibitor Cocktail Sigma 11873580001 Sodium Fluoride (NaF) Sigma 201154 Sodium pyrophosphate decahydrate (NaPyPh) Sigma 221368 b-Glycerophosphate disodium salt hydrate (BGP) Sigma G9422 Sodium Orthovanadate (NaO) New England Biolabs P0758L X-tremeGENETM HP DNA Transfection Reagent Sigma XTGHP-RO Paraformaldehyde Sigma 158127 Goat Serum Sigma G9023 RNaseA ThermoFisher Scientific EN0531 Propidium Iodide Sigma 537059 Benzonase Nuclease Sigma E1014 DynabeadsTM M-270 Epoxy ThermoFisher Scientific 14302D DyLight 800 NHS Ester ThermoFisher Scientific 46421 Triethanolamine Sigma T58300 Tricene MP Biomedicals 807416 Lithium dodecyl sulfate Sigma BP1309-25 Crystal Violet Sigma C581 Shield-1 MedChemExpress HY-112210 4-Hydroxytamoxifen MedChemExpress HY-16950 Dimethyl sulfoxide (DMSO) Sigma BP231 ProLongTM Gold Antifade Mountant with DNA Stain DAPI ThermoFisher Scientific P36931 HisPurTM Ni-NTA Magnetic Beads ThermoFisher Scientific 88831 Dithiothreitol (DTT) ThermoFisher Scientific BP172 Urea Sigma U5378 Polybrene Sigma TR-1003 Ammonium Bicarbonate Sigma A6141 Amersham Hybond-N+ Cytiva RPN303B Doxycycline hyclate Wisent 450-185 XG 3-Indoleacetic acid (IAA) MP Biomedicals ICN10203725 Critical commercial assays Wizard Genomic DNA Purification kit Promega A1120 Click-iTTM RNA Alexa FluorTM 594 Imaging Kit Invitrogen C10330 BioRad Lowry DC Assay BioRad 5000111 In-Fusion Snap Assembly Takara 638946 (Continued on next page) 22 Cell Reports 43, 114738, September 24, 2024 Article ll OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER Deposited data CRISPR-Cas9 rDNA dropout screen This study NCBI GEO: GSE253809 TCOF1-eGFP/eGFP-NLS affinity purification mass spectrometry and His10UFM1DSC affinity purification mass spectrometry This study PRIDE repository: PXD048568; project DOI: 10.6019/PXD048568 Experimental models: Cell lines hTERT-RPE1 ATCC N/A hTERT-RPE1 p53 / Cas9 Alexandre Orthwein N/A hTERT-RPE1 p53 / Cas9+ DD-HA-ER-I-PpoI This study N/A hTERT-RPE1 p53 / Cas9+ DD-HA-ER-I-PpoI + eGFP-NLS This study N/A hTERT-RPE1 p53 / Cas9+ DD-HA-ER-I-PpoI + TCOF1-eGFP This study N/A hTERT-RPE1 p53 / Cas9+ DD-HA-ER-I-PpoI + His10-UFM1DSC This study N/A hTERT-RPE1 p53 / Cas9+ DD-HA-ER-I-PpoI, UFL1 KO This study N/A hTERT-RPE1 p53 / Cas9+ DD-HA-ER-I-PpoI, DDRGK1 KO This study N/A U2OS + DD-HA-ER-I-PpoI This study N/A HCT116 SMC6-mAC (mAID-Clover) mCherry H3 Venegas et al.89 N/A Oligonucleotides Primers used for library preparation Hart et al.49 Table S4 sgRNAs Hart et al.49 Walczak et al.83 Platt et al.103 Table S4 Northern Blot Probes This study Table S4 Recombinant DNA Plasmid: pLX303-DD-HA-ER-I-PpoI (G418) This study N/A Plasmid: Lenti-Guide-GFP-T2A-His10-UFM1DSC This study N/A Plasmid: pRK10-His10-UFM1DSC This study N/A Plasmid: Lenti-Guide-Puro-UBA5 This study N/A Plasmid: Lenti-Guide-Puro-UFM1 This study N/A Plasmid: Lenti-Guide-Puro-DDRGK1 This study N/A Plasmid Lenti-Guide-Puro-UFSP2: This study N/A Plasmid: Lenti-Guide-Puro-UFC1#1 This study N/A Plasmid: Lenti-Guide-Puro-UFC1#2 This study N/A Plasmid: Lenti-Guide-GFP-UFL1#1 This study N/A Plasmid: Lenti-Guide-GFP-UFL1#2 This study N/A Plasmid: Lenti-Guide-Puro-UFL1#1 This study N/A Plasmid: Lenti-Guide-Puro-UFL1#2 This study N/A Plasmid: Lenti-Guide-Puro 50 ETS #1 This study N/A Plasmid: Lenti-Guide-Puro-LacZ This study N/A Plasmid: pSH-EF-IRES-eGFP-V5-NLS This study N/A Plasmid: pSH-EF-IRES-TCOF1-eGFP This study N/A Plasmid: Lenti-Guide-Puro FAM208A#1 This study N/A Plasmid: Lenti-Guide-Puro FAM208A#2 This study N/A Plasmid: Lenti-Guide-Puro SETDB1#1 This study N/A Plasmid: Lenti-Guide-Puro SETDB1#2 This study N/A Plasmid: Lenti-Guide-mCherry-AAVS1 Noordermeer et al.104 N/A Plasmid: pCas9-sgAAVS1-1 Li et al.105 N/A Plasmid: pCas9-sgAAVS1-2 Li et al.105 N/A Plasmid: pMD2.G Addgene 12259 Plasmid: psPAX2 Addgene 12260 (Continued on next page) Cell Reports 43, 114738, September 24, 2024 23 Article ll OPEN ACCESS

    Transfection:

    Article Title: Protein UFMylation regulates early events during ribosomal DNA-damage response.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse monoclonal anti-Treacle (H-6) Santa Cruz Biotechnology sc-374536 RRID:AB_10987865 Rabbit polyclonal anti-TCOF1 Millipore Sigma HPA038237 RRID:AB_10670660 Mouse monoclonal anti-MRE11 (12D7) GeneTex GTX70212 RRID:AB_372398 Mouse monoclonal anti-NBS1 (1D7) GeneTex GTX70224 RRID:AB_372445 Mouse monoclonal anti-TOPBP1 (B-7) Santa Cruz Biotechnology sc-271043 RRID:AB_10610636 Rabbit monoclonal anti-GAPDH (D16H11) Cell Signaling #5174 RRID:AB_10622025 Rabbit monoclonal anti-HA tag (C29F4) Cell Signaling #3724 RRID:AB_1549585 Rabbit polyclonal anti-UFL1 Abclonal A20528 Rabbit polyclonal anti-UFL1 Millipore Sigma HPA030558 RRID:AB_10600663 Rabbit monoclonal anti-UFM1 Abclonal A20875 Rabbit polyclonal anti-DDRGK1 Proteintech 21445-1-AP RRID:AB_2827383 Rabbit polyclonal anti-DDRGK1 Novus Biologicals NBP2-87256; RRID: AB_3428641 Mouse monoclonal anti-H3 Elabscience E-AB-22003 Rabbit polyclonal anti-GFP Abcam Ab290 RRID:AB_2313768 Mouse monoclonal anti-GFP Roche 11814460001 RRID:AB_390913 Rabbit monoclonal anti-Phopsho-Histone H2A.X Ser139 (20E3) Cell Signaling #9718 RRID:AB_2118009 Rabbit polyclonal anti-53BP1 Cell Signaling #4937 RRID:AB_10694558 Rabbit polyclonal anti-BRCA1 Abclonal A0212; RRID: AB_2757026 Rabbit polyclonal anti-ATM (D2E2) Cell Signaling #2873 RRID:AB_2062659 Rabbit monoclonal anti-V5 tag (D3H8Q) Cell Signaling #13202 RRID:AB_2687461 Rabbit polyclonal anti-Actin Sigma A2066, RRID:AB_476693 Mouse monoclonal anti-SMC6 (A-3) Santa Cruz Biotechnology sc-365742 RRID:AB_10846328 Mouse monoclonal anti-SMC5 (B-11) Santa Cruz Biotechnology sc-393282 Mouse monoclonal anti-Phospho-ATM Ser1981 Invitrogen MA12020 RRID:AB_1086244 F(ab’)2-Goat anti-Rabbit IgG (H + L) Cross-Adsorbed secondary antibody, Alexa FluorTM 680 Invitrogen A21077 RRID:AB_1500771 IRDye 800CW Goat anti-Rabbit IgG secondary antibody Licor 926–32211 RRID:AB_621843 IRDye 680LT Goat anti-Mouse IgG secondary antibody Licor 926–68020 RRID:AB_10706161 (Continued on next page) Cell Reports 43, 114738, September 24, 2024 21 .. REAGENT or RESOURCE SOURCE IDENTIFIER AmershamTM CyDyeTM 800 Goat-Anti-Mouse secondary antibody Cytiva 29360789 Alexa Fluor 488 goat anti-rabbit secondary antibody Invitrogen 22845951 Alexa Fluor 594 goat anti-mouse secondary antibody Invitrogen 2301112 Alexa Fluor 488 goat anti-mouse secondary antibody Invitrogen 2551357 Alexa Fluor 594 goat anti-rabbit secondary antibody Invitrogen 2268327 Nanobody Anti-GFP Rothbauer et al.102 GBP Chemicals, peptides, and recombinant proteins TRIzol Invitrogen 15596026 Trypsin Protease Promega V511A cOmpleteTM EDTA-free Protease Inhibitor Cocktail Sigma 11873580001 Sodium Fluoride (NaF) Sigma 201154 Sodium pyrophosphate decahydrate (NaPyPh) Sigma 221368 b-Glycerophosphate disodium salt hydrate (BGP) Sigma G9422 Sodium Orthovanadate (NaO) New England Biolabs P0758L X-tremeGENETM HP DNA Transfection Reagent Sigma XTGHP-RO Paraformaldehyde Sigma 158127 Goat Serum Sigma G9023 RNaseA ThermoFisher Scientific EN0531 Propidium Iodide Sigma 537059 Benzonase Nuclease Sigma E1014 DynabeadsTM M-270 Epoxy ThermoFisher Scientific 14302D DyLight 800 NHS Ester ThermoFisher Scientific 46421 Triethanolamine Sigma T58300 Tricene MP Biomedicals 807416 Lithium dodecyl sulfate Sigma BP1309-25 Crystal Violet Sigma C581 Shield-1 MedChemExpress HY-112210 4-Hydroxytamoxifen MedChemExpress HY-16950 Dimethyl sulfoxide (DMSO) Sigma BP231 ProLongTM Gold Antifade Mountant with DNA Stain DAPI ThermoFisher Scientific P36931 HisPurTM Ni-NTA Magnetic Beads ThermoFisher Scientific 88831 Dithiothreitol (DTT) ThermoFisher Scientific BP172 Urea Sigma U5378 Polybrene Sigma TR-1003 Ammonium Bicarbonate Sigma A6141 Amersham Hybond-N+ Cytiva RPN303B Doxycycline hyclate Wisent 450-185 XG 3-Indoleacetic acid (IAA) MP Biomedicals ICN10203725 Critical commercial assays Wizard Genomic DNA Purification kit Promega A1120 Click-iTTM RNA Alexa FluorTM 594 Imaging Kit Invitrogen C10330 BioRad Lowry DC Assay BioRad 5000111 In-Fusion Snap Assembly Takara 638946 (Continued on next page) 22 Cell Reports 43, 114738, September 24, 2024 Article ll OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER Deposited data CRISPR-Cas9 rDNA dropout screen This study NCBI GEO: GSE253809 TCOF1-eGFP/eGFP-NLS affinity purification mass spectrometry and His10UFM1DSC affinity purification mass spectrometry This study PRIDE repository: PXD048568; project DOI: 10.6019/PXD048568 Experimental models: Cell lines hTERT-RPE1 ATCC N/A hTERT-RPE1 p53 / Cas9 Alexandre Orthwein N/A hTERT-RPE1 p53 / Cas9+ DD-HA-ER-I-PpoI This study N/A hTERT-RPE1 p53 / Cas9+ DD-HA-ER-I-PpoI + eGFP-NLS This study N/A hTERT-RPE1 p53 / Cas9+ DD-HA-ER-I-PpoI + TCOF1-eGFP This study N/A hTERT-RPE1 p53 / Cas9+ DD-HA-ER-I-PpoI + His10-UFM1DSC This study N/A hTERT-RPE1 p53 / Cas9+ DD-HA-ER-I-PpoI, UFL1 KO This study N/A hTERT-RPE1 p53 / Cas9+ DD-HA-ER-I-PpoI, DDRGK1 KO This study N/A U2OS + DD-HA-ER-I-PpoI This study N/A HCT116 SMC6-mAC (mAID-Clover) mCherry H3 Venegas et al.89 N/A Oligonucleotides Primers used for library preparation Hart et al.49 Table S4 sgRNAs Hart et al.49 Walczak et al.83 Platt et al.103 Table S4 Northern Blot Probes This study Table S4 Recombinant DNA Plasmid: pLX303-DD-HA-ER-I-PpoI (G418) This study N/A Plasmid: Lenti-Guide-GFP-T2A-His10-UFM1DSC This study N/A Plasmid: pRK10-His10-UFM1DSC This study N/A Plasmid: Lenti-Guide-Puro-UBA5 This study N/A Plasmid: Lenti-Guide-Puro-UFM1 This study N/A Plasmid: Lenti-Guide-Puro-DDRGK1 This study N/A Plasmid Lenti-Guide-Puro-UFSP2: This study N/A Plasmid: Lenti-Guide-Puro-UFC1#1 This study N/A Plasmid: Lenti-Guide-Puro-UFC1#2 This study N/A Plasmid: Lenti-Guide-GFP-UFL1#1 This study N/A Plasmid: Lenti-Guide-GFP-UFL1#2 This study N/A Plasmid: Lenti-Guide-Puro-UFL1#1 This study N/A Plasmid: Lenti-Guide-Puro-UFL1#2 This study N/A Plasmid: Lenti-Guide-Puro 50 ETS #1 This study N/A Plasmid: Lenti-Guide-Puro-LacZ This study N/A Plasmid: pSH-EF-IRES-eGFP-V5-NLS This study N/A Plasmid: pSH-EF-IRES-TCOF1-eGFP This study N/A Plasmid: Lenti-Guide-Puro FAM208A#1 This study N/A Plasmid: Lenti-Guide-Puro FAM208A#2 This study N/A Plasmid: Lenti-Guide-Puro SETDB1#1 This study N/A Plasmid: Lenti-Guide-Puro SETDB1#2 This study N/A Plasmid: Lenti-Guide-mCherry-AAVS1 Noordermeer et al.104 N/A Plasmid: pCas9-sgAAVS1-1 Li et al.105 N/A Plasmid: pCas9-sgAAVS1-2 Li et al.105 N/A Plasmid: pMD2.G Addgene 12259 Plasmid: psPAX2 Addgene 12260 (Continued on next page) Cell Reports 43, 114738, September 24, 2024 23 Article ll OPEN ACCESS

    Staining:

    Article Title: Protein UFMylation regulates early events during ribosomal DNA-damage response.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse monoclonal anti-Treacle (H-6) Santa Cruz Biotechnology sc-374536 RRID:AB_10987865 Rabbit polyclonal anti-TCOF1 Millipore Sigma HPA038237 RRID:AB_10670660 Mouse monoclonal anti-MRE11 (12D7) GeneTex GTX70212 RRID:AB_372398 Mouse monoclonal anti-NBS1 (1D7) GeneTex GTX70224 RRID:AB_372445 Mouse monoclonal anti-TOPBP1 (B-7) Santa Cruz Biotechnology sc-271043 RRID:AB_10610636 Rabbit monoclonal anti-GAPDH (D16H11) Cell Signaling #5174 RRID:AB_10622025 Rabbit monoclonal anti-HA tag (C29F4) Cell Signaling #3724 RRID:AB_1549585 Rabbit polyclonal anti-UFL1 Abclonal A20528 Rabbit polyclonal anti-UFL1 Millipore Sigma HPA030558 RRID:AB_10600663 Rabbit monoclonal anti-UFM1 Abclonal A20875 Rabbit polyclonal anti-DDRGK1 Proteintech 21445-1-AP RRID:AB_2827383 Rabbit polyclonal anti-DDRGK1 Novus Biologicals NBP2-87256; RRID: AB_3428641 Mouse monoclonal anti-H3 Elabscience E-AB-22003 Rabbit polyclonal anti-GFP Abcam Ab290 RRID:AB_2313768 Mouse monoclonal anti-GFP Roche 11814460001 RRID:AB_390913 Rabbit monoclonal anti-Phopsho-Histone H2A.X Ser139 (20E3) Cell Signaling #9718 RRID:AB_2118009 Rabbit polyclonal anti-53BP1 Cell Signaling #4937 RRID:AB_10694558 Rabbit polyclonal anti-BRCA1 Abclonal A0212; RRID: AB_2757026 Rabbit polyclonal anti-ATM (D2E2) Cell Signaling #2873 RRID:AB_2062659 Rabbit monoclonal anti-V5 tag (D3H8Q) Cell Signaling #13202 RRID:AB_2687461 Rabbit polyclonal anti-Actin Sigma A2066, RRID:AB_476693 Mouse monoclonal anti-SMC6 (A-3) Santa Cruz Biotechnology sc-365742 RRID:AB_10846328 Mouse monoclonal anti-SMC5 (B-11) Santa Cruz Biotechnology sc-393282 Mouse monoclonal anti-Phospho-ATM Ser1981 Invitrogen MA12020 RRID:AB_1086244 F(ab’)2-Goat anti-Rabbit IgG (H + L) Cross-Adsorbed secondary antibody, Alexa FluorTM 680 Invitrogen A21077 RRID:AB_1500771 IRDye 800CW Goat anti-Rabbit IgG secondary antibody Licor 926–32211 RRID:AB_621843 IRDye 680LT Goat anti-Mouse IgG secondary antibody Licor 926–68020 RRID:AB_10706161 (Continued on next page) Cell Reports 43, 114738, September 24, 2024 21 .. REAGENT or RESOURCE SOURCE IDENTIFIER AmershamTM CyDyeTM 800 Goat-Anti-Mouse secondary antibody Cytiva 29360789 Alexa Fluor 488 goat anti-rabbit secondary antibody Invitrogen 22845951 Alexa Fluor 594 goat anti-mouse secondary antibody Invitrogen 2301112 Alexa Fluor 488 goat anti-mouse secondary antibody Invitrogen 2551357 Alexa Fluor 594 goat anti-rabbit secondary antibody Invitrogen 2268327 Nanobody Anti-GFP Rothbauer et al.102 GBP Chemicals, peptides, and recombinant proteins TRIzol Invitrogen 15596026 Trypsin Protease Promega V511A cOmpleteTM EDTA-free Protease Inhibitor Cocktail Sigma 11873580001 Sodium Fluoride (NaF) Sigma 201154 Sodium pyrophosphate decahydrate (NaPyPh) Sigma 221368 b-Glycerophosphate disodium salt hydrate (BGP) Sigma G9422 Sodium Orthovanadate (NaO) New England Biolabs P0758L X-tremeGENETM HP DNA Transfection Reagent Sigma XTGHP-RO Paraformaldehyde Sigma 158127 Goat Serum Sigma G9023 RNaseA ThermoFisher Scientific EN0531 Propidium Iodide Sigma 537059 Benzonase Nuclease Sigma E1014 DynabeadsTM M-270 Epoxy ThermoFisher Scientific 14302D DyLight 800 NHS Ester ThermoFisher Scientific 46421 Triethanolamine Sigma T58300 Tricene MP Biomedicals 807416 Lithium dodecyl sulfate Sigma BP1309-25 Crystal Violet Sigma C581 Shield-1 MedChemExpress HY-112210 4-Hydroxytamoxifen MedChemExpress HY-16950 Dimethyl sulfoxide (DMSO) Sigma BP231 ProLongTM Gold Antifade Mountant with DNA Stain DAPI ThermoFisher Scientific P36931 HisPurTM Ni-NTA Magnetic Beads ThermoFisher Scientific 88831 Dithiothreitol (DTT) ThermoFisher Scientific BP172 Urea Sigma U5378 Polybrene Sigma TR-1003 Ammonium Bicarbonate Sigma A6141 Amersham Hybond-N+ Cytiva RPN303B Doxycycline hyclate Wisent 450-185 XG 3-Indoleacetic acid (IAA) MP Biomedicals ICN10203725 Critical commercial assays Wizard Genomic DNA Purification kit Promega A1120 Click-iTTM RNA Alexa FluorTM 594 Imaging Kit Invitrogen C10330 BioRad Lowry DC Assay BioRad 5000111 In-Fusion Snap Assembly Takara 638946 (Continued on next page) 22 Cell Reports 43, 114738, September 24, 2024 Article ll OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER Deposited data CRISPR-Cas9 rDNA dropout screen This study NCBI GEO: GSE253809 TCOF1-eGFP/eGFP-NLS affinity purification mass spectrometry and His10UFM1DSC affinity purification mass spectrometry This study PRIDE repository: PXD048568; project DOI: 10.6019/PXD048568 Experimental models: Cell lines hTERT-RPE1 ATCC N/A hTERT-RPE1 p53 / Cas9 Alexandre Orthwein N/A hTERT-RPE1 p53 / Cas9+ DD-HA-ER-I-PpoI This study N/A hTERT-RPE1 p53 / Cas9+ DD-HA-ER-I-PpoI + eGFP-NLS This study N/A hTERT-RPE1 p53 / Cas9+ DD-HA-ER-I-PpoI + TCOF1-eGFP This study N/A hTERT-RPE1 p53 / Cas9+ DD-HA-ER-I-PpoI + His10-UFM1DSC This study N/A hTERT-RPE1 p53 / Cas9+ DD-HA-ER-I-PpoI, UFL1 KO This study N/A hTERT-RPE1 p53 / Cas9+ DD-HA-ER-I-PpoI, DDRGK1 KO This study N/A U2OS + DD-HA-ER-I-PpoI This study N/A HCT116 SMC6-mAC (mAID-Clover) mCherry H3 Venegas et al.89 N/A Oligonucleotides Primers used for library preparation Hart et al.49 Table S4 sgRNAs Hart et al.49 Walczak et al.83 Platt et al.103 Table S4 Northern Blot Probes This study Table S4 Recombinant DNA Plasmid: pLX303-DD-HA-ER-I-PpoI (G418) This study N/A Plasmid: Lenti-Guide-GFP-T2A-His10-UFM1DSC This study N/A Plasmid: pRK10-His10-UFM1DSC This study N/A Plasmid: Lenti-Guide-Puro-UBA5 This study N/A Plasmid: Lenti-Guide-Puro-UFM1 This study N/A Plasmid: Lenti-Guide-Puro-DDRGK1 This study N/A Plasmid Lenti-Guide-Puro-UFSP2: This study N/A Plasmid: Lenti-Guide-Puro-UFC1#1 This study N/A Plasmid: Lenti-Guide-Puro-UFC1#2 This study N/A Plasmid: Lenti-Guide-GFP-UFL1#1 This study N/A Plasmid: Lenti-Guide-GFP-UFL1#2 This study N/A Plasmid: Lenti-Guide-Puro-UFL1#1 This study N/A Plasmid: Lenti-Guide-Puro-UFL1#2 This study N/A Plasmid: Lenti-Guide-Puro 50 ETS #1 This study N/A Plasmid: Lenti-Guide-Puro-LacZ This study N/A Plasmid: pSH-EF-IRES-eGFP-V5-NLS This study N/A Plasmid: pSH-EF-IRES-TCOF1-eGFP This study N/A Plasmid: Lenti-Guide-Puro FAM208A#1 This study N/A Plasmid: Lenti-Guide-Puro FAM208A#2 This study N/A Plasmid: Lenti-Guide-Puro SETDB1#1 This study N/A Plasmid: Lenti-Guide-Puro SETDB1#2 This study N/A Plasmid: Lenti-Guide-mCherry-AAVS1 Noordermeer et al.104 N/A Plasmid: pCas9-sgAAVS1-1 Li et al.105 N/A Plasmid: pCas9-sgAAVS1-2 Li et al.105 N/A Plasmid: pMD2.G Addgene 12259 Plasmid: psPAX2 Addgene 12260 (Continued on next page) Cell Reports 43, 114738, September 24, 2024 23 Article ll OPEN ACCESS

    Magnetic Beads:

    Article Title: Protein UFMylation regulates early events during ribosomal DNA-damage response.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse monoclonal anti-Treacle (H-6) Santa Cruz Biotechnology sc-374536 RRID:AB_10987865 Rabbit polyclonal anti-TCOF1 Millipore Sigma HPA038237 RRID:AB_10670660 Mouse monoclonal anti-MRE11 (12D7) GeneTex GTX70212 RRID:AB_372398 Mouse monoclonal anti-NBS1 (1D7) GeneTex GTX70224 RRID:AB_372445 Mouse monoclonal anti-TOPBP1 (B-7) Santa Cruz Biotechnology sc-271043 RRID:AB_10610636 Rabbit monoclonal anti-GAPDH (D16H11) Cell Signaling #5174 RRID:AB_10622025 Rabbit monoclonal anti-HA tag (C29F4) Cell Signaling #3724 RRID:AB_1549585 Rabbit polyclonal anti-UFL1 Abclonal A20528 Rabbit polyclonal anti-UFL1 Millipore Sigma HPA030558 RRID:AB_10600663 Rabbit monoclonal anti-UFM1 Abclonal A20875 Rabbit polyclonal anti-DDRGK1 Proteintech 21445-1-AP RRID:AB_2827383 Rabbit polyclonal anti-DDRGK1 Novus Biologicals NBP2-87256; RRID: AB_3428641 Mouse monoclonal anti-H3 Elabscience E-AB-22003 Rabbit polyclonal anti-GFP Abcam Ab290 RRID:AB_2313768 Mouse monoclonal anti-GFP Roche 11814460001 RRID:AB_390913 Rabbit monoclonal anti-Phopsho-Histone H2A.X Ser139 (20E3) Cell Signaling #9718 RRID:AB_2118009 Rabbit polyclonal anti-53BP1 Cell Signaling #4937 RRID:AB_10694558 Rabbit polyclonal anti-BRCA1 Abclonal A0212; RRID: AB_2757026 Rabbit polyclonal anti-ATM (D2E2) Cell Signaling #2873 RRID:AB_2062659 Rabbit monoclonal anti-V5 tag (D3H8Q) Cell Signaling #13202 RRID:AB_2687461 Rabbit polyclonal anti-Actin Sigma A2066, RRID:AB_476693 Mouse monoclonal anti-SMC6 (A-3) Santa Cruz Biotechnology sc-365742 RRID:AB_10846328 Mouse monoclonal anti-SMC5 (B-11) Santa Cruz Biotechnology sc-393282 Mouse monoclonal anti-Phospho-ATM Ser1981 Invitrogen MA12020 RRID:AB_1086244 F(ab’)2-Goat anti-Rabbit IgG (H + L) Cross-Adsorbed secondary antibody, Alexa FluorTM 680 Invitrogen A21077 RRID:AB_1500771 IRDye 800CW Goat anti-Rabbit IgG secondary antibody Licor 926–32211 RRID:AB_621843 IRDye 680LT Goat anti-Mouse IgG secondary antibody Licor 926–68020 RRID:AB_10706161 (Continued on next page) Cell Reports 43, 114738, September 24, 2024 21 .. REAGENT or RESOURCE SOURCE IDENTIFIER AmershamTM CyDyeTM 800 Goat-Anti-Mouse secondary antibody Cytiva 29360789 Alexa Fluor 488 goat anti-rabbit secondary antibody Invitrogen 22845951 Alexa Fluor 594 goat anti-mouse secondary antibody Invitrogen 2301112 Alexa Fluor 488 goat anti-mouse secondary antibody Invitrogen 2551357 Alexa Fluor 594 goat anti-rabbit secondary antibody Invitrogen 2268327 Nanobody Anti-GFP Rothbauer et al.102 GBP Chemicals, peptides, and recombinant proteins TRIzol Invitrogen 15596026 Trypsin Protease Promega V511A cOmpleteTM EDTA-free Protease Inhibitor Cocktail Sigma 11873580001 Sodium Fluoride (NaF) Sigma 201154 Sodium pyrophosphate decahydrate (NaPyPh) Sigma 221368 b-Glycerophosphate disodium salt hydrate (BGP) Sigma G9422 Sodium Orthovanadate (NaO) New England Biolabs P0758L X-tremeGENETM HP DNA Transfection Reagent Sigma XTGHP-RO Paraformaldehyde Sigma 158127 Goat Serum Sigma G9023 RNaseA ThermoFisher Scientific EN0531 Propidium Iodide Sigma 537059 Benzonase Nuclease Sigma E1014 DynabeadsTM M-270 Epoxy ThermoFisher Scientific 14302D DyLight 800 NHS Ester ThermoFisher Scientific 46421 Triethanolamine Sigma T58300 Tricene MP Biomedicals 807416 Lithium dodecyl sulfate Sigma BP1309-25 Crystal Violet Sigma C581 Shield-1 MedChemExpress HY-112210 4-Hydroxytamoxifen MedChemExpress HY-16950 Dimethyl sulfoxide (DMSO) Sigma BP231 ProLongTM Gold Antifade Mountant with DNA Stain DAPI ThermoFisher Scientific P36931 HisPurTM Ni-NTA Magnetic Beads ThermoFisher Scientific 88831 Dithiothreitol (DTT) ThermoFisher Scientific BP172 Urea Sigma U5378 Polybrene Sigma TR-1003 Ammonium Bicarbonate Sigma A6141 Amersham Hybond-N+ Cytiva RPN303B Doxycycline hyclate Wisent 450-185 XG 3-Indoleacetic acid (IAA) MP Biomedicals ICN10203725 Critical commercial assays Wizard Genomic DNA Purification kit Promega A1120 Click-iTTM RNA Alexa FluorTM 594 Imaging Kit Invitrogen C10330 BioRad Lowry DC Assay BioRad 5000111 In-Fusion Snap Assembly Takara 638946 (Continued on next page) 22 Cell Reports 43, 114738, September 24, 2024 Article ll OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER Deposited data CRISPR-Cas9 rDNA dropout screen This study NCBI GEO: GSE253809 TCOF1-eGFP/eGFP-NLS affinity purification mass spectrometry and His10UFM1DSC affinity purification mass spectrometry This study PRIDE repository: PXD048568; project DOI: 10.6019/PXD048568 Experimental models: Cell lines hTERT-RPE1 ATCC N/A hTERT-RPE1 p53 / Cas9 Alexandre Orthwein N/A hTERT-RPE1 p53 / Cas9+ DD-HA-ER-I-PpoI This study N/A hTERT-RPE1 p53 / Cas9+ DD-HA-ER-I-PpoI + eGFP-NLS This study N/A hTERT-RPE1 p53 / Cas9+ DD-HA-ER-I-PpoI + TCOF1-eGFP This study N/A hTERT-RPE1 p53 / Cas9+ DD-HA-ER-I-PpoI + His10-UFM1DSC This study N/A hTERT-RPE1 p53 / Cas9+ DD-HA-ER-I-PpoI, UFL1 KO This study N/A hTERT-RPE1 p53 / Cas9+ DD-HA-ER-I-PpoI, DDRGK1 KO This study N/A U2OS + DD-HA-ER-I-PpoI This study N/A HCT116 SMC6-mAC (mAID-Clover) mCherry H3 Venegas et al.89 N/A Oligonucleotides Primers used for library preparation Hart et al.49 Table S4 sgRNAs Hart et al.49 Walczak et al.83 Platt et al.103 Table S4 Northern Blot Probes This study Table S4 Recombinant DNA Plasmid: pLX303-DD-HA-ER-I-PpoI (G418) This study N/A Plasmid: Lenti-Guide-GFP-T2A-His10-UFM1DSC This study N/A Plasmid: pRK10-His10-UFM1DSC This study N/A Plasmid: Lenti-Guide-Puro-UBA5 This study N/A Plasmid: Lenti-Guide-Puro-UFM1 This study N/A Plasmid: Lenti-Guide-Puro-DDRGK1 This study N/A Plasmid Lenti-Guide-Puro-UFSP2: This study N/A Plasmid: Lenti-Guide-Puro-UFC1#1 This study N/A Plasmid: Lenti-Guide-Puro-UFC1#2 This study N/A Plasmid: Lenti-Guide-GFP-UFL1#1 This study N/A Plasmid: Lenti-Guide-GFP-UFL1#2 This study N/A Plasmid: Lenti-Guide-Puro-UFL1#1 This study N/A Plasmid: Lenti-Guide-Puro-UFL1#2 This study N/A Plasmid: Lenti-Guide-Puro 50 ETS #1 This study N/A Plasmid: Lenti-Guide-Puro-LacZ This study N/A Plasmid: pSH-EF-IRES-eGFP-V5-NLS This study N/A Plasmid: pSH-EF-IRES-TCOF1-eGFP This study N/A Plasmid: Lenti-Guide-Puro FAM208A#1 This study N/A Plasmid: Lenti-Guide-Puro FAM208A#2 This study N/A Plasmid: Lenti-Guide-Puro SETDB1#1 This study N/A Plasmid: Lenti-Guide-Puro SETDB1#2 This study N/A Plasmid: Lenti-Guide-mCherry-AAVS1 Noordermeer et al.104 N/A Plasmid: pCas9-sgAAVS1-1 Li et al.105 N/A Plasmid: pCas9-sgAAVS1-2 Li et al.105 N/A Plasmid: pMD2.G Addgene 12259 Plasmid: psPAX2 Addgene 12260 (Continued on next page) Cell Reports 43, 114738, September 24, 2024 23 Article ll OPEN ACCESS

    DNA Purification:

    Article Title: Protein UFMylation regulates early events during ribosomal DNA-damage response.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse monoclonal anti-Treacle (H-6) Santa Cruz Biotechnology sc-374536 RRID:AB_10987865 Rabbit polyclonal anti-TCOF1 Millipore Sigma HPA038237 RRID:AB_10670660 Mouse monoclonal anti-MRE11 (12D7) GeneTex GTX70212 RRID:AB_372398 Mouse monoclonal anti-NBS1 (1D7) GeneTex GTX70224 RRID:AB_372445 Mouse monoclonal anti-TOPBP1 (B-7) Santa Cruz Biotechnology sc-271043 RRID:AB_10610636 Rabbit monoclonal anti-GAPDH (D16H11) Cell Signaling #5174 RRID:AB_10622025 Rabbit monoclonal anti-HA tag (C29F4) Cell Signaling #3724 RRID:AB_1549585 Rabbit polyclonal anti-UFL1 Abclonal A20528 Rabbit polyclonal anti-UFL1 Millipore Sigma HPA030558 RRID:AB_10600663 Rabbit monoclonal anti-UFM1 Abclonal A20875 Rabbit polyclonal anti-DDRGK1 Proteintech 21445-1-AP RRID:AB_2827383 Rabbit polyclonal anti-DDRGK1 Novus Biologicals NBP2-87256; RRID: AB_3428641 Mouse monoclonal anti-H3 Elabscience E-AB-22003 Rabbit polyclonal anti-GFP Abcam Ab290 RRID:AB_2313768 Mouse monoclonal anti-GFP Roche 11814460001 RRID:AB_390913 Rabbit monoclonal anti-Phopsho-Histone H2A.X Ser139 (20E3) Cell Signaling #9718 RRID:AB_2118009 Rabbit polyclonal anti-53BP1 Cell Signaling #4937 RRID:AB_10694558 Rabbit polyclonal anti-BRCA1 Abclonal A0212; RRID: AB_2757026 Rabbit polyclonal anti-ATM (D2E2) Cell Signaling #2873 RRID:AB_2062659 Rabbit monoclonal anti-V5 tag (D3H8Q) Cell Signaling #13202 RRID:AB_2687461 Rabbit polyclonal anti-Actin Sigma A2066, RRID:AB_476693 Mouse monoclonal anti-SMC6 (A-3) Santa Cruz Biotechnology sc-365742 RRID:AB_10846328 Mouse monoclonal anti-SMC5 (B-11) Santa Cruz Biotechnology sc-393282 Mouse monoclonal anti-Phospho-ATM Ser1981 Invitrogen MA12020 RRID:AB_1086244 F(ab’)2-Goat anti-Rabbit IgG (H + L) Cross-Adsorbed secondary antibody, Alexa FluorTM 680 Invitrogen A21077 RRID:AB_1500771 IRDye 800CW Goat anti-Rabbit IgG secondary antibody Licor 926–32211 RRID:AB_621843 IRDye 680LT Goat anti-Mouse IgG secondary antibody Licor 926–68020 RRID:AB_10706161 (Continued on next page) Cell Reports 43, 114738, September 24, 2024 21 .. REAGENT or RESOURCE SOURCE IDENTIFIER AmershamTM CyDyeTM 800 Goat-Anti-Mouse secondary antibody Cytiva 29360789 Alexa Fluor 488 goat anti-rabbit secondary antibody Invitrogen 22845951 Alexa Fluor 594 goat anti-mouse secondary antibody Invitrogen 2301112 Alexa Fluor 488 goat anti-mouse secondary antibody Invitrogen 2551357 Alexa Fluor 594 goat anti-rabbit secondary antibody Invitrogen 2268327 Nanobody Anti-GFP Rothbauer et al.102 GBP Chemicals, peptides, and recombinant proteins TRIzol Invitrogen 15596026 Trypsin Protease Promega V511A cOmpleteTM EDTA-free Protease Inhibitor Cocktail Sigma 11873580001 Sodium Fluoride (NaF) Sigma 201154 Sodium pyrophosphate decahydrate (NaPyPh) Sigma 221368 b-Glycerophosphate disodium salt hydrate (BGP) Sigma G9422 Sodium Orthovanadate (NaO) New England Biolabs P0758L X-tremeGENETM HP DNA Transfection Reagent Sigma XTGHP-RO Paraformaldehyde Sigma 158127 Goat Serum Sigma G9023 RNaseA ThermoFisher Scientific EN0531 Propidium Iodide Sigma 537059 Benzonase Nuclease Sigma E1014 DynabeadsTM M-270 Epoxy ThermoFisher Scientific 14302D DyLight 800 NHS Ester ThermoFisher Scientific 46421 Triethanolamine Sigma T58300 Tricene MP Biomedicals 807416 Lithium dodecyl sulfate Sigma BP1309-25 Crystal Violet Sigma C581 Shield-1 MedChemExpress HY-112210 4-Hydroxytamoxifen MedChemExpress HY-16950 Dimethyl sulfoxide (DMSO) Sigma BP231 ProLongTM Gold Antifade Mountant with DNA Stain DAPI ThermoFisher Scientific P36931 HisPurTM Ni-NTA Magnetic Beads ThermoFisher Scientific 88831 Dithiothreitol (DTT) ThermoFisher Scientific BP172 Urea Sigma U5378 Polybrene Sigma TR-1003 Ammonium Bicarbonate Sigma A6141 Amersham Hybond-N+ Cytiva RPN303B Doxycycline hyclate Wisent 450-185 XG 3-Indoleacetic acid (IAA) MP Biomedicals ICN10203725 Critical commercial assays Wizard Genomic DNA Purification kit Promega A1120 Click-iTTM RNA Alexa FluorTM 594 Imaging Kit Invitrogen C10330 BioRad Lowry DC Assay BioRad 5000111 In-Fusion Snap Assembly Takara 638946 (Continued on next page) 22 Cell Reports 43, 114738, September 24, 2024 Article ll OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER Deposited data CRISPR-Cas9 rDNA dropout screen This study NCBI GEO: GSE253809 TCOF1-eGFP/eGFP-NLS affinity purification mass spectrometry and His10UFM1DSC affinity purification mass spectrometry This study PRIDE repository: PXD048568; project DOI: 10.6019/PXD048568 Experimental models: Cell lines hTERT-RPE1 ATCC N/A hTERT-RPE1 p53 / Cas9 Alexandre Orthwein N/A hTERT-RPE1 p53 / Cas9+ DD-HA-ER-I-PpoI This study N/A hTERT-RPE1 p53 / Cas9+ DD-HA-ER-I-PpoI + eGFP-NLS This study N/A hTERT-RPE1 p53 / Cas9+ DD-HA-ER-I-PpoI + TCOF1-eGFP This study N/A hTERT-RPE1 p53 / Cas9+ DD-HA-ER-I-PpoI + His10-UFM1DSC This study N/A hTERT-RPE1 p53 / Cas9+ DD-HA-ER-I-PpoI, UFL1 KO This study N/A hTERT-RPE1 p53 / Cas9+ DD-HA-ER-I-PpoI, DDRGK1 KO This study N/A U2OS + DD-HA-ER-I-PpoI This study N/A HCT116 SMC6-mAC (mAID-Clover) mCherry H3 Venegas et al.89 N/A Oligonucleotides Primers used for library preparation Hart et al.49 Table S4 sgRNAs Hart et al.49 Walczak et al.83 Platt et al.103 Table S4 Northern Blot Probes This study Table S4 Recombinant DNA Plasmid: pLX303-DD-HA-ER-I-PpoI (G418) This study N/A Plasmid: Lenti-Guide-GFP-T2A-His10-UFM1DSC This study N/A Plasmid: pRK10-His10-UFM1DSC This study N/A Plasmid: Lenti-Guide-Puro-UBA5 This study N/A Plasmid: Lenti-Guide-Puro-UFM1 This study N/A Plasmid: Lenti-Guide-Puro-DDRGK1 This study N/A Plasmid Lenti-Guide-Puro-UFSP2: This study N/A Plasmid: Lenti-Guide-Puro-UFC1#1 This study N/A Plasmid: Lenti-Guide-Puro-UFC1#2 This study N/A Plasmid: Lenti-Guide-GFP-UFL1#1 This study N/A Plasmid: Lenti-Guide-GFP-UFL1#2 This study N/A Plasmid: Lenti-Guide-Puro-UFL1#1 This study N/A Plasmid: Lenti-Guide-Puro-UFL1#2 This study N/A Plasmid: Lenti-Guide-Puro 50 ETS #1 This study N/A Plasmid: Lenti-Guide-Puro-LacZ This study N/A Plasmid: pSH-EF-IRES-eGFP-V5-NLS This study N/A Plasmid: pSH-EF-IRES-TCOF1-eGFP This study N/A Plasmid: Lenti-Guide-Puro FAM208A#1 This study N/A Plasmid: Lenti-Guide-Puro FAM208A#2 This study N/A Plasmid: Lenti-Guide-Puro SETDB1#1 This study N/A Plasmid: Lenti-Guide-Puro SETDB1#2 This study N/A Plasmid: Lenti-Guide-mCherry-AAVS1 Noordermeer et al.104 N/A Plasmid: pCas9-sgAAVS1-1 Li et al.105 N/A Plasmid: pCas9-sgAAVS1-2 Li et al.105 N/A Plasmid: pMD2.G Addgene 12259 Plasmid: psPAX2 Addgene 12260 (Continued on next page) Cell Reports 43, 114738, September 24, 2024 23 Article ll OPEN ACCESS

    Imaging:

    Article Title: Protein UFMylation regulates early events during ribosomal DNA-damage response.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse monoclonal anti-Treacle (H-6) Santa Cruz Biotechnology sc-374536 RRID:AB_10987865 Rabbit polyclonal anti-TCOF1 Millipore Sigma HPA038237 RRID:AB_10670660 Mouse monoclonal anti-MRE11 (12D7) GeneTex GTX70212 RRID:AB_372398 Mouse monoclonal anti-NBS1 (1D7) GeneTex GTX70224 RRID:AB_372445 Mouse monoclonal anti-TOPBP1 (B-7) Santa Cruz Biotechnology sc-271043 RRID:AB_10610636 Rabbit monoclonal anti-GAPDH (D16H11) Cell Signaling #5174 RRID:AB_10622025 Rabbit monoclonal anti-HA tag (C29F4) Cell Signaling #3724 RRID:AB_1549585 Rabbit polyclonal anti-UFL1 Abclonal A20528 Rabbit polyclonal anti-UFL1 Millipore Sigma HPA030558 RRID:AB_10600663 Rabbit monoclonal anti-UFM1 Abclonal A20875 Rabbit polyclonal anti-DDRGK1 Proteintech 21445-1-AP RRID:AB_2827383 Rabbit polyclonal anti-DDRGK1 Novus Biologicals NBP2-87256; RRID: AB_3428641 Mouse monoclonal anti-H3 Elabscience E-AB-22003 Rabbit polyclonal anti-GFP Abcam Ab290 RRID:AB_2313768 Mouse monoclonal anti-GFP Roche 11814460001 RRID:AB_390913 Rabbit monoclonal anti-Phopsho-Histone H2A.X Ser139 (20E3) Cell Signaling #9718 RRID:AB_2118009 Rabbit polyclonal anti-53BP1 Cell Signaling #4937 RRID:AB_10694558 Rabbit polyclonal anti-BRCA1 Abclonal A0212; RRID: AB_2757026 Rabbit polyclonal anti-ATM (D2E2) Cell Signaling #2873 RRID:AB_2062659 Rabbit monoclonal anti-V5 tag (D3H8Q) Cell Signaling #13202 RRID:AB_2687461 Rabbit polyclonal anti-Actin Sigma A2066, RRID:AB_476693 Mouse monoclonal anti-SMC6 (A-3) Santa Cruz Biotechnology sc-365742 RRID:AB_10846328 Mouse monoclonal anti-SMC5 (B-11) Santa Cruz Biotechnology sc-393282 Mouse monoclonal anti-Phospho-ATM Ser1981 Invitrogen MA12020 RRID:AB_1086244 F(ab’)2-Goat anti-Rabbit IgG (H + L) Cross-Adsorbed secondary antibody, Alexa FluorTM 680 Invitrogen A21077 RRID:AB_1500771 IRDye 800CW Goat anti-Rabbit IgG secondary antibody Licor 926–32211 RRID:AB_621843 IRDye 680LT Goat anti-Mouse IgG secondary antibody Licor 926–68020 RRID:AB_10706161 (Continued on next page) Cell Reports 43, 114738, September 24, 2024 21 .. REAGENT or RESOURCE SOURCE IDENTIFIER AmershamTM CyDyeTM 800 Goat-Anti-Mouse secondary antibody Cytiva 29360789 Alexa Fluor 488 goat anti-rabbit secondary antibody Invitrogen 22845951 Alexa Fluor 594 goat anti-mouse secondary antibody Invitrogen 2301112 Alexa Fluor 488 goat anti-mouse secondary antibody Invitrogen 2551357 Alexa Fluor 594 goat anti-rabbit secondary antibody Invitrogen 2268327 Nanobody Anti-GFP Rothbauer et al.102 GBP Chemicals, peptides, and recombinant proteins TRIzol Invitrogen 15596026 Trypsin Protease Promega V511A cOmpleteTM EDTA-free Protease Inhibitor Cocktail Sigma 11873580001 Sodium Fluoride (NaF) Sigma 201154 Sodium pyrophosphate decahydrate (NaPyPh) Sigma 221368 b-Glycerophosphate disodium salt hydrate (BGP) Sigma G9422 Sodium Orthovanadate (NaO) New England Biolabs P0758L X-tremeGENETM HP DNA Transfection Reagent Sigma XTGHP-RO Paraformaldehyde Sigma 158127 Goat Serum Sigma G9023 RNaseA ThermoFisher Scientific EN0531 Propidium Iodide Sigma 537059 Benzonase Nuclease Sigma E1014 DynabeadsTM M-270 Epoxy ThermoFisher Scientific 14302D DyLight 800 NHS Ester ThermoFisher Scientific 46421 Triethanolamine Sigma T58300 Tricene MP Biomedicals 807416 Lithium dodecyl sulfate Sigma BP1309-25 Crystal Violet Sigma C581 Shield-1 MedChemExpress HY-112210 4-Hydroxytamoxifen MedChemExpress HY-16950 Dimethyl sulfoxide (DMSO) Sigma BP231 ProLongTM Gold Antifade Mountant with DNA Stain DAPI ThermoFisher Scientific P36931 HisPurTM Ni-NTA Magnetic Beads ThermoFisher Scientific 88831 Dithiothreitol (DTT) ThermoFisher Scientific BP172 Urea Sigma U5378 Polybrene Sigma TR-1003 Ammonium Bicarbonate Sigma A6141 Amersham Hybond-N+ Cytiva RPN303B Doxycycline hyclate Wisent 450-185 XG 3-Indoleacetic acid (IAA) MP Biomedicals ICN10203725 Critical commercial assays Wizard Genomic DNA Purification kit Promega A1120 Click-iTTM RNA Alexa FluorTM 594 Imaging Kit Invitrogen C10330 BioRad Lowry DC Assay BioRad 5000111 In-Fusion Snap Assembly Takara 638946 (Continued on next page) 22 Cell Reports 43, 114738, September 24, 2024 Article ll OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER Deposited data CRISPR-Cas9 rDNA dropout screen This study NCBI GEO: GSE253809 TCOF1-eGFP/eGFP-NLS affinity purification mass spectrometry and His10UFM1DSC affinity purification mass spectrometry This study PRIDE repository: PXD048568; project DOI: 10.6019/PXD048568 Experimental models: Cell lines hTERT-RPE1 ATCC N/A hTERT-RPE1 p53 / Cas9 Alexandre Orthwein N/A hTERT-RPE1 p53 / Cas9+ DD-HA-ER-I-PpoI This study N/A hTERT-RPE1 p53 / Cas9+ DD-HA-ER-I-PpoI + eGFP-NLS This study N/A hTERT-RPE1 p53 / Cas9+ DD-HA-ER-I-PpoI + TCOF1-eGFP This study N/A hTERT-RPE1 p53 / Cas9+ DD-HA-ER-I-PpoI + His10-UFM1DSC This study N/A hTERT-RPE1 p53 / Cas9+ DD-HA-ER-I-PpoI, UFL1 KO This study N/A hTERT-RPE1 p53 / Cas9+ DD-HA-ER-I-PpoI, DDRGK1 KO This study N/A U2OS + DD-HA-ER-I-PpoI This study N/A HCT116 SMC6-mAC (mAID-Clover) mCherry H3 Venegas et al.89 N/A Oligonucleotides Primers used for library preparation Hart et al.49 Table S4 sgRNAs Hart et al.49 Walczak et al.83 Platt et al.103 Table S4 Northern Blot Probes This study Table S4 Recombinant DNA Plasmid: pLX303-DD-HA-ER-I-PpoI (G418) This study N/A Plasmid: Lenti-Guide-GFP-T2A-His10-UFM1DSC This study N/A Plasmid: pRK10-His10-UFM1DSC This study N/A Plasmid: Lenti-Guide-Puro-UBA5 This study N/A Plasmid: Lenti-Guide-Puro-UFM1 This study N/A Plasmid: Lenti-Guide-Puro-DDRGK1 This study N/A Plasmid Lenti-Guide-Puro-UFSP2: This study N/A Plasmid: Lenti-Guide-Puro-UFC1#1 This study N/A Plasmid: Lenti-Guide-Puro-UFC1#2 This study N/A Plasmid: Lenti-Guide-GFP-UFL1#1 This study N/A Plasmid: Lenti-Guide-GFP-UFL1#2 This study N/A Plasmid: Lenti-Guide-Puro-UFL1#1 This study N/A Plasmid: Lenti-Guide-Puro-UFL1#2 This study N/A Plasmid: Lenti-Guide-Puro 50 ETS #1 This study N/A Plasmid: Lenti-Guide-Puro-LacZ This study N/A Plasmid: pSH-EF-IRES-eGFP-V5-NLS This study N/A Plasmid: pSH-EF-IRES-TCOF1-eGFP This study N/A Plasmid: Lenti-Guide-Puro FAM208A#1 This study N/A Plasmid: Lenti-Guide-Puro FAM208A#2 This study N/A Plasmid: Lenti-Guide-Puro SETDB1#1 This study N/A Plasmid: Lenti-Guide-Puro SETDB1#2 This study N/A Plasmid: Lenti-Guide-mCherry-AAVS1 Noordermeer et al.104 N/A Plasmid: pCas9-sgAAVS1-1 Li et al.105 N/A Plasmid: pCas9-sgAAVS1-2 Li et al.105 N/A Plasmid: pMD2.G Addgene 12259 Plasmid: psPAX2 Addgene 12260 (Continued on next page) Cell Reports 43, 114738, September 24, 2024 23 Article ll OPEN ACCESS



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