Affinity Purification:Article Title: Tolerance to colibactin correlates with homologous recombination proficiency and resistance to irinotecan in colorectal cancer cells
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit anti-gamma-H2AX Antibody, Affinity Purified Bethyl Cat# A300-081A; RRID:AB_203288 Anti-RAD51 Millipore Cat# ABE257; RRID:AB_10850319 Donkey Anti-Rabbit IgG (H + L) Polyclonal Antibody, Alexa Fluor 555 Conjugated Molecular Probes Cat# A-31572; RRID:AB_162543 Donkey anti-Mouse IgG (H + L) ReadyProbes Secondary Antibody, Alexa FluorTM 488 Thermo Fisher Scientific Cat# R37114; RRID:AB_2556542 Phospho-Histone H2A.X (Ser139) (D7T2V) Mouse mAb Cell Signaling Technology Cat# 80312; RRID:AB_2799949 Histone H2A.X (D17A3) XP Rabbit mAb Cell Signaling Technology Cat# 7631; RRID:AB_10860771 Anti-Vinculin, clone V284 Millipore Cat# 05–386; RRID:AB_11212640 ATM (phospho S1981) antibody [EP1890Y] Abcam Cat# ab81292; RRID:AB_1640207 Rabbit Anti-ATM Monoclonal Antibody, Unconjugated, Clone D2E2 Cell Signaling Technology Cat# 2873; RRID:AB_2062659 Rabbit anti-Phospho RPA32 (S33) Antibody, Affinity Purified Bethyl Cat# A300-246A; RRID:AB_2180847 Recombinant Anti-RPA32/RPA2 antibody [4E4] Abcam Cat# ab252861; RRID:AB_292764 Rad51C (2H11) Santa Cruz Biotechnology Cat# sc-56214; RRID:AB_2238197 Phospho-Chk1 (Ser345) (133D3) Rabbit mAb Cell Signaling Technology Cat# 2348; RRID:AB_331212 Chk1 (2G1D5) Mouse mAb Cell Signaling Technology Cat# 2360; RRID:AB_2080320 Phospho-Chk2 (Thr68) (C13C1) Rabbit mAb Cell Signaling Technology Cat# 2197; RRID:AB_2080501 Mouse Anti-Chk2 Monoclonal Antibody, Unconjugated, Clone 1C12 Cell Signaling Technology Cat# 3440; RRID:AB_2229490 ATRIP Antibody Cell Signaling Technology Cat# 2737, RRID:AB_823659 FANCD2 Antibody - BSA Free Novus Biologicals Cat# NB100-182, RRID:AB_10002867 ERCC1 (D61F5) Rabbit mAb Cell Signaling Technology Cat# 5437, RRID:AB_10831838 REV1 Antibody (A-11) Santa Cruz Biotechnology Cat# sc-393022, RRID:AB_2885169 Bacterial and virus strains Escherichia coli DH10B pBeloBAC empty vector Prof. Jean Philippe Nougayrede21 N/A Escherichia coli DH10B pBeloBAC-pks Prof. Jean Philippe Nougayrede21 N/A Chemicals, peptides, and recombinant proteins DAPI (40,6-diamidino-2-phenylindole, dihydrochloride) Thermo Scientific Cat# 62247 Fetal Bovine Serum (South America) Sterile Filtered Euroclone Cat# ECS0180L L-Glutamine solution Sigma-Aldrich Cat# G7513 Antibiotic Antimycotic Solution (1003), Stabilized Sigma-Aldrich Cat# A5955 Trypsin-EDTA Solution Sigma-Aldrich Cat# T3924 Crystal Violet Solution Sigma-Aldrich Cat# V5265-500ML Oxaliplatin MedChemExpress Cat# HY-17371 SN38 MedChemExpress Cat# HY-13704 Olaparib MedChemExpress Cat# HY-10162 AZD0156 MedChemExpress Cat# HY-100016 Critical commercial assays Venor GeM Classic Minerva Biolabs Cat# 11-1250 PowerPlex 16 HS System Promega Cat# DC2100 (Continued on next page) Cell Reports Medicine 5, 101376, February 20, 2024 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER PierceTM BCA Protein Assay Kit Thermo Scientific Cat# 23225 Western Blotting AmershamTM ECLTM Prime Cytica Cat# RPN2236 LipofectamineTM 3000 Transfection Reagent Invitrogen Cat# L3000001 NEBNext High-Fidelity 2X PCR Master Mix New England Biolabs GmbH Cat# M0541S CellTiter-Glo Luminescent Cell Viability Assay Promega Cat# G7573 Maxwell RSC DNA FFPE Kit Promega Cat# AS1450 Deposited data RNA-Seq data This study ENA:PRJEB68048 Experimental models: Cell lines Human: COGA-5 cell line Laboratory of L.A. Huber RRID:CVCL_A076 Human: DLD-1 cell line ATCC RRID:CVCL_0248 Human: HCT 116 cell line NCI60 RRID:CVCL_0291 Human: OUMS-23 cell line JCRB RRID:CVCL_3088 Human: WiDr cell line Laboratory of R. Bernards RRID:CVCL_2760 Human: SW480 cell line ATCC RRID:CVCL_0546 Human: DiFi cell line Laboratory of J. Baselga RRID:CVCL_6895 Human: HT29 cell line NCI60 RRID:CVCL_A8EZ Human: HROC183 cell line Laboratory of M. Linnebacher RRID:CVCL_1D16 Human: Co-115 cell line Laboratory of R. Hamelin RRID:CVCL_D102 Human: SNU-977 cell line KCLB RRID:CVCL_5109 Human: HROC284Met cell line Laboratory of M. Linnebacher RRID:CVCL_1U91 Human: MDST8 cell line ECACC RRID:CVCL_2588 Human: GEO cell line Laboratory of G. Tortora RRID:CVCL_0271 Human: KM20 cell line KCLB RRID:CVCL_L095 Human: KM12 cell line NCI60 RRID:CVCL_1331 Human: RW-7213 cell line Laboratory of D. Arango RRID:CVCL_D175 Human: SNU-1411 cell line KCLB RRID:CVCL_5025 Human: LS411N cell line ATCC RRID:CVCL_1385 Human: LS1034 cell line ATCC RRID:CVCL_1382 Human: VACO 432 cell line Labboratory of B. Vogelstein RRID:CVCL_5402 Human: HCC2998 cell line NCI60 RRID:CVCL_1266 Human: CL-11 cell line DSMZ RRID:CVCL_1978 Human: HROC69 cell line Laboratory of M. Linnebacher RRID:CVCL_1G06 Human: JVE015 cell line LUMC RRID:CVCL_EG16 Human: CRC0174_XL cell line Lead contact N/A Human: SK-CO-1 cell line ATCC RRID:CVCL_0626 Human: HROC131 T0 M3 cell line Laboratory of M. Linnebacher RRID:CVCL_1D13 Human: HDC-114 cell line Laboratory of M. Schwab RRID:CVCL_A376 Human: SW1116 cell line ATCC RRID:CVCL_0544 Human: CRC0740_XL cell line Lead contact N/A Human: SNU-61 cell line KCLB RRID:CVCL_5078 Human: HROC59 cell line Laboratory of M. Linnebacher RRID:CVCL_1G04 Human: HROC39 cell line Laboratory of M. Linnebacher RRID:CVCL_1U81 Human: C106 cell line ECACC RRID:CVCL_M011 Human: OX-CO-3 cell line Laboratory of V. Cerundolo RRID:CVCL_B452 Human: HROC278Met T2 M2 cell line Laboratory of M. Linnebacher RRID:CVCL_1U90 Human: NCI-H498 cell line ATCC RRID:CVCL_1563 Human: KP363T cell line LUMC RRID:CVCL_EG34 (Continued on next page) e2 Cell Reports Medicine 5, 101376, February 20, 2024 Article ll OPEN ACCESS
Article Title: Circadian PERIOD proteins regulate TC-DSB repair through anchoring to the nuclear envelope.
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REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse Anti-53BP1 Monoclonal Antibody, Unconjugated, Clone 19 BD Biosciences Cat# 612522; RRID:AB_2206766 Rabbit Anti-ATM (phospho S1981) antibody [EP1890Y] Abcam Cat# ab81292; RRID:AB_1640207 Rabbit Anti-BMAL1 Polyclonal Antibody, Unconjugated Abcam Cat# ab3350; RRID:AB_303729 Rabbit Anti-CLOCK Polyclonal Antibody, Unconjugated Abcam Cat# ab3517; RRID:AB_303866 Rabbit Anti-Cry1 Polyclonal Antibody, Affinity Purified Bethyl, Discontinued Cat# A302-614A; RRID:AB_10555376 Rabbit Anti-Cryptochrome 2 Polyclonal antibody Proteintech Cat# 13997-1-AP; RRID:AB_10860100 Mouse Anti-DDX5 (p68) Monoclonal Antibody, Unconjugated, Clone 204 Millipore Cat# 05-850; RRID:AB_327052 Rabbit Anti-DDX17 Polyclonal antibody Proteintech Cat# 19910-1-AP; RRID:AB_10667004 Mouse Anti-GAPDH Monoclonal Antibody, 6C5 Sigma-Aldrich Cat# MAB374; RRID:AB_2107445 Rabbit Anti-Histone H2A.X, phospho (Ser139) Monoclonal Antibody, Unconjugated, Clone EP854(2)Y Abcam Cat# ab81299; RRID:AB_1640564 Mouse Anti-phospho-Histone H2A.X (Ser139) Monoclonal Antibody, clone JBW301 Sigma-Aldrich Cat# 05-636 RRID:AB_309864 Rabbit Anti-Lamin B1 Polyclonal antibody - Nuclear Envelope Marker Abcam Cat# ab16048; RRID:AB_443298 Rabbit Anti-Mouse Myosin I beta, Nuclear Antibody, Unconjugated Sigma-Aldrich Cat# M3567; RRID:AB_477180 Rabbit Anti-NONO Polyclonal antibody Proteintech Cat# 11058-1-AP; RRID:AB_2152167 Rabbit Anti-Nup153 Polyclonal antibody Abcam Cat# ab84872; RRID:AB_1859766 Rabbit Phospho-p53 (Ser15) Antibody #9284 Cell Signaling Technology Cat# 9284; RRID:AB_331464 Mouse Anti-PCNA (PC10) Monoclonal Antibody Santa Cruz Biotechnology Cat# sc-56; RRID:AB_628110 Rabbit Anti-PER2 Polyclonal antibody Proteintech, Discontinued Cat# 20359-1-AP; RRID:AB_10733224 Rabbit Anti-PER2 Monoclonal antibody [EPR11381(2)] Abcam, Discontinued Cat# ab179813 Rabbit Anti-RAD51 (H-92) Polyclonal antibody Santa Cruz Biotechnology, Discontinued Cat# sc-8349; RRID:AB_2253533 Goat Anti-RNF4 Polyclonal antibody R and D Systems Cat# AF7964; RRID:AB_3644534 Rabbit Anti-RPA32/RPA2 Polyclonal antibody Abcam Cat# ab10359; RRID:AB_297095 Rabbit Anti-SUN1 Polyclonal antibody Sigma-Aldrich Cat# HPA008346; RRID:AB_1080462 Rabbit Anti-SUN1 Monoclonal antibody [EPR6554] Abcam Cat# ab124770; RRID:AB_10976056 Rabbit Anti-SUN2 Monoclonal antibody [EPR6557] Abcam Cat# ab124916; RRID:AB_10972497 (Continued on next page) ll OPEN ACCESSArticle Molecular Cell 85, 1–18.e1–e11, December 18, 2025 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Mouse Anti-alpha-Tubulin Monoclonal Antibody Sigma-Aldrich Cat# T6199; RRID:AB_477583 Goat anti-Rabbit IgG (H+L) Highly CrossAdsorbed Secondary Antibody, Alexa FluorTM 488 Thermo Fisher Scientific Cat# A-11034; RRID:AB_2576217 Goat anti-Rabbit IgG (H+L) Highly CrossAdsorbed Secondary Antibody, Alexa FluorTM 594 Thermo Fisher Scientific Cat# A-11037; RRID:AB_2534095 Goat anti-Mouse IgG (H+L) Highly CrossAdsorbed Secondary Antibody, Alexa FluorTM 488 Thermo Fisher Scientific Cat# A-11029; RRID:AB_2534088 Goat anti-Mouse IgG (H+L) Highly CrossAdsorbed Secondary Antibody, Alexa FluorTM 594 Thermo Fisher Scientific Cat# A-11032; RRID:AB_2534091 Anti-Mouse IgG (Fc specific)–Peroxidase antibody produced in goat Sigma-Aldrich Cat# A2554; RRID:AB_258008 Anti-Rabbit IgG (whole molecule)Peroxidase antibody produced in goat Sigma-Aldrich Cat# A0545; RRID:AB_257896 Chemicals, peptides, and recombinant proteins 4-hydroxytamoxifen (OHT) Sigma-Aldrich Cat# H7904 Auxin: Indole-3-acetic acid sodium salt (IAA) Sigma-Aldrich Cat# I5148 etoposide Sigma-Aldrich Cat# E1383 doxorubicin Sigma-Aldrich Cat# D1515 ATM inhibitor (ATMi) KU-55933 Sigma-Aldrich Cat# SML1109 ATR inhibitor (ATRi) ETP-46464 Sigma-Aldrich Cat# SML1321 DNA-PK inhibitor (DNA-PKi) NU-7441 Selleckchem Cat# S2638 dexamethasone (Dex) Sigma-Aldrich Cat# D4902 Citifluor Clinisciences Cat# AF1-25 EdU (5-éthynyl-2’-désoxyuridine) Thermo Fisher Scientific Cat# A10044 Hoechst 33342 Thermo Fisher Scientific Cat# 62249 AMV reverse transcriptase Promega Cat# M510F Crystal Violet Solution Sigma-Aldrich Cat# V5265 TB GreenTM Premix Ex TaqTM (Tli RNaseH Plus) Takara Cat# RR420L PrimeSTAR Max DNA Polymerase Takara Cat# R045A Nuclease Benzonase Sigma-Aldrich Cat# E1014 RNAseH New England Biolabs Cat# M0297 AsiSI New England Biolabs Cat# R0630 BanI New England Biolabs Cat# R0118 BanII New England Biolabs Cat# R0119 cOmpleteTM Protease Inhibitor Cocktail Roche Cat# 11 836 153 001 Phosphatase Inhibitor Cocktail 2 Sigma-Aldrich Cat# P5726 Critical commercial assays Kit de prolifération cellulaire EdU Click-iTTM pour imagerie, colorant Alexa FluorTM 647 Thermo Fisher Scientific Cat# C10340 NEBuilder HiFi DNA Assembly Cloning Kit New England Biolabs Cat# E5520S QIAprep Spin Miniprep Kit Qiagen Cat# 27104 EndoFree Plasmid Maxi Kit Qiagen Cat# 12362 DNeasy Blood & Tissue Kit Qiagen Cat# 69504 RNeasy Mini Kit Qiagen Cat# 74104 (Continued on next page) ll OPEN ACCESS Article e2 Molecular Cell 85, 1–18.e1–e11, December 18, 2025
Article Title: Tolerance to colibactin correlates with homologous recombination proficiency and resistance to irinotecan in colorectal cancer cells.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit anti-gamma-H2AX Antibody, Affinity Purified Bethyl Cat# A300-081A; RRID:AB_203288 Anti-RAD51 Millipore Cat# ABE257; RRID:AB_10850319 Donkey Anti-Rabbit IgG (H + L) Polyclonal Antibody, Alexa Fluor 555 Conjugated Molecular Probes Cat# A-31572; RRID:AB_162543 Donkey anti-Mouse IgG (H + L) ReadyProbes Secondary Antibody, Alexa FluorTM 488 Thermo Fisher Scientific Cat# R37114; RRID:AB_2556542 Phospho-Histone H2A.X (Ser139) (D7T2V) Mouse mAb Cell Signaling Technology Cat# 80312; RRID:AB_2799949 Histone H2A.X (D17A3) XP Rabbit mAb Cell Signaling Technology Cat# 7631; RRID:AB_10860771 Anti-Vinculin, clone V284 Millipore Cat# 05–386; RRID:AB_11212640 ATM (phospho S1981) antibody [EP1890Y] Abcam Cat# ab81292; RRID:AB_1640207 Rabbit Anti-ATM Monoclonal Antibody, Unconjugated, Clone D2E2 Cell Signaling Technology Cat# 2873; RRID:AB_2062659 Rabbit anti-Phospho RPA32 (S33) Antibody, Affinity Purified Bethyl Cat# A300-246A; RRID:AB_2180847 Recombinant Anti-RPA32/RPA2 antibody [4E4] Abcam Cat# ab252861; RRID:AB_292764 Rad51C (2H11) Santa Cruz Biotechnology Cat# sc-56214; RRID:AB_2238197 Phospho-Chk1 (Ser345) (133D3) Rabbit mAb Cell Signaling Technology Cat# 2348; RRID:AB_331212 Chk1 (2G1D5) Mouse mAb Cell Signaling Technology Cat# 2360; RRID:AB_2080320 Phospho-Chk2 (Thr68) (C13C1) Rabbit mAb Cell Signaling Technology Cat# 2197; RRID:AB_2080501 Mouse Anti-Chk2 Monoclonal Antibody, Unconjugated, Clone 1C12 Cell Signaling Technology Cat# 3440; RRID:AB_2229490 ATRIP Antibody Cell Signaling Technology Cat# 2737, RRID:AB_823659 FANCD2 Antibody - BSA Free Novus Biologicals Cat# NB100-182, RRID:AB_10002867 ERCC1 (D61F5) Rabbit mAb Cell Signaling Technology Cat# 5437, RRID:AB_10831838 REV1 Antibody (A-11) Santa Cruz Biotechnology Cat# sc-393022, RRID:AB_2885169 Bacterial and virus strains Escherichia coli DH10B pBeloBAC empty vector Prof. Jean Philippe Nougayrede21 N/A Escherichia coli DH10B pBeloBAC-pks Prof. Jean Philippe Nougayrede21 N/A Chemicals, peptides, and recombinant proteins DAPI (40,6-diamidino-2-phenylindole, dihydrochloride) Thermo Scientific Cat# 62247 Fetal Bovine Serum (South America) Sterile Filtered Euroclone Cat# ECS0180L L-Glutamine solution Sigma-Aldrich Cat# G7513 Antibiotic Antimycotic Solution (1003), Stabilized Sigma-Aldrich Cat# A5955 Trypsin-EDTA Solution Sigma-Aldrich Cat# T3924 Crystal Violet Solution Sigma-Aldrich Cat# V5265-500ML Oxaliplatin MedChemExpress Cat# HY-17371 SN38 MedChemExpress Cat# HY-13704 Olaparib MedChemExpress Cat# HY-10162 AZD0156 MedChemExpress Cat# HY-100016 Critical commercial assays Venor GeM Classic Minerva Biolabs Cat# 11-1250 PowerPlex 16 HS System Promega Cat# DC2100 (Continued on next page) Cell Reports Medicine 5, 101376, February 20, 2024 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Human: SW480 ATM KO cell line This study N/A Human: SW480 ATRIP KO cell line This study N/A Human: SW480 ERCC1 KO cell line This study N/A Human: SW480 FANCD2 KO cell line This study N/A Human: SW480 REV1 KO cell line This study N/A Human: A2780 cell line ECACC RRID:CVCL_0134 Human: UWB1.289 cell line ATCC RRID:CVCL_B079 Human: UWB1.289+BRCA1 cell line ATCC RRID:CVCL_B078 Human: KP363T olaparib-resistant cell line This study N/A Human: HROC278MET olaparib-resistant cell line This study N/A Human: KP363T colibactin-tolerant cell line This study N/A Human: KP363T empty long term cell line This study N/A Human: HROC39 colibactin-tolerant cell line This study N/A Oligonucleotides sgRNA targeting ATM 50- CCAAGGCTATTCAGTG TGCG-30 Durinikova et al.33 N/A sgRNA targeting ATRIP 50-GCGAGACTCACTACA TCAGA-30 This study N/A sgRNA targeting ERCC1 50-GCTCTGTGTAGATCG GAATA-30 This study N/A sgRNA targeting FANCD2 50-AAGAAGACTGTCAA AATCTG-30 This study N/A sgRNA targeting REV1 50-AAACTAATGATGTTGC ATGG-30 This study N/A CLBI forward primer 50-CGCTTCATCAACACGC TTTA-30 This study N/A CLBI reverse primer 50-GCAAAAACCGGCTACT TGTC-30 This study N/A CLBO forward primer 50-CGTCGTTATTTACCGC ACCT-30 This study N/A CLBO reverse primer 50-CACTACGCGACCAAGA CAGA-30 This study N/A Recombinant DNA Plasmid: pDRGFP Addgene RRID:Addgene_26475 Plasmid: pCBASceI Addgene RRID:Addgene_26477 Plasmid: lentiCRISPR v2 Addgene RRID:Addgene_52961 Software and algorithms GeneMapper Software v.6 Applied Biosystems RRID:SCR_014290 GraphPad Prism v.8 GraphPad RRID:SCR_002798 ImageJ v1.53a https://ImageJ.nih.gov/ij/ N/A MapSplice v2.2.1 http://www.netlab.uky.edu/p/bioinfo/ http://www.netlab.uky.edu/p/bioinfo/ Samtools v1.14 https://samtools.sourceforge.net/ https://samtools.sourceforge.net/ Ubu 1.2 UNC-Chapel Hill Bioinformatics Utilities https://github.com/mozack/ubu/blob/master/ src/main/java/edu/unc/bioinf/ubu/Ubu.java Rsem v1.3.3 https://github.com/deweylab/RSEM https://github.com/deweylab/RSEM R v4.1 The R Foundation for Statistical Computing https://www.R-project.org/ Tximport Bioconductor https://bioconductor.org/packages/release/ bioc/html/tximport.html Deseq2 Bioconductor https://bioconductor.org/packages/release/ bioc/html/DESeq2.html (Continued on next page) Please cite this article in press as: Sogari et al., Tolerance to colibactin correlates with homologous recombination proficiency and resistance to irinotecan in colorectal cancer cells, Cell Reports Medicine (2023), https://doi.org/10.1016/j.xcrm.2023.101376 Cell Reports Medicine 5, 101376, February 20, 2024 e3 Article ll OPEN ACCESS
Article Title: Alpha-synuclein abundance and localization are regulated by the RNA-binding protein PUMILIO1.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse neuron-specific beta-III Tubulin antibody R and D Systems Cat# MAB1195 RRID: AB_357520 Rabbit anti-Pumilio 1 antibody Abcam Cat# ab92545 RRID:AB_10563695 Anti-Synuclein, alpha Millipore Cat# AB5038 RRID:AB_91648 Goat anti-Pumilio 1, Affinity Purified Bethyl Cat# A300-201A RRID:AB_2253218 Rabbit Anti-Argonaute 2 Monoclonal Cell Signaling Technology Cat# 2897 RRID:AB_2096291 Recombinant Anti-Alpha-synuclein Abcam Cat# ab212184 RRID:AB_2941889 Mouse Anti-Rabbit GADPH Monoclonal Millipore Cat# CB1001 RRID:AB_2107426 alpha Tubulin Abcam Cat# ab24246 RRID:AB_447954 Ataxin 1 - 11750 Huda Zoghbi Lab; Baylor College of Medicine Cat# ATXN1-11750 RRID:AB_2721278 Rabbit control IgG (Purified Rabbit IgG) Bethyl Cat# P120-201 RRID:AB_479830 Mouse neuron-specific anti-beta-III Tubulin Abcam Cat# ab7751 RRID:AB_306045 Chemicals, peptides, and recombinant proteins Dulbecco’s Modified Eagle Medium (DMEM) Thermo Fisher Scientific N/A Fetal Bovine Serum N/A Matrigel in StemFlex Medium Thermo Fisher Scientific Cat# A3349401 mTeSR TM Plus StemCell Technologies Cat# 100-1130 DMEM-F12 Thermo Fisher Scientific Cat# 12634010 Neurobasal-A Thermo Fisher Scientific Cat# 10-888-022 MEM Non-Essential Amino Acids Solution (100X) Thermo Fisher Scientific Cat# 11140050 Penicillin-Streptomycin Millipore Sigma Cat# P4333 β-mercaptoethanol Thermo Fisher Scientific Cat# 31350010 Doxycycline Millipore Sigma Cat# D9891-5G Glutamax Thermo Fisher Scientific Cat# 35050-061 N2 Thermo Fisher Scientific Cat# 17502-048 B27 without Vitamin A Gibco Cat# 12587-010 Geltrex Thermo Fisher Scientific Cat# A1413202 Brain Derived Neurotrophic Factor Gibco Cat# 450-02-50UG Adenosine-3 ′ ,5 ′ -cyclic monophosphate Millipore Sigma Cat# 28745-100MG L-Ascorbic Acid Millipore Sigma Cat# A92902-25G Glial-Derived Neurotrophic Factor Peprotech Cat# 450-10-50 B27 without Vitamin A Gibco Cat# 12587-010 jetPRIME Transfection Reagent Genesee Cat# 55-133 .. Triton X-100 Fisher Scientific Cat# BP151500 (Continued on next page) 16 Cell Reports 44, 116145, August 26, 2025
Article Title: Beta-coronaviruses exploit cellular stress responses by modulating TFEB and TFE3 activity.
Article Snippet: Antibodies Caspase-3 (D3R6Y) Rabbit mAb Cell Signaling Technology Cat# 9664; RRID:AB_2798429 Cleaved Caspase-3 (Asp175) (5A1E) Rabbit mAb Cell Signaling Technology Cat# 9664, RRID:AB_2070042 PARP Antibody Cell Signaling Technology Cat# 9542, RRID:AB_2160739 Cleaved PARP (Asp214) (D64E10) XP Rabbit mAb Cell Signaling Technology Cat# 5625, RRID:AB_10699459 Caspase-9 (C9) Mouse mAb Cell Signaling Technology Cat# 9508, RRID:AB_2068620 Cleaved Caspase-9 (Asp330) (E5Z7N) Rabbit mAb Cell Signaling Technology Cat# 52873, RRID:AB_2799423 Caspase-7 (D2Q3L) Rabbit Antibody Cell Signaling Technology Cat# 12827, RRID:AB_2687912 Cleaved Caspase-7 (Asp198) (D6H1) Rabbit mAb Cell Signaling Technology Cat# 8438; RRID:AB_11178377 Anti-rabbit IgG, HRP-linked Antibody Cell Signaling Technology Cat# 7074, RRID:AB_2099233 Anti-mouse IgG, HRP-linked Antibody Cell Signaling Technology Cat# 7076, RRID:AB_330924 TFE3 Antibody Cell Signaling Technology Cat# 14779, RRID:AB_2687582 TFEB Antibody Cell Signaling Technology Cat# 4240, RRID:AB_11220225 GAPDH Monoclonal Antibody (6C5) Thermo Fisher Scientific Cat# AM4300, RRID:AB_2536381 Goat anti-Rabbit IgG (Heavy Chain), Superclonal Recombinant Secondary Antibody, Alexa Fluor 488 Thermo Fisher Scientific Cat# A27034, RRID:AB_2536097 .. Recombinant Secondary Antibody, Alexa Fluor 555 Thermo Fisher Scientific Cat# A27039, RRID:AB_2536100 LAMP-1 (human) DSHB Cat# H4A3, RRID:AB_2296838 p70 S6 Kinase Antibody Cell Signaling Technology Cat# 9202, RRID:AB_331676 Phospho-p70 S6 Kinase (Thr389) Antibody Cell Signaling Technology Cat# 9205, RRID:AB_330944 Phospho-4E-BP1 (Ser65) Antibody Cell Signaling Technology Cat# 9451, RRID:AB_330947 4E-BP1 (53H11) Rabbit mAb Cell Signaling Technology Cat# 9644, RRID:AB_2097841 Phospho-Stat3 (Tyr705) (D3A7) XP Rabbit mAb Cell Signaling Technology Cat# 9145, RRID:AB_2491009 Stat3 (D3Z2G) Rabbit mAb #12640 Cell Signaling Technology Cat# 12640, RRID:AB_2629499 Calnexin (C5C9) Rabbit mAb Cell Signaling Technology Cat# 2679, RRID:AB_2228381 Pan-Calcineurin A Antibody Cell Signaling Technology Cat# 2614, RRID:AB_2168458 Phospho-TFEB (Ser211) (E9S8N) Rabbit mAb Cell Signaling Technology Cat# 37681, RRID:AB_2799117 Phospho-Stat3 (Ser727) Cell Signaling Technology Cat# 34911, RRID:AB_2737598 Histone H3 (D1H2) XP Rabbit mAb Cell Signaling Technology Cat# 4499, RRID:AB_10544537 NFAT1 (D43B1) XP Rabbit mAb Cell Signaling Technology Cat# 5861, RRID:AB_10834808 Rabbit anti-TFEB Antibody, Affinity Purified Bethyl Cat# A303-673A, RRID:AB_1120475 Anti-TFE3 antibody produced in rabbit Sigma-Aldrich Cat# HPA023881, RRID:AB_1857931 Anti-phospho S321 TFE3 Martina et al., 201655 N/A Anti-MHV(MJ1.3) Ghosh et al., 202030 N/A .. Unconjugated Bio-Rad Cat# AHP1586, RRID:AB_2303333 Anti-p18 INK, C-Terminal antibody produced in rabbit Sigma-Aldrich Cat# SAB4500079, RRID:AB_10742707 NF-kB p65 (D14E12) XP Rabbit mAb #8242 Cell Signaling Technology Cat# 8242, RRID:AB_10859369 Phospho-NF-kB p65 (Ser536) (93H1) Rabbit mAb #3033 Cell Signaling Technology Cat# 3033, RRID:AB_331284 Phospho-IkBa (Ser32) (14D4) Rabbit mAb #2859 Cell Signaling Technology Cat# 2859, RRID:AB_561111 (Continued on next page) 18 iScience 26, 106169, March 17, 2023
Recombinant:Article Title: Tolerance to colibactin correlates with homologous recombination proficiency and resistance to irinotecan in colorectal cancer cells
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit anti-gamma-H2AX Antibody, Affinity Purified Bethyl Cat# A300-081A; RRID:AB_203288 Anti-RAD51 Millipore Cat# ABE257; RRID:AB_10850319 Donkey Anti-Rabbit IgG (H + L) Polyclonal Antibody, Alexa Fluor 555 Conjugated Molecular Probes Cat# A-31572; RRID:AB_162543 Donkey anti-Mouse IgG (H + L) ReadyProbes Secondary Antibody, Alexa FluorTM 488 Thermo Fisher Scientific Cat# R37114; RRID:AB_2556542 Phospho-Histone H2A.X (Ser139) (D7T2V) Mouse mAb Cell Signaling Technology Cat# 80312; RRID:AB_2799949 Histone H2A.X (D17A3) XP Rabbit mAb Cell Signaling Technology Cat# 7631; RRID:AB_10860771 Anti-Vinculin, clone V284 Millipore Cat# 05–386; RRID:AB_11212640 ATM (phospho S1981) antibody [EP1890Y] Abcam Cat# ab81292; RRID:AB_1640207 Rabbit Anti-ATM Monoclonal Antibody, Unconjugated, Clone D2E2 Cell Signaling Technology Cat# 2873; RRID:AB_2062659 Rabbit anti-Phospho RPA32 (S33) Antibody, Affinity Purified Bethyl Cat# A300-246A; RRID:AB_2180847 Recombinant Anti-RPA32/RPA2 antibody [4E4] Abcam Cat# ab252861; RRID:AB_292764 Rad51C (2H11) Santa Cruz Biotechnology Cat# sc-56214; RRID:AB_2238197 Phospho-Chk1 (Ser345) (133D3) Rabbit mAb Cell Signaling Technology Cat# 2348; RRID:AB_331212 Chk1 (2G1D5) Mouse mAb Cell Signaling Technology Cat# 2360; RRID:AB_2080320 Phospho-Chk2 (Thr68) (C13C1) Rabbit mAb Cell Signaling Technology Cat# 2197; RRID:AB_2080501 Mouse Anti-Chk2 Monoclonal Antibody, Unconjugated, Clone 1C12 Cell Signaling Technology Cat# 3440; RRID:AB_2229490 ATRIP Antibody Cell Signaling Technology Cat# 2737, RRID:AB_823659 FANCD2 Antibody - BSA Free Novus Biologicals Cat# NB100-182, RRID:AB_10002867 ERCC1 (D61F5) Rabbit mAb Cell Signaling Technology Cat# 5437, RRID:AB_10831838 REV1 Antibody (A-11) Santa Cruz Biotechnology Cat# sc-393022, RRID:AB_2885169 Bacterial and virus strains Escherichia coli DH10B pBeloBAC empty vector Prof. Jean Philippe Nougayrede21 N/A Escherichia coli DH10B pBeloBAC-pks Prof. Jean Philippe Nougayrede21 N/A Chemicals, peptides, and recombinant proteins DAPI (40,6-diamidino-2-phenylindole, dihydrochloride) Thermo Scientific Cat# 62247 Fetal Bovine Serum (South America) Sterile Filtered Euroclone Cat# ECS0180L L-Glutamine solution Sigma-Aldrich Cat# G7513 Antibiotic Antimycotic Solution (1003), Stabilized Sigma-Aldrich Cat# A5955 Trypsin-EDTA Solution Sigma-Aldrich Cat# T3924 Crystal Violet Solution Sigma-Aldrich Cat# V5265-500ML Oxaliplatin MedChemExpress Cat# HY-17371 SN38 MedChemExpress Cat# HY-13704 Olaparib MedChemExpress Cat# HY-10162 AZD0156 MedChemExpress Cat# HY-100016 Critical commercial assays Venor GeM Classic Minerva Biolabs Cat# 11-1250 PowerPlex 16 HS System Promega Cat# DC2100 (Continued on next page) Cell Reports Medicine 5, 101376, February 20, 2024 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER PierceTM BCA Protein Assay Kit Thermo Scientific Cat# 23225 Western Blotting AmershamTM ECLTM Prime Cytica Cat# RPN2236 LipofectamineTM 3000 Transfection Reagent Invitrogen Cat# L3000001 NEBNext High-Fidelity 2X PCR Master Mix New England Biolabs GmbH Cat# M0541S CellTiter-Glo Luminescent Cell Viability Assay Promega Cat# G7573 Maxwell RSC DNA FFPE Kit Promega Cat# AS1450 Deposited data RNA-Seq data This study ENA:PRJEB68048 Experimental models: Cell lines Human: COGA-5 cell line Laboratory of L.A. Huber RRID:CVCL_A076 Human: DLD-1 cell line ATCC RRID:CVCL_0248 Human: HCT 116 cell line NCI60 RRID:CVCL_0291 Human: OUMS-23 cell line JCRB RRID:CVCL_3088 Human: WiDr cell line Laboratory of R. Bernards RRID:CVCL_2760 Human: SW480 cell line ATCC RRID:CVCL_0546 Human: DiFi cell line Laboratory of J. Baselga RRID:CVCL_6895 Human: HT29 cell line NCI60 RRID:CVCL_A8EZ Human: HROC183 cell line Laboratory of M. Linnebacher RRID:CVCL_1D16 Human: Co-115 cell line Laboratory of R. Hamelin RRID:CVCL_D102 Human: SNU-977 cell line KCLB RRID:CVCL_5109 Human: HROC284Met cell line Laboratory of M. Linnebacher RRID:CVCL_1U91 Human: MDST8 cell line ECACC RRID:CVCL_2588 Human: GEO cell line Laboratory of G. Tortora RRID:CVCL_0271 Human: KM20 cell line KCLB RRID:CVCL_L095 Human: KM12 cell line NCI60 RRID:CVCL_1331 Human: RW-7213 cell line Laboratory of D. Arango RRID:CVCL_D175 Human: SNU-1411 cell line KCLB RRID:CVCL_5025 Human: LS411N cell line ATCC RRID:CVCL_1385 Human: LS1034 cell line ATCC RRID:CVCL_1382 Human: VACO 432 cell line Labboratory of B. Vogelstein RRID:CVCL_5402 Human: HCC2998 cell line NCI60 RRID:CVCL_1266 Human: CL-11 cell line DSMZ RRID:CVCL_1978 Human: HROC69 cell line Laboratory of M. Linnebacher RRID:CVCL_1G06 Human: JVE015 cell line LUMC RRID:CVCL_EG16 Human: CRC0174_XL cell line Lead contact N/A Human: SK-CO-1 cell line ATCC RRID:CVCL_0626 Human: HROC131 T0 M3 cell line Laboratory of M. Linnebacher RRID:CVCL_1D13 Human: HDC-114 cell line Laboratory of M. Schwab RRID:CVCL_A376 Human: SW1116 cell line ATCC RRID:CVCL_0544 Human: CRC0740_XL cell line Lead contact N/A Human: SNU-61 cell line KCLB RRID:CVCL_5078 Human: HROC59 cell line Laboratory of M. Linnebacher RRID:CVCL_1G04 Human: HROC39 cell line Laboratory of M. Linnebacher RRID:CVCL_1U81 Human: C106 cell line ECACC RRID:CVCL_M011 Human: OX-CO-3 cell line Laboratory of V. Cerundolo RRID:CVCL_B452 Human: HROC278Met T2 M2 cell line Laboratory of M. Linnebacher RRID:CVCL_1U90 Human: NCI-H498 cell line ATCC RRID:CVCL_1563 Human: KP363T cell line LUMC RRID:CVCL_EG34 (Continued on next page) e2 Cell Reports Medicine 5, 101376, February 20, 2024 Article ll OPEN ACCESS
Article Title: Tolerance to colibactin correlates with homologous recombination proficiency and resistance to irinotecan in colorectal cancer cells.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit anti-gamma-H2AX Antibody, Affinity Purified Bethyl Cat# A300-081A; RRID:AB_203288 Anti-RAD51 Millipore Cat# ABE257; RRID:AB_10850319 Donkey Anti-Rabbit IgG (H + L) Polyclonal Antibody, Alexa Fluor 555 Conjugated Molecular Probes Cat# A-31572; RRID:AB_162543 Donkey anti-Mouse IgG (H + L) ReadyProbes Secondary Antibody, Alexa FluorTM 488 Thermo Fisher Scientific Cat# R37114; RRID:AB_2556542 Phospho-Histone H2A.X (Ser139) (D7T2V) Mouse mAb Cell Signaling Technology Cat# 80312; RRID:AB_2799949 Histone H2A.X (D17A3) XP Rabbit mAb Cell Signaling Technology Cat# 7631; RRID:AB_10860771 Anti-Vinculin, clone V284 Millipore Cat# 05–386; RRID:AB_11212640 ATM (phospho S1981) antibody [EP1890Y] Abcam Cat# ab81292; RRID:AB_1640207 Rabbit Anti-ATM Monoclonal Antibody, Unconjugated, Clone D2E2 Cell Signaling Technology Cat# 2873; RRID:AB_2062659 Rabbit anti-Phospho RPA32 (S33) Antibody, Affinity Purified Bethyl Cat# A300-246A; RRID:AB_2180847 Recombinant Anti-RPA32/RPA2 antibody [4E4] Abcam Cat# ab252861; RRID:AB_292764 Rad51C (2H11) Santa Cruz Biotechnology Cat# sc-56214; RRID:AB_2238197 Phospho-Chk1 (Ser345) (133D3) Rabbit mAb Cell Signaling Technology Cat# 2348; RRID:AB_331212 Chk1 (2G1D5) Mouse mAb Cell Signaling Technology Cat# 2360; RRID:AB_2080320 Phospho-Chk2 (Thr68) (C13C1) Rabbit mAb Cell Signaling Technology Cat# 2197; RRID:AB_2080501 Mouse Anti-Chk2 Monoclonal Antibody, Unconjugated, Clone 1C12 Cell Signaling Technology Cat# 3440; RRID:AB_2229490 ATRIP Antibody Cell Signaling Technology Cat# 2737, RRID:AB_823659 FANCD2 Antibody - BSA Free Novus Biologicals Cat# NB100-182, RRID:AB_10002867 ERCC1 (D61F5) Rabbit mAb Cell Signaling Technology Cat# 5437, RRID:AB_10831838 REV1 Antibody (A-11) Santa Cruz Biotechnology Cat# sc-393022, RRID:AB_2885169 Bacterial and virus strains Escherichia coli DH10B pBeloBAC empty vector Prof. Jean Philippe Nougayrede21 N/A Escherichia coli DH10B pBeloBAC-pks Prof. Jean Philippe Nougayrede21 N/A Chemicals, peptides, and recombinant proteins DAPI (40,6-diamidino-2-phenylindole, dihydrochloride) Thermo Scientific Cat# 62247 Fetal Bovine Serum (South America) Sterile Filtered Euroclone Cat# ECS0180L L-Glutamine solution Sigma-Aldrich Cat# G7513 Antibiotic Antimycotic Solution (1003), Stabilized Sigma-Aldrich Cat# A5955 Trypsin-EDTA Solution Sigma-Aldrich Cat# T3924 Crystal Violet Solution Sigma-Aldrich Cat# V5265-500ML Oxaliplatin MedChemExpress Cat# HY-17371 SN38 MedChemExpress Cat# HY-13704 Olaparib MedChemExpress Cat# HY-10162 AZD0156 MedChemExpress Cat# HY-100016 Critical commercial assays Venor GeM Classic Minerva Biolabs Cat# 11-1250 PowerPlex 16 HS System Promega Cat# DC2100 (Continued on next page) Cell Reports Medicine 5, 101376, February 20, 2024 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Human: SW480 ATM KO cell line This study N/A Human: SW480 ATRIP KO cell line This study N/A Human: SW480 ERCC1 KO cell line This study N/A Human: SW480 FANCD2 KO cell line This study N/A Human: SW480 REV1 KO cell line This study N/A Human: A2780 cell line ECACC RRID:CVCL_0134 Human: UWB1.289 cell line ATCC RRID:CVCL_B079 Human: UWB1.289+BRCA1 cell line ATCC RRID:CVCL_B078 Human: KP363T olaparib-resistant cell line This study N/A Human: HROC278MET olaparib-resistant cell line This study N/A Human: KP363T colibactin-tolerant cell line This study N/A Human: KP363T empty long term cell line This study N/A Human: HROC39 colibactin-tolerant cell line This study N/A Oligonucleotides sgRNA targeting ATM 50- CCAAGGCTATTCAGTG TGCG-30 Durinikova et al.33 N/A sgRNA targeting ATRIP 50-GCGAGACTCACTACA TCAGA-30 This study N/A sgRNA targeting ERCC1 50-GCTCTGTGTAGATCG GAATA-30 This study N/A sgRNA targeting FANCD2 50-AAGAAGACTGTCAA AATCTG-30 This study N/A sgRNA targeting REV1 50-AAACTAATGATGTTGC ATGG-30 This study N/A CLBI forward primer 50-CGCTTCATCAACACGC TTTA-30 This study N/A CLBI reverse primer 50-GCAAAAACCGGCTACT TGTC-30 This study N/A CLBO forward primer 50-CGTCGTTATTTACCGC ACCT-30 This study N/A CLBO reverse primer 50-CACTACGCGACCAAGA CAGA-30 This study N/A Recombinant DNA Plasmid: pDRGFP Addgene RRID:Addgene_26475 Plasmid: pCBASceI Addgene RRID:Addgene_26477 Plasmid: lentiCRISPR v2 Addgene RRID:Addgene_52961 Software and algorithms GeneMapper Software v.6 Applied Biosystems RRID:SCR_014290 GraphPad Prism v.8 GraphPad RRID:SCR_002798 ImageJ v1.53a https://ImageJ.nih.gov/ij/ N/A MapSplice v2.2.1 http://www.netlab.uky.edu/p/bioinfo/ http://www.netlab.uky.edu/p/bioinfo/ Samtools v1.14 https://samtools.sourceforge.net/ https://samtools.sourceforge.net/ Ubu 1.2 UNC-Chapel Hill Bioinformatics Utilities https://github.com/mozack/ubu/blob/master/ src/main/java/edu/unc/bioinf/ubu/Ubu.java Rsem v1.3.3 https://github.com/deweylab/RSEM https://github.com/deweylab/RSEM R v4.1 The R Foundation for Statistical Computing https://www.R-project.org/ Tximport Bioconductor https://bioconductor.org/packages/release/ bioc/html/tximport.html Deseq2 Bioconductor https://bioconductor.org/packages/release/ bioc/html/DESeq2.html (Continued on next page) Please cite this article in press as: Sogari et al., Tolerance to colibactin correlates with homologous recombination proficiency and resistance to irinotecan in colorectal cancer cells, Cell Reports Medicine (2023), https://doi.org/10.1016/j.xcrm.2023.101376 Cell Reports Medicine 5, 101376, February 20, 2024 e3 Article ll OPEN ACCESS
Article Title: Alpha-synuclein abundance and localization are regulated by the RNA-binding protein PUMILIO1.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse neuron-specific beta-III Tubulin antibody R and D Systems Cat# MAB1195 RRID: AB_357520 Rabbit anti-Pumilio 1 antibody Abcam Cat# ab92545 RRID:AB_10563695 Anti-Synuclein, alpha Millipore Cat# AB5038 RRID:AB_91648 Goat anti-Pumilio 1, Affinity Purified Bethyl Cat# A300-201A RRID:AB_2253218 Rabbit Anti-Argonaute 2 Monoclonal Cell Signaling Technology Cat# 2897 RRID:AB_2096291 Recombinant Anti-Alpha-synuclein Abcam Cat# ab212184 RRID:AB_2941889 Mouse Anti-Rabbit GADPH Monoclonal Millipore Cat# CB1001 RRID:AB_2107426 alpha Tubulin Abcam Cat# ab24246 RRID:AB_447954 Ataxin 1 - 11750 Huda Zoghbi Lab; Baylor College of Medicine Cat# ATXN1-11750 RRID:AB_2721278 Rabbit control IgG (Purified Rabbit IgG) Bethyl Cat# P120-201 RRID:AB_479830 Mouse neuron-specific anti-beta-III Tubulin Abcam Cat# ab7751 RRID:AB_306045 Chemicals, peptides, and recombinant proteins Dulbecco’s Modified Eagle Medium (DMEM) Thermo Fisher Scientific N/A Fetal Bovine Serum N/A Matrigel in StemFlex Medium Thermo Fisher Scientific Cat# A3349401 mTeSR TM Plus StemCell Technologies Cat# 100-1130 DMEM-F12 Thermo Fisher Scientific Cat# 12634010 Neurobasal-A Thermo Fisher Scientific Cat# 10-888-022 MEM Non-Essential Amino Acids Solution (100X) Thermo Fisher Scientific Cat# 11140050 Penicillin-Streptomycin Millipore Sigma Cat# P4333 β-mercaptoethanol Thermo Fisher Scientific Cat# 31350010 Doxycycline Millipore Sigma Cat# D9891-5G Glutamax Thermo Fisher Scientific Cat# 35050-061 N2 Thermo Fisher Scientific Cat# 17502-048 B27 without Vitamin A Gibco Cat# 12587-010 Geltrex Thermo Fisher Scientific Cat# A1413202 Brain Derived Neurotrophic Factor Gibco Cat# 450-02-50UG Adenosine-3 ′ ,5 ′ -cyclic monophosphate Millipore Sigma Cat# 28745-100MG L-Ascorbic Acid Millipore Sigma Cat# A92902-25G Glial-Derived Neurotrophic Factor Peprotech Cat# 450-10-50 B27 without Vitamin A Gibco Cat# 12587-010 jetPRIME Transfection Reagent Genesee Cat# 55-133 .. Triton X-100 Fisher Scientific Cat# BP151500 (Continued on next page) 16 Cell Reports 44, 116145, August 26, 2025
Article Title: Beta-coronaviruses exploit cellular stress responses by modulating TFEB and TFE3 activity.
Article Snippet: Antibodies Caspase-3 (D3R6Y) Rabbit mAb Cell Signaling Technology Cat# 9664; RRID:AB_2798429 Cleaved Caspase-3 (Asp175) (5A1E) Rabbit mAb Cell Signaling Technology Cat# 9664, RRID:AB_2070042 PARP Antibody Cell Signaling Technology Cat# 9542, RRID:AB_2160739 Cleaved PARP (Asp214) (D64E10) XP Rabbit mAb Cell Signaling Technology Cat# 5625, RRID:AB_10699459 Caspase-9 (C9) Mouse mAb Cell Signaling Technology Cat# 9508, RRID:AB_2068620 Cleaved Caspase-9 (Asp330) (E5Z7N) Rabbit mAb Cell Signaling Technology Cat# 52873, RRID:AB_2799423 Caspase-7 (D2Q3L) Rabbit Antibody Cell Signaling Technology Cat# 12827, RRID:AB_2687912 Cleaved Caspase-7 (Asp198) (D6H1) Rabbit mAb Cell Signaling Technology Cat# 8438; RRID:AB_11178377 Anti-rabbit IgG, HRP-linked Antibody Cell Signaling Technology Cat# 7074, RRID:AB_2099233 Anti-mouse IgG, HRP-linked Antibody Cell Signaling Technology Cat# 7076, RRID:AB_330924 TFE3 Antibody Cell Signaling Technology Cat# 14779, RRID:AB_2687582 TFEB Antibody Cell Signaling Technology Cat# 4240, RRID:AB_11220225 GAPDH Monoclonal Antibody (6C5) Thermo Fisher Scientific Cat# AM4300, RRID:AB_2536381 Goat anti-Rabbit IgG (Heavy Chain), Superclonal Recombinant Secondary Antibody, Alexa Fluor 488 Thermo Fisher Scientific Cat# A27034, RRID:AB_2536097 .. Recombinant Secondary Antibody, Alexa Fluor 555 Thermo Fisher Scientific Cat# A27039, RRID:AB_2536100 LAMP-1 (human) DSHB Cat# H4A3, RRID:AB_2296838 p70 S6 Kinase Antibody Cell Signaling Technology Cat# 9202, RRID:AB_331676 Phospho-p70 S6 Kinase (Thr389) Antibody Cell Signaling Technology Cat# 9205, RRID:AB_330944 Phospho-4E-BP1 (Ser65) Antibody Cell Signaling Technology Cat# 9451, RRID:AB_330947 4E-BP1 (53H11) Rabbit mAb Cell Signaling Technology Cat# 9644, RRID:AB_2097841 Phospho-Stat3 (Tyr705) (D3A7) XP Rabbit mAb Cell Signaling Technology Cat# 9145, RRID:AB_2491009 Stat3 (D3Z2G) Rabbit mAb #12640 Cell Signaling Technology Cat# 12640, RRID:AB_2629499 Calnexin (C5C9) Rabbit mAb Cell Signaling Technology Cat# 2679, RRID:AB_2228381 Pan-Calcineurin A Antibody Cell Signaling Technology Cat# 2614, RRID:AB_2168458 Phospho-TFEB (Ser211) (E9S8N) Rabbit mAb Cell Signaling Technology Cat# 37681, RRID:AB_2799117 Phospho-Stat3 (Ser727) Cell Signaling Technology Cat# 34911, RRID:AB_2737598 Histone H3 (D1H2) XP Rabbit mAb Cell Signaling Technology Cat# 4499, RRID:AB_10544537 NFAT1 (D43B1) XP Rabbit mAb Cell Signaling Technology Cat# 5861, RRID:AB_10834808 Rabbit anti-TFEB Antibody, Affinity Purified Bethyl Cat# A303-673A, RRID:AB_1120475 Anti-TFE3 antibody produced in rabbit Sigma-Aldrich Cat# HPA023881, RRID:AB_1857931 Anti-phospho S321 TFE3 Martina et al., 201655 N/A Anti-MHV(MJ1.3) Ghosh et al., 202030 N/A .. Unconjugated Bio-Rad Cat# AHP1586, RRID:AB_2303333 Anti-p18 INK, C-Terminal antibody produced in rabbit Sigma-Aldrich Cat# SAB4500079, RRID:AB_10742707 NF-kB p65 (D14E12) XP Rabbit mAb #8242 Cell Signaling Technology Cat# 8242, RRID:AB_10859369 Phospho-NF-kB p65 (Ser536) (93H1) Rabbit mAb #3033 Cell Signaling Technology Cat# 3033, RRID:AB_331284 Phospho-IkBa (Ser32) (14D4) Rabbit mAb #2859 Cell Signaling Technology Cat# 2859, RRID:AB_561111 (Continued on next page) 18 iScience 26, 106169, March 17, 2023
Virus:Article Title: Tolerance to colibactin correlates with homologous recombination proficiency and resistance to irinotecan in colorectal cancer cells
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit anti-gamma-H2AX Antibody, Affinity Purified Bethyl Cat# A300-081A; RRID:AB_203288 Anti-RAD51 Millipore Cat# ABE257; RRID:AB_10850319 Donkey Anti-Rabbit IgG (H + L) Polyclonal Antibody, Alexa Fluor 555 Conjugated Molecular Probes Cat# A-31572; RRID:AB_162543 Donkey anti-Mouse IgG (H + L) ReadyProbes Secondary Antibody, Alexa FluorTM 488 Thermo Fisher Scientific Cat# R37114; RRID:AB_2556542 Phospho-Histone H2A.X (Ser139) (D7T2V) Mouse mAb Cell Signaling Technology Cat# 80312; RRID:AB_2799949 Histone H2A.X (D17A3) XP Rabbit mAb Cell Signaling Technology Cat# 7631; RRID:AB_10860771 Anti-Vinculin, clone V284 Millipore Cat# 05–386; RRID:AB_11212640 ATM (phospho S1981) antibody [EP1890Y] Abcam Cat# ab81292; RRID:AB_1640207 Rabbit Anti-ATM Monoclonal Antibody, Unconjugated, Clone D2E2 Cell Signaling Technology Cat# 2873; RRID:AB_2062659 Rabbit anti-Phospho RPA32 (S33) Antibody, Affinity Purified Bethyl Cat# A300-246A; RRID:AB_2180847 Recombinant Anti-RPA32/RPA2 antibody [4E4] Abcam Cat# ab252861; RRID:AB_292764 Rad51C (2H11) Santa Cruz Biotechnology Cat# sc-56214; RRID:AB_2238197 Phospho-Chk1 (Ser345) (133D3) Rabbit mAb Cell Signaling Technology Cat# 2348; RRID:AB_331212 Chk1 (2G1D5) Mouse mAb Cell Signaling Technology Cat# 2360; RRID:AB_2080320 Phospho-Chk2 (Thr68) (C13C1) Rabbit mAb Cell Signaling Technology Cat# 2197; RRID:AB_2080501 Mouse Anti-Chk2 Monoclonal Antibody, Unconjugated, Clone 1C12 Cell Signaling Technology Cat# 3440; RRID:AB_2229490 ATRIP Antibody Cell Signaling Technology Cat# 2737, RRID:AB_823659 FANCD2 Antibody - BSA Free Novus Biologicals Cat# NB100-182, RRID:AB_10002867 ERCC1 (D61F5) Rabbit mAb Cell Signaling Technology Cat# 5437, RRID:AB_10831838 REV1 Antibody (A-11) Santa Cruz Biotechnology Cat# sc-393022, RRID:AB_2885169 Bacterial and virus strains Escherichia coli DH10B pBeloBAC empty vector Prof. Jean Philippe Nougayrede21 N/A Escherichia coli DH10B pBeloBAC-pks Prof. Jean Philippe Nougayrede21 N/A Chemicals, peptides, and recombinant proteins DAPI (40,6-diamidino-2-phenylindole, dihydrochloride) Thermo Scientific Cat# 62247 Fetal Bovine Serum (South America) Sterile Filtered Euroclone Cat# ECS0180L L-Glutamine solution Sigma-Aldrich Cat# G7513 Antibiotic Antimycotic Solution (1003), Stabilized Sigma-Aldrich Cat# A5955 Trypsin-EDTA Solution Sigma-Aldrich Cat# T3924 Crystal Violet Solution Sigma-Aldrich Cat# V5265-500ML Oxaliplatin MedChemExpress Cat# HY-17371 SN38 MedChemExpress Cat# HY-13704 Olaparib MedChemExpress Cat# HY-10162 AZD0156 MedChemExpress Cat# HY-100016 Critical commercial assays Venor GeM Classic Minerva Biolabs Cat# 11-1250 PowerPlex 16 HS System Promega Cat# DC2100 (Continued on next page) Cell Reports Medicine 5, 101376, February 20, 2024 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER PierceTM BCA Protein Assay Kit Thermo Scientific Cat# 23225 Western Blotting AmershamTM ECLTM Prime Cytica Cat# RPN2236 LipofectamineTM 3000 Transfection Reagent Invitrogen Cat# L3000001 NEBNext High-Fidelity 2X PCR Master Mix New England Biolabs GmbH Cat# M0541S CellTiter-Glo Luminescent Cell Viability Assay Promega Cat# G7573 Maxwell RSC DNA FFPE Kit Promega Cat# AS1450 Deposited data RNA-Seq data This study ENA:PRJEB68048 Experimental models: Cell lines Human: COGA-5 cell line Laboratory of L.A. Huber RRID:CVCL_A076 Human: DLD-1 cell line ATCC RRID:CVCL_0248 Human: HCT 116 cell line NCI60 RRID:CVCL_0291 Human: OUMS-23 cell line JCRB RRID:CVCL_3088 Human: WiDr cell line Laboratory of R. Bernards RRID:CVCL_2760 Human: SW480 cell line ATCC RRID:CVCL_0546 Human: DiFi cell line Laboratory of J. Baselga RRID:CVCL_6895 Human: HT29 cell line NCI60 RRID:CVCL_A8EZ Human: HROC183 cell line Laboratory of M. Linnebacher RRID:CVCL_1D16 Human: Co-115 cell line Laboratory of R. Hamelin RRID:CVCL_D102 Human: SNU-977 cell line KCLB RRID:CVCL_5109 Human: HROC284Met cell line Laboratory of M. Linnebacher RRID:CVCL_1U91 Human: MDST8 cell line ECACC RRID:CVCL_2588 Human: GEO cell line Laboratory of G. Tortora RRID:CVCL_0271 Human: KM20 cell line KCLB RRID:CVCL_L095 Human: KM12 cell line NCI60 RRID:CVCL_1331 Human: RW-7213 cell line Laboratory of D. Arango RRID:CVCL_D175 Human: SNU-1411 cell line KCLB RRID:CVCL_5025 Human: LS411N cell line ATCC RRID:CVCL_1385 Human: LS1034 cell line ATCC RRID:CVCL_1382 Human: VACO 432 cell line Labboratory of B. Vogelstein RRID:CVCL_5402 Human: HCC2998 cell line NCI60 RRID:CVCL_1266 Human: CL-11 cell line DSMZ RRID:CVCL_1978 Human: HROC69 cell line Laboratory of M. Linnebacher RRID:CVCL_1G06 Human: JVE015 cell line LUMC RRID:CVCL_EG16 Human: CRC0174_XL cell line Lead contact N/A Human: SK-CO-1 cell line ATCC RRID:CVCL_0626 Human: HROC131 T0 M3 cell line Laboratory of M. Linnebacher RRID:CVCL_1D13 Human: HDC-114 cell line Laboratory of M. Schwab RRID:CVCL_A376 Human: SW1116 cell line ATCC RRID:CVCL_0544 Human: CRC0740_XL cell line Lead contact N/A Human: SNU-61 cell line KCLB RRID:CVCL_5078 Human: HROC59 cell line Laboratory of M. Linnebacher RRID:CVCL_1G04 Human: HROC39 cell line Laboratory of M. Linnebacher RRID:CVCL_1U81 Human: C106 cell line ECACC RRID:CVCL_M011 Human: OX-CO-3 cell line Laboratory of V. Cerundolo RRID:CVCL_B452 Human: HROC278Met T2 M2 cell line Laboratory of M. Linnebacher RRID:CVCL_1U90 Human: NCI-H498 cell line ATCC RRID:CVCL_1563 Human: KP363T cell line LUMC RRID:CVCL_EG34 (Continued on next page) e2 Cell Reports Medicine 5, 101376, February 20, 2024 Article ll OPEN ACCESS
Article Title: Tolerance to colibactin correlates with homologous recombination proficiency and resistance to irinotecan in colorectal cancer cells.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit anti-gamma-H2AX Antibody, Affinity Purified Bethyl Cat# A300-081A; RRID:AB_203288 Anti-RAD51 Millipore Cat# ABE257; RRID:AB_10850319 Donkey Anti-Rabbit IgG (H + L) Polyclonal Antibody, Alexa Fluor 555 Conjugated Molecular Probes Cat# A-31572; RRID:AB_162543 Donkey anti-Mouse IgG (H + L) ReadyProbes Secondary Antibody, Alexa FluorTM 488 Thermo Fisher Scientific Cat# R37114; RRID:AB_2556542 Phospho-Histone H2A.X (Ser139) (D7T2V) Mouse mAb Cell Signaling Technology Cat# 80312; RRID:AB_2799949 Histone H2A.X (D17A3) XP Rabbit mAb Cell Signaling Technology Cat# 7631; RRID:AB_10860771 Anti-Vinculin, clone V284 Millipore Cat# 05–386; RRID:AB_11212640 ATM (phospho S1981) antibody [EP1890Y] Abcam Cat# ab81292; RRID:AB_1640207 Rabbit Anti-ATM Monoclonal Antibody, Unconjugated, Clone D2E2 Cell Signaling Technology Cat# 2873; RRID:AB_2062659 Rabbit anti-Phospho RPA32 (S33) Antibody, Affinity Purified Bethyl Cat# A300-246A; RRID:AB_2180847 Recombinant Anti-RPA32/RPA2 antibody [4E4] Abcam Cat# ab252861; RRID:AB_292764 Rad51C (2H11) Santa Cruz Biotechnology Cat# sc-56214; RRID:AB_2238197 Phospho-Chk1 (Ser345) (133D3) Rabbit mAb Cell Signaling Technology Cat# 2348; RRID:AB_331212 Chk1 (2G1D5) Mouse mAb Cell Signaling Technology Cat# 2360; RRID:AB_2080320 Phospho-Chk2 (Thr68) (C13C1) Rabbit mAb Cell Signaling Technology Cat# 2197; RRID:AB_2080501 Mouse Anti-Chk2 Monoclonal Antibody, Unconjugated, Clone 1C12 Cell Signaling Technology Cat# 3440; RRID:AB_2229490 ATRIP Antibody Cell Signaling Technology Cat# 2737, RRID:AB_823659 FANCD2 Antibody - BSA Free Novus Biologicals Cat# NB100-182, RRID:AB_10002867 ERCC1 (D61F5) Rabbit mAb Cell Signaling Technology Cat# 5437, RRID:AB_10831838 REV1 Antibody (A-11) Santa Cruz Biotechnology Cat# sc-393022, RRID:AB_2885169 Bacterial and virus strains Escherichia coli DH10B pBeloBAC empty vector Prof. Jean Philippe Nougayrede21 N/A Escherichia coli DH10B pBeloBAC-pks Prof. Jean Philippe Nougayrede21 N/A Chemicals, peptides, and recombinant proteins DAPI (40,6-diamidino-2-phenylindole, dihydrochloride) Thermo Scientific Cat# 62247 Fetal Bovine Serum (South America) Sterile Filtered Euroclone Cat# ECS0180L L-Glutamine solution Sigma-Aldrich Cat# G7513 Antibiotic Antimycotic Solution (1003), Stabilized Sigma-Aldrich Cat# A5955 Trypsin-EDTA Solution Sigma-Aldrich Cat# T3924 Crystal Violet Solution Sigma-Aldrich Cat# V5265-500ML Oxaliplatin MedChemExpress Cat# HY-17371 SN38 MedChemExpress Cat# HY-13704 Olaparib MedChemExpress Cat# HY-10162 AZD0156 MedChemExpress Cat# HY-100016 Critical commercial assays Venor GeM Classic Minerva Biolabs Cat# 11-1250 PowerPlex 16 HS System Promega Cat# DC2100 (Continued on next page) Cell Reports Medicine 5, 101376, February 20, 2024 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Human: SW480 ATM KO cell line This study N/A Human: SW480 ATRIP KO cell line This study N/A Human: SW480 ERCC1 KO cell line This study N/A Human: SW480 FANCD2 KO cell line This study N/A Human: SW480 REV1 KO cell line This study N/A Human: A2780 cell line ECACC RRID:CVCL_0134 Human: UWB1.289 cell line ATCC RRID:CVCL_B079 Human: UWB1.289+BRCA1 cell line ATCC RRID:CVCL_B078 Human: KP363T olaparib-resistant cell line This study N/A Human: HROC278MET olaparib-resistant cell line This study N/A Human: KP363T colibactin-tolerant cell line This study N/A Human: KP363T empty long term cell line This study N/A Human: HROC39 colibactin-tolerant cell line This study N/A Oligonucleotides sgRNA targeting ATM 50- CCAAGGCTATTCAGTG TGCG-30 Durinikova et al.33 N/A sgRNA targeting ATRIP 50-GCGAGACTCACTACA TCAGA-30 This study N/A sgRNA targeting ERCC1 50-GCTCTGTGTAGATCG GAATA-30 This study N/A sgRNA targeting FANCD2 50-AAGAAGACTGTCAA AATCTG-30 This study N/A sgRNA targeting REV1 50-AAACTAATGATGTTGC ATGG-30 This study N/A CLBI forward primer 50-CGCTTCATCAACACGC TTTA-30 This study N/A CLBI reverse primer 50-GCAAAAACCGGCTACT TGTC-30 This study N/A CLBO forward primer 50-CGTCGTTATTTACCGC ACCT-30 This study N/A CLBO reverse primer 50-CACTACGCGACCAAGA CAGA-30 This study N/A Recombinant DNA Plasmid: pDRGFP Addgene RRID:Addgene_26475 Plasmid: pCBASceI Addgene RRID:Addgene_26477 Plasmid: lentiCRISPR v2 Addgene RRID:Addgene_52961 Software and algorithms GeneMapper Software v.6 Applied Biosystems RRID:SCR_014290 GraphPad Prism v.8 GraphPad RRID:SCR_002798 ImageJ v1.53a https://ImageJ.nih.gov/ij/ N/A MapSplice v2.2.1 http://www.netlab.uky.edu/p/bioinfo/ http://www.netlab.uky.edu/p/bioinfo/ Samtools v1.14 https://samtools.sourceforge.net/ https://samtools.sourceforge.net/ Ubu 1.2 UNC-Chapel Hill Bioinformatics Utilities https://github.com/mozack/ubu/blob/master/ src/main/java/edu/unc/bioinf/ubu/Ubu.java Rsem v1.3.3 https://github.com/deweylab/RSEM https://github.com/deweylab/RSEM R v4.1 The R Foundation for Statistical Computing https://www.R-project.org/ Tximport Bioconductor https://bioconductor.org/packages/release/ bioc/html/tximport.html Deseq2 Bioconductor https://bioconductor.org/packages/release/ bioc/html/DESeq2.html (Continued on next page) Please cite this article in press as: Sogari et al., Tolerance to colibactin correlates with homologous recombination proficiency and resistance to irinotecan in colorectal cancer cells, Cell Reports Medicine (2023), https://doi.org/10.1016/j.xcrm.2023.101376 Cell Reports Medicine 5, 101376, February 20, 2024 e3 Article ll OPEN ACCESS
Plasmid Preparation:Article Title: Tolerance to colibactin correlates with homologous recombination proficiency and resistance to irinotecan in colorectal cancer cells
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit anti-gamma-H2AX Antibody, Affinity Purified Bethyl Cat# A300-081A; RRID:AB_203288 Anti-RAD51 Millipore Cat# ABE257; RRID:AB_10850319 Donkey Anti-Rabbit IgG (H + L) Polyclonal Antibody, Alexa Fluor 555 Conjugated Molecular Probes Cat# A-31572; RRID:AB_162543 Donkey anti-Mouse IgG (H + L) ReadyProbes Secondary Antibody, Alexa FluorTM 488 Thermo Fisher Scientific Cat# R37114; RRID:AB_2556542 Phospho-Histone H2A.X (Ser139) (D7T2V) Mouse mAb Cell Signaling Technology Cat# 80312; RRID:AB_2799949 Histone H2A.X (D17A3) XP Rabbit mAb Cell Signaling Technology Cat# 7631; RRID:AB_10860771 Anti-Vinculin, clone V284 Millipore Cat# 05–386; RRID:AB_11212640 ATM (phospho S1981) antibody [EP1890Y] Abcam Cat# ab81292; RRID:AB_1640207 Rabbit Anti-ATM Monoclonal Antibody, Unconjugated, Clone D2E2 Cell Signaling Technology Cat# 2873; RRID:AB_2062659 Rabbit anti-Phospho RPA32 (S33) Antibody, Affinity Purified Bethyl Cat# A300-246A; RRID:AB_2180847 Recombinant Anti-RPA32/RPA2 antibody [4E4] Abcam Cat# ab252861; RRID:AB_292764 Rad51C (2H11) Santa Cruz Biotechnology Cat# sc-56214; RRID:AB_2238197 Phospho-Chk1 (Ser345) (133D3) Rabbit mAb Cell Signaling Technology Cat# 2348; RRID:AB_331212 Chk1 (2G1D5) Mouse mAb Cell Signaling Technology Cat# 2360; RRID:AB_2080320 Phospho-Chk2 (Thr68) (C13C1) Rabbit mAb Cell Signaling Technology Cat# 2197; RRID:AB_2080501 Mouse Anti-Chk2 Monoclonal Antibody, Unconjugated, Clone 1C12 Cell Signaling Technology Cat# 3440; RRID:AB_2229490 ATRIP Antibody Cell Signaling Technology Cat# 2737, RRID:AB_823659 FANCD2 Antibody - BSA Free Novus Biologicals Cat# NB100-182, RRID:AB_10002867 ERCC1 (D61F5) Rabbit mAb Cell Signaling Technology Cat# 5437, RRID:AB_10831838 REV1 Antibody (A-11) Santa Cruz Biotechnology Cat# sc-393022, RRID:AB_2885169 Bacterial and virus strains Escherichia coli DH10B pBeloBAC empty vector Prof. Jean Philippe Nougayrede21 N/A Escherichia coli DH10B pBeloBAC-pks Prof. Jean Philippe Nougayrede21 N/A Chemicals, peptides, and recombinant proteins DAPI (40,6-diamidino-2-phenylindole, dihydrochloride) Thermo Scientific Cat# 62247 Fetal Bovine Serum (South America) Sterile Filtered Euroclone Cat# ECS0180L L-Glutamine solution Sigma-Aldrich Cat# G7513 Antibiotic Antimycotic Solution (1003), Stabilized Sigma-Aldrich Cat# A5955 Trypsin-EDTA Solution Sigma-Aldrich Cat# T3924 Crystal Violet Solution Sigma-Aldrich Cat# V5265-500ML Oxaliplatin MedChemExpress Cat# HY-17371 SN38 MedChemExpress Cat# HY-13704 Olaparib MedChemExpress Cat# HY-10162 AZD0156 MedChemExpress Cat# HY-100016 Critical commercial assays Venor GeM Classic Minerva Biolabs Cat# 11-1250 PowerPlex 16 HS System Promega Cat# DC2100 (Continued on next page) Cell Reports Medicine 5, 101376, February 20, 2024 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER PierceTM BCA Protein Assay Kit Thermo Scientific Cat# 23225 Western Blotting AmershamTM ECLTM Prime Cytica Cat# RPN2236 LipofectamineTM 3000 Transfection Reagent Invitrogen Cat# L3000001 NEBNext High-Fidelity 2X PCR Master Mix New England Biolabs GmbH Cat# M0541S CellTiter-Glo Luminescent Cell Viability Assay Promega Cat# G7573 Maxwell RSC DNA FFPE Kit Promega Cat# AS1450 Deposited data RNA-Seq data This study ENA:PRJEB68048 Experimental models: Cell lines Human: COGA-5 cell line Laboratory of L.A. Huber RRID:CVCL_A076 Human: DLD-1 cell line ATCC RRID:CVCL_0248 Human: HCT 116 cell line NCI60 RRID:CVCL_0291 Human: OUMS-23 cell line JCRB RRID:CVCL_3088 Human: WiDr cell line Laboratory of R. Bernards RRID:CVCL_2760 Human: SW480 cell line ATCC RRID:CVCL_0546 Human: DiFi cell line Laboratory of J. Baselga RRID:CVCL_6895 Human: HT29 cell line NCI60 RRID:CVCL_A8EZ Human: HROC183 cell line Laboratory of M. Linnebacher RRID:CVCL_1D16 Human: Co-115 cell line Laboratory of R. Hamelin RRID:CVCL_D102 Human: SNU-977 cell line KCLB RRID:CVCL_5109 Human: HROC284Met cell line Laboratory of M. Linnebacher RRID:CVCL_1U91 Human: MDST8 cell line ECACC RRID:CVCL_2588 Human: GEO cell line Laboratory of G. Tortora RRID:CVCL_0271 Human: KM20 cell line KCLB RRID:CVCL_L095 Human: KM12 cell line NCI60 RRID:CVCL_1331 Human: RW-7213 cell line Laboratory of D. Arango RRID:CVCL_D175 Human: SNU-1411 cell line KCLB RRID:CVCL_5025 Human: LS411N cell line ATCC RRID:CVCL_1385 Human: LS1034 cell line ATCC RRID:CVCL_1382 Human: VACO 432 cell line Labboratory of B. Vogelstein RRID:CVCL_5402 Human: HCC2998 cell line NCI60 RRID:CVCL_1266 Human: CL-11 cell line DSMZ RRID:CVCL_1978 Human: HROC69 cell line Laboratory of M. Linnebacher RRID:CVCL_1G06 Human: JVE015 cell line LUMC RRID:CVCL_EG16 Human: CRC0174_XL cell line Lead contact N/A Human: SK-CO-1 cell line ATCC RRID:CVCL_0626 Human: HROC131 T0 M3 cell line Laboratory of M. Linnebacher RRID:CVCL_1D13 Human: HDC-114 cell line Laboratory of M. Schwab RRID:CVCL_A376 Human: SW1116 cell line ATCC RRID:CVCL_0544 Human: CRC0740_XL cell line Lead contact N/A Human: SNU-61 cell line KCLB RRID:CVCL_5078 Human: HROC59 cell line Laboratory of M. Linnebacher RRID:CVCL_1G04 Human: HROC39 cell line Laboratory of M. Linnebacher RRID:CVCL_1U81 Human: C106 cell line ECACC RRID:CVCL_M011 Human: OX-CO-3 cell line Laboratory of V. Cerundolo RRID:CVCL_B452 Human: HROC278Met T2 M2 cell line Laboratory of M. Linnebacher RRID:CVCL_1U90 Human: NCI-H498 cell line ATCC RRID:CVCL_1563 Human: KP363T cell line LUMC RRID:CVCL_EG34 (Continued on next page) e2 Cell Reports Medicine 5, 101376, February 20, 2024 Article ll OPEN ACCESS
Article Title: Tolerance to colibactin correlates with homologous recombination proficiency and resistance to irinotecan in colorectal cancer cells.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit anti-gamma-H2AX Antibody, Affinity Purified Bethyl Cat# A300-081A; RRID:AB_203288 Anti-RAD51 Millipore Cat# ABE257; RRID:AB_10850319 Donkey Anti-Rabbit IgG (H + L) Polyclonal Antibody, Alexa Fluor 555 Conjugated Molecular Probes Cat# A-31572; RRID:AB_162543 Donkey anti-Mouse IgG (H + L) ReadyProbes Secondary Antibody, Alexa FluorTM 488 Thermo Fisher Scientific Cat# R37114; RRID:AB_2556542 Phospho-Histone H2A.X (Ser139) (D7T2V) Mouse mAb Cell Signaling Technology Cat# 80312; RRID:AB_2799949 Histone H2A.X (D17A3) XP Rabbit mAb Cell Signaling Technology Cat# 7631; RRID:AB_10860771 Anti-Vinculin, clone V284 Millipore Cat# 05–386; RRID:AB_11212640 ATM (phospho S1981) antibody [EP1890Y] Abcam Cat# ab81292; RRID:AB_1640207 Rabbit Anti-ATM Monoclonal Antibody, Unconjugated, Clone D2E2 Cell Signaling Technology Cat# 2873; RRID:AB_2062659 Rabbit anti-Phospho RPA32 (S33) Antibody, Affinity Purified Bethyl Cat# A300-246A; RRID:AB_2180847 Recombinant Anti-RPA32/RPA2 antibody [4E4] Abcam Cat# ab252861; RRID:AB_292764 Rad51C (2H11) Santa Cruz Biotechnology Cat# sc-56214; RRID:AB_2238197 Phospho-Chk1 (Ser345) (133D3) Rabbit mAb Cell Signaling Technology Cat# 2348; RRID:AB_331212 Chk1 (2G1D5) Mouse mAb Cell Signaling Technology Cat# 2360; RRID:AB_2080320 Phospho-Chk2 (Thr68) (C13C1) Rabbit mAb Cell Signaling Technology Cat# 2197; RRID:AB_2080501 Mouse Anti-Chk2 Monoclonal Antibody, Unconjugated, Clone 1C12 Cell Signaling Technology Cat# 3440; RRID:AB_2229490 ATRIP Antibody Cell Signaling Technology Cat# 2737, RRID:AB_823659 FANCD2 Antibody - BSA Free Novus Biologicals Cat# NB100-182, RRID:AB_10002867 ERCC1 (D61F5) Rabbit mAb Cell Signaling Technology Cat# 5437, RRID:AB_10831838 REV1 Antibody (A-11) Santa Cruz Biotechnology Cat# sc-393022, RRID:AB_2885169 Bacterial and virus strains Escherichia coli DH10B pBeloBAC empty vector Prof. Jean Philippe Nougayrede21 N/A Escherichia coli DH10B pBeloBAC-pks Prof. Jean Philippe Nougayrede21 N/A Chemicals, peptides, and recombinant proteins DAPI (40,6-diamidino-2-phenylindole, dihydrochloride) Thermo Scientific Cat# 62247 Fetal Bovine Serum (South America) Sterile Filtered Euroclone Cat# ECS0180L L-Glutamine solution Sigma-Aldrich Cat# G7513 Antibiotic Antimycotic Solution (1003), Stabilized Sigma-Aldrich Cat# A5955 Trypsin-EDTA Solution Sigma-Aldrich Cat# T3924 Crystal Violet Solution Sigma-Aldrich Cat# V5265-500ML Oxaliplatin MedChemExpress Cat# HY-17371 SN38 MedChemExpress Cat# HY-13704 Olaparib MedChemExpress Cat# HY-10162 AZD0156 MedChemExpress Cat# HY-100016 Critical commercial assays Venor GeM Classic Minerva Biolabs Cat# 11-1250 PowerPlex 16 HS System Promega Cat# DC2100 (Continued on next page) Cell Reports Medicine 5, 101376, February 20, 2024 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Human: SW480 ATM KO cell line This study N/A Human: SW480 ATRIP KO cell line This study N/A Human: SW480 ERCC1 KO cell line This study N/A Human: SW480 FANCD2 KO cell line This study N/A Human: SW480 REV1 KO cell line This study N/A Human: A2780 cell line ECACC RRID:CVCL_0134 Human: UWB1.289 cell line ATCC RRID:CVCL_B079 Human: UWB1.289+BRCA1 cell line ATCC RRID:CVCL_B078 Human: KP363T olaparib-resistant cell line This study N/A Human: HROC278MET olaparib-resistant cell line This study N/A Human: KP363T colibactin-tolerant cell line This study N/A Human: KP363T empty long term cell line This study N/A Human: HROC39 colibactin-tolerant cell line This study N/A Oligonucleotides sgRNA targeting ATM 50- CCAAGGCTATTCAGTG TGCG-30 Durinikova et al.33 N/A sgRNA targeting ATRIP 50-GCGAGACTCACTACA TCAGA-30 This study N/A sgRNA targeting ERCC1 50-GCTCTGTGTAGATCG GAATA-30 This study N/A sgRNA targeting FANCD2 50-AAGAAGACTGTCAA AATCTG-30 This study N/A sgRNA targeting REV1 50-AAACTAATGATGTTGC ATGG-30 This study N/A CLBI forward primer 50-CGCTTCATCAACACGC TTTA-30 This study N/A CLBI reverse primer 50-GCAAAAACCGGCTACT TGTC-30 This study N/A CLBO forward primer 50-CGTCGTTATTTACCGC ACCT-30 This study N/A CLBO reverse primer 50-CACTACGCGACCAAGA CAGA-30 This study N/A Recombinant DNA Plasmid: pDRGFP Addgene RRID:Addgene_26475 Plasmid: pCBASceI Addgene RRID:Addgene_26477 Plasmid: lentiCRISPR v2 Addgene RRID:Addgene_52961 Software and algorithms GeneMapper Software v.6 Applied Biosystems RRID:SCR_014290 GraphPad Prism v.8 GraphPad RRID:SCR_002798 ImageJ v1.53a https://ImageJ.nih.gov/ij/ N/A MapSplice v2.2.1 http://www.netlab.uky.edu/p/bioinfo/ http://www.netlab.uky.edu/p/bioinfo/ Samtools v1.14 https://samtools.sourceforge.net/ https://samtools.sourceforge.net/ Ubu 1.2 UNC-Chapel Hill Bioinformatics Utilities https://github.com/mozack/ubu/blob/master/ src/main/java/edu/unc/bioinf/ubu/Ubu.java Rsem v1.3.3 https://github.com/deweylab/RSEM https://github.com/deweylab/RSEM R v4.1 The R Foundation for Statistical Computing https://www.R-project.org/ Tximport Bioconductor https://bioconductor.org/packages/release/ bioc/html/tximport.html Deseq2 Bioconductor https://bioconductor.org/packages/release/ bioc/html/DESeq2.html (Continued on next page) Please cite this article in press as: Sogari et al., Tolerance to colibactin correlates with homologous recombination proficiency and resistance to irinotecan in colorectal cancer cells, Cell Reports Medicine (2023), https://doi.org/10.1016/j.xcrm.2023.101376 Cell Reports Medicine 5, 101376, February 20, 2024 e3 Article ll OPEN ACCESS
Sterility:Article Title: Tolerance to colibactin correlates with homologous recombination proficiency and resistance to irinotecan in colorectal cancer cells
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit anti-gamma-H2AX Antibody, Affinity Purified Bethyl Cat# A300-081A; RRID:AB_203288 Anti-RAD51 Millipore Cat# ABE257; RRID:AB_10850319 Donkey Anti-Rabbit IgG (H + L) Polyclonal Antibody, Alexa Fluor 555 Conjugated Molecular Probes Cat# A-31572; RRID:AB_162543 Donkey anti-Mouse IgG (H + L) ReadyProbes Secondary Antibody, Alexa FluorTM 488 Thermo Fisher Scientific Cat# R37114; RRID:AB_2556542 Phospho-Histone H2A.X (Ser139) (D7T2V) Mouse mAb Cell Signaling Technology Cat# 80312; RRID:AB_2799949 Histone H2A.X (D17A3) XP Rabbit mAb Cell Signaling Technology Cat# 7631; RRID:AB_10860771 Anti-Vinculin, clone V284 Millipore Cat# 05–386; RRID:AB_11212640 ATM (phospho S1981) antibody [EP1890Y] Abcam Cat# ab81292; RRID:AB_1640207 Rabbit Anti-ATM Monoclonal Antibody, Unconjugated, Clone D2E2 Cell Signaling Technology Cat# 2873; RRID:AB_2062659 Rabbit anti-Phospho RPA32 (S33) Antibody, Affinity Purified Bethyl Cat# A300-246A; RRID:AB_2180847 Recombinant Anti-RPA32/RPA2 antibody [4E4] Abcam Cat# ab252861; RRID:AB_292764 Rad51C (2H11) Santa Cruz Biotechnology Cat# sc-56214; RRID:AB_2238197 Phospho-Chk1 (Ser345) (133D3) Rabbit mAb Cell Signaling Technology Cat# 2348; RRID:AB_331212 Chk1 (2G1D5) Mouse mAb Cell Signaling Technology Cat# 2360; RRID:AB_2080320 Phospho-Chk2 (Thr68) (C13C1) Rabbit mAb Cell Signaling Technology Cat# 2197; RRID:AB_2080501 Mouse Anti-Chk2 Monoclonal Antibody, Unconjugated, Clone 1C12 Cell Signaling Technology Cat# 3440; RRID:AB_2229490 ATRIP Antibody Cell Signaling Technology Cat# 2737, RRID:AB_823659 FANCD2 Antibody - BSA Free Novus Biologicals Cat# NB100-182, RRID:AB_10002867 ERCC1 (D61F5) Rabbit mAb Cell Signaling Technology Cat# 5437, RRID:AB_10831838 REV1 Antibody (A-11) Santa Cruz Biotechnology Cat# sc-393022, RRID:AB_2885169 Bacterial and virus strains Escherichia coli DH10B pBeloBAC empty vector Prof. Jean Philippe Nougayrede21 N/A Escherichia coli DH10B pBeloBAC-pks Prof. Jean Philippe Nougayrede21 N/A Chemicals, peptides, and recombinant proteins DAPI (40,6-diamidino-2-phenylindole, dihydrochloride) Thermo Scientific Cat# 62247 Fetal Bovine Serum (South America) Sterile Filtered Euroclone Cat# ECS0180L L-Glutamine solution Sigma-Aldrich Cat# G7513 Antibiotic Antimycotic Solution (1003), Stabilized Sigma-Aldrich Cat# A5955 Trypsin-EDTA Solution Sigma-Aldrich Cat# T3924 Crystal Violet Solution Sigma-Aldrich Cat# V5265-500ML Oxaliplatin MedChemExpress Cat# HY-17371 SN38 MedChemExpress Cat# HY-13704 Olaparib MedChemExpress Cat# HY-10162 AZD0156 MedChemExpress Cat# HY-100016 Critical commercial assays Venor GeM Classic Minerva Biolabs Cat# 11-1250 PowerPlex 16 HS System Promega Cat# DC2100 (Continued on next page) Cell Reports Medicine 5, 101376, February 20, 2024 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER PierceTM BCA Protein Assay Kit Thermo Scientific Cat# 23225 Western Blotting AmershamTM ECLTM Prime Cytica Cat# RPN2236 LipofectamineTM 3000 Transfection Reagent Invitrogen Cat# L3000001 NEBNext High-Fidelity 2X PCR Master Mix New England Biolabs GmbH Cat# M0541S CellTiter-Glo Luminescent Cell Viability Assay Promega Cat# G7573 Maxwell RSC DNA FFPE Kit Promega Cat# AS1450 Deposited data RNA-Seq data This study ENA:PRJEB68048 Experimental models: Cell lines Human: COGA-5 cell line Laboratory of L.A. Huber RRID:CVCL_A076 Human: DLD-1 cell line ATCC RRID:CVCL_0248 Human: HCT 116 cell line NCI60 RRID:CVCL_0291 Human: OUMS-23 cell line JCRB RRID:CVCL_3088 Human: WiDr cell line Laboratory of R. Bernards RRID:CVCL_2760 Human: SW480 cell line ATCC RRID:CVCL_0546 Human: DiFi cell line Laboratory of J. Baselga RRID:CVCL_6895 Human: HT29 cell line NCI60 RRID:CVCL_A8EZ Human: HROC183 cell line Laboratory of M. Linnebacher RRID:CVCL_1D16 Human: Co-115 cell line Laboratory of R. Hamelin RRID:CVCL_D102 Human: SNU-977 cell line KCLB RRID:CVCL_5109 Human: HROC284Met cell line Laboratory of M. Linnebacher RRID:CVCL_1U91 Human: MDST8 cell line ECACC RRID:CVCL_2588 Human: GEO cell line Laboratory of G. Tortora RRID:CVCL_0271 Human: KM20 cell line KCLB RRID:CVCL_L095 Human: KM12 cell line NCI60 RRID:CVCL_1331 Human: RW-7213 cell line Laboratory of D. Arango RRID:CVCL_D175 Human: SNU-1411 cell line KCLB RRID:CVCL_5025 Human: LS411N cell line ATCC RRID:CVCL_1385 Human: LS1034 cell line ATCC RRID:CVCL_1382 Human: VACO 432 cell line Labboratory of B. Vogelstein RRID:CVCL_5402 Human: HCC2998 cell line NCI60 RRID:CVCL_1266 Human: CL-11 cell line DSMZ RRID:CVCL_1978 Human: HROC69 cell line Laboratory of M. Linnebacher RRID:CVCL_1G06 Human: JVE015 cell line LUMC RRID:CVCL_EG16 Human: CRC0174_XL cell line Lead contact N/A Human: SK-CO-1 cell line ATCC RRID:CVCL_0626 Human: HROC131 T0 M3 cell line Laboratory of M. Linnebacher RRID:CVCL_1D13 Human: HDC-114 cell line Laboratory of M. Schwab RRID:CVCL_A376 Human: SW1116 cell line ATCC RRID:CVCL_0544 Human: CRC0740_XL cell line Lead contact N/A Human: SNU-61 cell line KCLB RRID:CVCL_5078 Human: HROC59 cell line Laboratory of M. Linnebacher RRID:CVCL_1G04 Human: HROC39 cell line Laboratory of M. Linnebacher RRID:CVCL_1U81 Human: C106 cell line ECACC RRID:CVCL_M011 Human: OX-CO-3 cell line Laboratory of V. Cerundolo RRID:CVCL_B452 Human: HROC278Met T2 M2 cell line Laboratory of M. Linnebacher RRID:CVCL_1U90 Human: NCI-H498 cell line ATCC RRID:CVCL_1563 Human: KP363T cell line LUMC RRID:CVCL_EG34 (Continued on next page) e2 Cell Reports Medicine 5, 101376, February 20, 2024 Article ll OPEN ACCESS
Article Title: Tolerance to colibactin correlates with homologous recombination proficiency and resistance to irinotecan in colorectal cancer cells.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit anti-gamma-H2AX Antibody, Affinity Purified Bethyl Cat# A300-081A; RRID:AB_203288 Anti-RAD51 Millipore Cat# ABE257; RRID:AB_10850319 Donkey Anti-Rabbit IgG (H + L) Polyclonal Antibody, Alexa Fluor 555 Conjugated Molecular Probes Cat# A-31572; RRID:AB_162543 Donkey anti-Mouse IgG (H + L) ReadyProbes Secondary Antibody, Alexa FluorTM 488 Thermo Fisher Scientific Cat# R37114; RRID:AB_2556542 Phospho-Histone H2A.X (Ser139) (D7T2V) Mouse mAb Cell Signaling Technology Cat# 80312; RRID:AB_2799949 Histone H2A.X (D17A3) XP Rabbit mAb Cell Signaling Technology Cat# 7631; RRID:AB_10860771 Anti-Vinculin, clone V284 Millipore Cat# 05–386; RRID:AB_11212640 ATM (phospho S1981) antibody [EP1890Y] Abcam Cat# ab81292; RRID:AB_1640207 Rabbit Anti-ATM Monoclonal Antibody, Unconjugated, Clone D2E2 Cell Signaling Technology Cat# 2873; RRID:AB_2062659 Rabbit anti-Phospho RPA32 (S33) Antibody, Affinity Purified Bethyl Cat# A300-246A; RRID:AB_2180847 Recombinant Anti-RPA32/RPA2 antibody [4E4] Abcam Cat# ab252861; RRID:AB_292764 Rad51C (2H11) Santa Cruz Biotechnology Cat# sc-56214; RRID:AB_2238197 Phospho-Chk1 (Ser345) (133D3) Rabbit mAb Cell Signaling Technology Cat# 2348; RRID:AB_331212 Chk1 (2G1D5) Mouse mAb Cell Signaling Technology Cat# 2360; RRID:AB_2080320 Phospho-Chk2 (Thr68) (C13C1) Rabbit mAb Cell Signaling Technology Cat# 2197; RRID:AB_2080501 Mouse Anti-Chk2 Monoclonal Antibody, Unconjugated, Clone 1C12 Cell Signaling Technology Cat# 3440; RRID:AB_2229490 ATRIP Antibody Cell Signaling Technology Cat# 2737, RRID:AB_823659 FANCD2 Antibody - BSA Free Novus Biologicals Cat# NB100-182, RRID:AB_10002867 ERCC1 (D61F5) Rabbit mAb Cell Signaling Technology Cat# 5437, RRID:AB_10831838 REV1 Antibody (A-11) Santa Cruz Biotechnology Cat# sc-393022, RRID:AB_2885169 Bacterial and virus strains Escherichia coli DH10B pBeloBAC empty vector Prof. Jean Philippe Nougayrede21 N/A Escherichia coli DH10B pBeloBAC-pks Prof. Jean Philippe Nougayrede21 N/A Chemicals, peptides, and recombinant proteins DAPI (40,6-diamidino-2-phenylindole, dihydrochloride) Thermo Scientific Cat# 62247 Fetal Bovine Serum (South America) Sterile Filtered Euroclone Cat# ECS0180L L-Glutamine solution Sigma-Aldrich Cat# G7513 Antibiotic Antimycotic Solution (1003), Stabilized Sigma-Aldrich Cat# A5955 Trypsin-EDTA Solution Sigma-Aldrich Cat# T3924 Crystal Violet Solution Sigma-Aldrich Cat# V5265-500ML Oxaliplatin MedChemExpress Cat# HY-17371 SN38 MedChemExpress Cat# HY-13704 Olaparib MedChemExpress Cat# HY-10162 AZD0156 MedChemExpress Cat# HY-100016 Critical commercial assays Venor GeM Classic Minerva Biolabs Cat# 11-1250 PowerPlex 16 HS System Promega Cat# DC2100 (Continued on next page) Cell Reports Medicine 5, 101376, February 20, 2024 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Human: SW480 ATM KO cell line This study N/A Human: SW480 ATRIP KO cell line This study N/A Human: SW480 ERCC1 KO cell line This study N/A Human: SW480 FANCD2 KO cell line This study N/A Human: SW480 REV1 KO cell line This study N/A Human: A2780 cell line ECACC RRID:CVCL_0134 Human: UWB1.289 cell line ATCC RRID:CVCL_B079 Human: UWB1.289+BRCA1 cell line ATCC RRID:CVCL_B078 Human: KP363T olaparib-resistant cell line This study N/A Human: HROC278MET olaparib-resistant cell line This study N/A Human: KP363T colibactin-tolerant cell line This study N/A Human: KP363T empty long term cell line This study N/A Human: HROC39 colibactin-tolerant cell line This study N/A Oligonucleotides sgRNA targeting ATM 50- CCAAGGCTATTCAGTG TGCG-30 Durinikova et al.33 N/A sgRNA targeting ATRIP 50-GCGAGACTCACTACA TCAGA-30 This study N/A sgRNA targeting ERCC1 50-GCTCTGTGTAGATCG GAATA-30 This study N/A sgRNA targeting FANCD2 50-AAGAAGACTGTCAA AATCTG-30 This study N/A sgRNA targeting REV1 50-AAACTAATGATGTTGC ATGG-30 This study N/A CLBI forward primer 50-CGCTTCATCAACACGC TTTA-30 This study N/A CLBI reverse primer 50-GCAAAAACCGGCTACT TGTC-30 This study N/A CLBO forward primer 50-CGTCGTTATTTACCGC ACCT-30 This study N/A CLBO reverse primer 50-CACTACGCGACCAAGA CAGA-30 This study N/A Recombinant DNA Plasmid: pDRGFP Addgene RRID:Addgene_26475 Plasmid: pCBASceI Addgene RRID:Addgene_26477 Plasmid: lentiCRISPR v2 Addgene RRID:Addgene_52961 Software and algorithms GeneMapper Software v.6 Applied Biosystems RRID:SCR_014290 GraphPad Prism v.8 GraphPad RRID:SCR_002798 ImageJ v1.53a https://ImageJ.nih.gov/ij/ N/A MapSplice v2.2.1 http://www.netlab.uky.edu/p/bioinfo/ http://www.netlab.uky.edu/p/bioinfo/ Samtools v1.14 https://samtools.sourceforge.net/ https://samtools.sourceforge.net/ Ubu 1.2 UNC-Chapel Hill Bioinformatics Utilities https://github.com/mozack/ubu/blob/master/ src/main/java/edu/unc/bioinf/ubu/Ubu.java Rsem v1.3.3 https://github.com/deweylab/RSEM https://github.com/deweylab/RSEM R v4.1 The R Foundation for Statistical Computing https://www.R-project.org/ Tximport Bioconductor https://bioconductor.org/packages/release/ bioc/html/tximport.html Deseq2 Bioconductor https://bioconductor.org/packages/release/ bioc/html/DESeq2.html (Continued on next page) Please cite this article in press as: Sogari et al., Tolerance to colibactin correlates with homologous recombination proficiency and resistance to irinotecan in colorectal cancer cells, Cell Reports Medicine (2023), https://doi.org/10.1016/j.xcrm.2023.101376 Cell Reports Medicine 5, 101376, February 20, 2024 e3 Article ll OPEN ACCESS
Marker:Article Title: Circadian PERIOD proteins regulate TC-DSB repair through anchoring to the nuclear envelope.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse Anti-53BP1 Monoclonal Antibody, Unconjugated, Clone 19 BD Biosciences Cat# 612522; RRID:AB_2206766 Rabbit Anti-ATM (phospho S1981) antibody [EP1890Y] Abcam Cat# ab81292; RRID:AB_1640207 Rabbit Anti-BMAL1 Polyclonal Antibody, Unconjugated Abcam Cat# ab3350; RRID:AB_303729 Rabbit Anti-CLOCK Polyclonal Antibody, Unconjugated Abcam Cat# ab3517; RRID:AB_303866 Rabbit Anti-Cry1 Polyclonal Antibody, Affinity Purified Bethyl, Discontinued Cat# A302-614A; RRID:AB_10555376 Rabbit Anti-Cryptochrome 2 Polyclonal antibody Proteintech Cat# 13997-1-AP; RRID:AB_10860100 Mouse Anti-DDX5 (p68) Monoclonal Antibody, Unconjugated, Clone 204 Millipore Cat# 05-850; RRID:AB_327052 Rabbit Anti-DDX17 Polyclonal antibody Proteintech Cat# 19910-1-AP; RRID:AB_10667004 Mouse Anti-GAPDH Monoclonal Antibody, 6C5 Sigma-Aldrich Cat# MAB374; RRID:AB_2107445 Rabbit Anti-Histone H2A.X, phospho (Ser139) Monoclonal Antibody, Unconjugated, Clone EP854(2)Y Abcam Cat# ab81299; RRID:AB_1640564 Mouse Anti-phospho-Histone H2A.X (Ser139) Monoclonal Antibody, clone JBW301 Sigma-Aldrich Cat# 05-636 RRID:AB_309864 Rabbit Anti-Lamin B1 Polyclonal antibody - Nuclear Envelope Marker Abcam Cat# ab16048; RRID:AB_443298 Rabbit Anti-Mouse Myosin I beta, Nuclear Antibody, Unconjugated Sigma-Aldrich Cat# M3567; RRID:AB_477180 Rabbit Anti-NONO Polyclonal antibody Proteintech Cat# 11058-1-AP; RRID:AB_2152167 Rabbit Anti-Nup153 Polyclonal antibody Abcam Cat# ab84872; RRID:AB_1859766 Rabbit Phospho-p53 (Ser15) Antibody #9284 Cell Signaling Technology Cat# 9284; RRID:AB_331464 Mouse Anti-PCNA (PC10) Monoclonal Antibody Santa Cruz Biotechnology Cat# sc-56; RRID:AB_628110 Rabbit Anti-PER2 Polyclonal antibody Proteintech, Discontinued Cat# 20359-1-AP; RRID:AB_10733224 Rabbit Anti-PER2 Monoclonal antibody [EPR11381(2)] Abcam, Discontinued Cat# ab179813 Rabbit Anti-RAD51 (H-92) Polyclonal antibody Santa Cruz Biotechnology, Discontinued Cat# sc-8349; RRID:AB_2253533 Goat Anti-RNF4 Polyclonal antibody R and D Systems Cat# AF7964; RRID:AB_3644534 Rabbit Anti-RPA32/RPA2 Polyclonal antibody Abcam Cat# ab10359; RRID:AB_297095 Rabbit Anti-SUN1 Polyclonal antibody Sigma-Aldrich Cat# HPA008346; RRID:AB_1080462 Rabbit Anti-SUN1 Monoclonal antibody [EPR6554] Abcam Cat# ab124770; RRID:AB_10976056 Rabbit Anti-SUN2 Monoclonal antibody [EPR6557] Abcam Cat# ab124916; RRID:AB_10972497 (Continued on next page) ll OPEN ACCESSArticle Molecular Cell 85, 1–18.e1–e11, December 18, 2025 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Mouse Anti-alpha-Tubulin Monoclonal Antibody Sigma-Aldrich Cat# T6199; RRID:AB_477583 Goat anti-Rabbit IgG (H+L) Highly CrossAdsorbed Secondary Antibody, Alexa FluorTM 488 Thermo Fisher Scientific Cat# A-11034; RRID:AB_2576217 Goat anti-Rabbit IgG (H+L) Highly CrossAdsorbed Secondary Antibody, Alexa FluorTM 594 Thermo Fisher Scientific Cat# A-11037; RRID:AB_2534095 Goat anti-Mouse IgG (H+L) Highly CrossAdsorbed Secondary Antibody, Alexa FluorTM 488 Thermo Fisher Scientific Cat# A-11029; RRID:AB_2534088 Goat anti-Mouse IgG (H+L) Highly CrossAdsorbed Secondary Antibody, Alexa FluorTM 594 Thermo Fisher Scientific Cat# A-11032; RRID:AB_2534091 Anti-Mouse IgG (Fc specific)–Peroxidase antibody produced in goat Sigma-Aldrich Cat# A2554; RRID:AB_258008 Anti-Rabbit IgG (whole molecule)Peroxidase antibody produced in goat Sigma-Aldrich Cat# A0545; RRID:AB_257896 Chemicals, peptides, and recombinant proteins 4-hydroxytamoxifen (OHT) Sigma-Aldrich Cat# H7904 Auxin: Indole-3-acetic acid sodium salt (IAA) Sigma-Aldrich Cat# I5148 etoposide Sigma-Aldrich Cat# E1383 doxorubicin Sigma-Aldrich Cat# D1515 ATM inhibitor (ATMi) KU-55933 Sigma-Aldrich Cat# SML1109 ATR inhibitor (ATRi) ETP-46464 Sigma-Aldrich Cat# SML1321 DNA-PK inhibitor (DNA-PKi) NU-7441 Selleckchem Cat# S2638 dexamethasone (Dex) Sigma-Aldrich Cat# D4902 Citifluor Clinisciences Cat# AF1-25 EdU (5-éthynyl-2’-désoxyuridine) Thermo Fisher Scientific Cat# A10044 Hoechst 33342 Thermo Fisher Scientific Cat# 62249 AMV reverse transcriptase Promega Cat# M510F Crystal Violet Solution Sigma-Aldrich Cat# V5265 TB GreenTM Premix Ex TaqTM (Tli RNaseH Plus) Takara Cat# RR420L PrimeSTAR Max DNA Polymerase Takara Cat# R045A Nuclease Benzonase Sigma-Aldrich Cat# E1014 RNAseH New England Biolabs Cat# M0297 AsiSI New England Biolabs Cat# R0630 BanI New England Biolabs Cat# R0118 BanII New England Biolabs Cat# R0119 cOmpleteTM Protease Inhibitor Cocktail Roche Cat# 11 836 153 001 Phosphatase Inhibitor Cocktail 2 Sigma-Aldrich Cat# P5726 Critical commercial assays Kit de prolifération cellulaire EdU Click-iTTM pour imagerie, colorant Alexa FluorTM 647 Thermo Fisher Scientific Cat# C10340 NEBuilder HiFi DNA Assembly Cloning Kit New England Biolabs Cat# E5520S QIAprep Spin Miniprep Kit Qiagen Cat# 27104 EndoFree Plasmid Maxi Kit Qiagen Cat# 12362 DNeasy Blood & Tissue Kit Qiagen Cat# 69504 RNeasy Mini Kit Qiagen Cat# 74104 (Continued on next page) ll OPEN ACCESS Article e2 Molecular Cell 85, 1–18.e1–e11, December 18, 2025
Control:Article Title: Alpha-synuclein abundance and localization are regulated by the RNA-binding protein PUMILIO1.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse neuron-specific beta-III Tubulin antibody R and D Systems Cat# MAB1195 RRID: AB_357520 Rabbit anti-Pumilio 1 antibody Abcam Cat# ab92545 RRID:AB_10563695 Anti-Synuclein, alpha Millipore Cat# AB5038 RRID:AB_91648 Goat anti-Pumilio 1, Affinity Purified Bethyl Cat# A300-201A RRID:AB_2253218 Rabbit Anti-Argonaute 2 Monoclonal Cell Signaling Technology Cat# 2897 RRID:AB_2096291 Recombinant Anti-Alpha-synuclein Abcam Cat# ab212184 RRID:AB_2941889 Mouse Anti-Rabbit GADPH Monoclonal Millipore Cat# CB1001 RRID:AB_2107426 alpha Tubulin Abcam Cat# ab24246 RRID:AB_447954 Ataxin 1 - 11750 Huda Zoghbi Lab; Baylor College of Medicine Cat# ATXN1-11750 RRID:AB_2721278 Rabbit control IgG (Purified Rabbit IgG) Bethyl Cat# P120-201 RRID:AB_479830 Mouse neuron-specific anti-beta-III Tubulin Abcam Cat# ab7751 RRID:AB_306045 Chemicals, peptides, and recombinant proteins Dulbecco’s Modified Eagle Medium (DMEM) Thermo Fisher Scientific N/A Fetal Bovine Serum N/A Matrigel in StemFlex Medium Thermo Fisher Scientific Cat# A3349401 mTeSR TM Plus StemCell Technologies Cat# 100-1130 DMEM-F12 Thermo Fisher Scientific Cat# 12634010 Neurobasal-A Thermo Fisher Scientific Cat# 10-888-022 MEM Non-Essential Amino Acids Solution (100X) Thermo Fisher Scientific Cat# 11140050 Penicillin-Streptomycin Millipore Sigma Cat# P4333 β-mercaptoethanol Thermo Fisher Scientific Cat# 31350010 Doxycycline Millipore Sigma Cat# D9891-5G Glutamax Thermo Fisher Scientific Cat# 35050-061 N2 Thermo Fisher Scientific Cat# 17502-048 B27 without Vitamin A Gibco Cat# 12587-010 Geltrex Thermo Fisher Scientific Cat# A1413202 Brain Derived Neurotrophic Factor Gibco Cat# 450-02-50UG Adenosine-3 ′ ,5 ′ -cyclic monophosphate Millipore Sigma Cat# 28745-100MG L-Ascorbic Acid Millipore Sigma Cat# A92902-25G Glial-Derived Neurotrophic Factor Peprotech Cat# 450-10-50 B27 without Vitamin A Gibco Cat# 12587-010 jetPRIME Transfection Reagent Genesee Cat# 55-133 .. Triton X-100 Fisher Scientific Cat# BP151500 (Continued on next page) 16 Cell Reports 44, 116145, August 26, 2025
Purification:Article Title: Alpha-synuclein abundance and localization are regulated by the RNA-binding protein PUMILIO1.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse neuron-specific beta-III Tubulin antibody R and D Systems Cat# MAB1195 RRID: AB_357520 Rabbit anti-Pumilio 1 antibody Abcam Cat# ab92545 RRID:AB_10563695 Anti-Synuclein, alpha Millipore Cat# AB5038 RRID:AB_91648 Goat anti-Pumilio 1, Affinity Purified Bethyl Cat# A300-201A RRID:AB_2253218 Rabbit Anti-Argonaute 2 Monoclonal Cell Signaling Technology Cat# 2897 RRID:AB_2096291 Recombinant Anti-Alpha-synuclein Abcam Cat# ab212184 RRID:AB_2941889 Mouse Anti-Rabbit GADPH Monoclonal Millipore Cat# CB1001 RRID:AB_2107426 alpha Tubulin Abcam Cat# ab24246 RRID:AB_447954 Ataxin 1 - 11750 Huda Zoghbi Lab; Baylor College of Medicine Cat# ATXN1-11750 RRID:AB_2721278 Rabbit control IgG (Purified Rabbit IgG) Bethyl Cat# P120-201 RRID:AB_479830 Mouse neuron-specific anti-beta-III Tubulin Abcam Cat# ab7751 RRID:AB_306045 Chemicals, peptides, and recombinant proteins Dulbecco’s Modified Eagle Medium (DMEM) Thermo Fisher Scientific N/A Fetal Bovine Serum N/A Matrigel in StemFlex Medium Thermo Fisher Scientific Cat# A3349401 mTeSR TM Plus StemCell Technologies Cat# 100-1130 DMEM-F12 Thermo Fisher Scientific Cat# 12634010 Neurobasal-A Thermo Fisher Scientific Cat# 10-888-022 MEM Non-Essential Amino Acids Solution (100X) Thermo Fisher Scientific Cat# 11140050 Penicillin-Streptomycin Millipore Sigma Cat# P4333 β-mercaptoethanol Thermo Fisher Scientific Cat# 31350010 Doxycycline Millipore Sigma Cat# D9891-5G Glutamax Thermo Fisher Scientific Cat# 35050-061 N2 Thermo Fisher Scientific Cat# 17502-048 B27 without Vitamin A Gibco Cat# 12587-010 Geltrex Thermo Fisher Scientific Cat# A1413202 Brain Derived Neurotrophic Factor Gibco Cat# 450-02-50UG Adenosine-3 ′ ,5 ′ -cyclic monophosphate Millipore Sigma Cat# 28745-100MG L-Ascorbic Acid Millipore Sigma Cat# A92902-25G Glial-Derived Neurotrophic Factor Peprotech Cat# 450-10-50 B27 without Vitamin A Gibco Cat# 12587-010 jetPRIME Transfection Reagent Genesee Cat# 55-133 .. Triton X-100 Fisher Scientific Cat# BP151500 (Continued on next page) 16 Cell Reports 44, 116145, August 26, 2025
Modification:Article Title: Alpha-synuclein abundance and localization are regulated by the RNA-binding protein PUMILIO1.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse neuron-specific beta-III Tubulin antibody R and D Systems Cat# MAB1195 RRID: AB_357520 Rabbit anti-Pumilio 1 antibody Abcam Cat# ab92545 RRID:AB_10563695 Anti-Synuclein, alpha Millipore Cat# AB5038 RRID:AB_91648 Goat anti-Pumilio 1, Affinity Purified Bethyl Cat# A300-201A RRID:AB_2253218 Rabbit Anti-Argonaute 2 Monoclonal Cell Signaling Technology Cat# 2897 RRID:AB_2096291 Recombinant Anti-Alpha-synuclein Abcam Cat# ab212184 RRID:AB_2941889 Mouse Anti-Rabbit GADPH Monoclonal Millipore Cat# CB1001 RRID:AB_2107426 alpha Tubulin Abcam Cat# ab24246 RRID:AB_447954 Ataxin 1 - 11750 Huda Zoghbi Lab; Baylor College of Medicine Cat# ATXN1-11750 RRID:AB_2721278 Rabbit control IgG (Purified Rabbit IgG) Bethyl Cat# P120-201 RRID:AB_479830 Mouse neuron-specific anti-beta-III Tubulin Abcam Cat# ab7751 RRID:AB_306045 Chemicals, peptides, and recombinant proteins Dulbecco’s Modified Eagle Medium (DMEM) Thermo Fisher Scientific N/A Fetal Bovine Serum N/A Matrigel in StemFlex Medium Thermo Fisher Scientific Cat# A3349401 mTeSR TM Plus StemCell Technologies Cat# 100-1130 DMEM-F12 Thermo Fisher Scientific Cat# 12634010 Neurobasal-A Thermo Fisher Scientific Cat# 10-888-022 MEM Non-Essential Amino Acids Solution (100X) Thermo Fisher Scientific Cat# 11140050 Penicillin-Streptomycin Millipore Sigma Cat# P4333 β-mercaptoethanol Thermo Fisher Scientific Cat# 31350010 Doxycycline Millipore Sigma Cat# D9891-5G Glutamax Thermo Fisher Scientific Cat# 35050-061 N2 Thermo Fisher Scientific Cat# 17502-048 B27 without Vitamin A Gibco Cat# 12587-010 Geltrex Thermo Fisher Scientific Cat# A1413202 Brain Derived Neurotrophic Factor Gibco Cat# 450-02-50UG Adenosine-3 ′ ,5 ′ -cyclic monophosphate Millipore Sigma Cat# 28745-100MG L-Ascorbic Acid Millipore Sigma Cat# A92902-25G Glial-Derived Neurotrophic Factor Peprotech Cat# 450-10-50 B27 without Vitamin A Gibco Cat# 12587-010 jetPRIME Transfection Reagent Genesee Cat# 55-133 .. Triton X-100 Fisher Scientific Cat# BP151500 (Continued on next page) 16 Cell Reports 44, 116145, August 26, 2025
Derivative Assay:Article Title: Alpha-synuclein abundance and localization are regulated by the RNA-binding protein PUMILIO1.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse neuron-specific beta-III Tubulin antibody R and D Systems Cat# MAB1195 RRID: AB_357520 Rabbit anti-Pumilio 1 antibody Abcam Cat# ab92545 RRID:AB_10563695 Anti-Synuclein, alpha Millipore Cat# AB5038 RRID:AB_91648 Goat anti-Pumilio 1, Affinity Purified Bethyl Cat# A300-201A RRID:AB_2253218 Rabbit Anti-Argonaute 2 Monoclonal Cell Signaling Technology Cat# 2897 RRID:AB_2096291 Recombinant Anti-Alpha-synuclein Abcam Cat# ab212184 RRID:AB_2941889 Mouse Anti-Rabbit GADPH Monoclonal Millipore Cat# CB1001 RRID:AB_2107426 alpha Tubulin Abcam Cat# ab24246 RRID:AB_447954 Ataxin 1 - 11750 Huda Zoghbi Lab; Baylor College of Medicine Cat# ATXN1-11750 RRID:AB_2721278 Rabbit control IgG (Purified Rabbit IgG) Bethyl Cat# P120-201 RRID:AB_479830 Mouse neuron-specific anti-beta-III Tubulin Abcam Cat# ab7751 RRID:AB_306045 Chemicals, peptides, and recombinant proteins Dulbecco’s Modified Eagle Medium (DMEM) Thermo Fisher Scientific N/A Fetal Bovine Serum N/A Matrigel in StemFlex Medium Thermo Fisher Scientific Cat# A3349401 mTeSR TM Plus StemCell Technologies Cat# 100-1130 DMEM-F12 Thermo Fisher Scientific Cat# 12634010 Neurobasal-A Thermo Fisher Scientific Cat# 10-888-022 MEM Non-Essential Amino Acids Solution (100X) Thermo Fisher Scientific Cat# 11140050 Penicillin-Streptomycin Millipore Sigma Cat# P4333 β-mercaptoethanol Thermo Fisher Scientific Cat# 31350010 Doxycycline Millipore Sigma Cat# D9891-5G Glutamax Thermo Fisher Scientific Cat# 35050-061 N2 Thermo Fisher Scientific Cat# 17502-048 B27 without Vitamin A Gibco Cat# 12587-010 Geltrex Thermo Fisher Scientific Cat# A1413202 Brain Derived Neurotrophic Factor Gibco Cat# 450-02-50UG Adenosine-3 ′ ,5 ′ -cyclic monophosphate Millipore Sigma Cat# 28745-100MG L-Ascorbic Acid Millipore Sigma Cat# A92902-25G Glial-Derived Neurotrophic Factor Peprotech Cat# 450-10-50 B27 without Vitamin A Gibco Cat# 12587-010 jetPRIME Transfection Reagent Genesee Cat# 55-133 .. Triton X-100 Fisher Scientific Cat# BP151500 (Continued on next page) 16 Cell Reports 44, 116145, August 26, 2025
Transfection:Article Title: Alpha-synuclein abundance and localization are regulated by the RNA-binding protein PUMILIO1.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse neuron-specific beta-III Tubulin antibody R and D Systems Cat# MAB1195 RRID: AB_357520 Rabbit anti-Pumilio 1 antibody Abcam Cat# ab92545 RRID:AB_10563695 Anti-Synuclein, alpha Millipore Cat# AB5038 RRID:AB_91648 Goat anti-Pumilio 1, Affinity Purified Bethyl Cat# A300-201A RRID:AB_2253218 Rabbit Anti-Argonaute 2 Monoclonal Cell Signaling Technology Cat# 2897 RRID:AB_2096291 Recombinant Anti-Alpha-synuclein Abcam Cat# ab212184 RRID:AB_2941889 Mouse Anti-Rabbit GADPH Monoclonal Millipore Cat# CB1001 RRID:AB_2107426 alpha Tubulin Abcam Cat# ab24246 RRID:AB_447954 Ataxin 1 - 11750 Huda Zoghbi Lab; Baylor College of Medicine Cat# ATXN1-11750 RRID:AB_2721278 Rabbit control IgG (Purified Rabbit IgG) Bethyl Cat# P120-201 RRID:AB_479830 Mouse neuron-specific anti-beta-III Tubulin Abcam Cat# ab7751 RRID:AB_306045 Chemicals, peptides, and recombinant proteins Dulbecco’s Modified Eagle Medium (DMEM) Thermo Fisher Scientific N/A Fetal Bovine Serum N/A Matrigel in StemFlex Medium Thermo Fisher Scientific Cat# A3349401 mTeSR TM Plus StemCell Technologies Cat# 100-1130 DMEM-F12 Thermo Fisher Scientific Cat# 12634010 Neurobasal-A Thermo Fisher Scientific Cat# 10-888-022 MEM Non-Essential Amino Acids Solution (100X) Thermo Fisher Scientific Cat# 11140050 Penicillin-Streptomycin Millipore Sigma Cat# P4333 β-mercaptoethanol Thermo Fisher Scientific Cat# 31350010 Doxycycline Millipore Sigma Cat# D9891-5G Glutamax Thermo Fisher Scientific Cat# 35050-061 N2 Thermo Fisher Scientific Cat# 17502-048 B27 without Vitamin A Gibco Cat# 12587-010 Geltrex Thermo Fisher Scientific Cat# A1413202 Brain Derived Neurotrophic Factor Gibco Cat# 450-02-50UG Adenosine-3 ′ ,5 ′ -cyclic monophosphate Millipore Sigma Cat# 28745-100MG L-Ascorbic Acid Millipore Sigma Cat# A92902-25G Glial-Derived Neurotrophic Factor Peprotech Cat# 450-10-50 B27 without Vitamin A Gibco Cat# 12587-010 jetPRIME Transfection Reagent Genesee Cat# 55-133 .. Triton X-100 Fisher Scientific Cat# BP151500 (Continued on next page) 16 Cell Reports 44, 116145, August 26, 2025
Produced:
Article Title: Beta-coronaviruses exploit cellular stress responses by modulating TFEB and TFE3 activity.
Article Snippet: Antibodies Caspase-3 (D3R6Y) Rabbit mAb Cell Signaling Technology Cat# 9664; RRID:AB_2798429 Cleaved Caspase-3 (Asp175) (5A1E) Rabbit mAb Cell Signaling Technology Cat# 9664, RRID:AB_2070042 PARP Antibody Cell Signaling Technology Cat# 9542, RRID:AB_2160739 Cleaved PARP (Asp214) (D64E10) XP Rabbit mAb Cell Signaling Technology Cat# 5625, RRID:AB_10699459 Caspase-9 (C9) Mouse mAb Cell Signaling Technology Cat# 9508, RRID:AB_2068620 Cleaved Caspase-9 (Asp330) (E5Z7N) Rabbit mAb Cell Signaling Technology Cat# 52873, RRID:AB_2799423 Caspase-7 (D2Q3L) Rabbit Antibody Cell Signaling Technology Cat# 12827, RRID:AB_2687912 Cleaved Caspase-7 (Asp198) (D6H1) Rabbit mAb Cell Signaling Technology Cat# 8438; RRID:AB_11178377 Anti-rabbit IgG, HRP-linked Antibody Cell Signaling Technology Cat# 7074, RRID:AB_2099233 Anti-mouse IgG, HRP-linked Antibody Cell Signaling Technology Cat# 7076, RRID:AB_330924 TFE3 Antibody Cell Signaling Technology Cat# 14779, RRID:AB_2687582 TFEB Antibody Cell Signaling Technology Cat# 4240, RRID:AB_11220225 GAPDH Monoclonal Antibody (6C5) Thermo Fisher Scientific Cat# AM4300, RRID:AB_2536381 Goat anti-Rabbit IgG (Heavy Chain), Superclonal Recombinant Secondary Antibody, Alexa Fluor 488 Thermo Fisher Scientific Cat# A27034, RRID:AB_2536097 .. Recombinant Secondary Antibody, Alexa Fluor 555 Thermo Fisher Scientific Cat# A27039, RRID:AB_2536100 LAMP-1 (human) DSHB Cat# H4A3, RRID:AB_2296838 p70 S6 Kinase Antibody Cell Signaling Technology Cat# 9202, RRID:AB_331676 Phospho-p70 S6 Kinase (Thr389) Antibody Cell Signaling Technology Cat# 9205, RRID:AB_330944 Phospho-4E-BP1 (Ser65) Antibody Cell Signaling Technology Cat# 9451, RRID:AB_330947 4E-BP1 (53H11) Rabbit mAb Cell Signaling Technology Cat# 9644, RRID:AB_2097841 Phospho-Stat3 (Tyr705) (D3A7) XP Rabbit mAb Cell Signaling Technology Cat# 9145, RRID:AB_2491009 Stat3 (D3Z2G) Rabbit mAb #12640 Cell Signaling Technology Cat# 12640, RRID:AB_2629499 Calnexin (C5C9) Rabbit mAb Cell Signaling Technology Cat# 2679, RRID:AB_2228381 Pan-Calcineurin A Antibody Cell Signaling Technology Cat# 2614, RRID:AB_2168458 Phospho-TFEB (Ser211) (E9S8N) Rabbit mAb Cell Signaling Technology Cat# 37681, RRID:AB_2799117 Phospho-Stat3 (Ser727) Cell Signaling Technology Cat# 34911, RRID:AB_2737598 Histone H3 (D1H2) XP Rabbit mAb Cell Signaling Technology Cat# 4499, RRID:AB_10544537 NFAT1 (D43B1) XP Rabbit mAb Cell Signaling Technology Cat# 5861, RRID:AB_10834808 Rabbit anti-TFEB Antibody, Affinity Purified Bethyl Cat# A303-673A, RRID:AB_1120475 Anti-TFE3 antibody produced in rabbit Sigma-Aldrich Cat# HPA023881, RRID:AB_1857931 Anti-phospho S321 TFE3 Martina et al., 201655 N/A Anti-MHV(MJ1.3) Ghosh et al., 202030 N/A .. Unconjugated Bio-Rad Cat# AHP1586, RRID:AB_2303333 Anti-p18 INK, C-Terminal antibody produced in rabbit Sigma-Aldrich Cat# SAB4500079, RRID:AB_10742707 NF-kB p65 (D14E12) XP Rabbit mAb #8242 Cell Signaling Technology Cat# 8242, RRID:AB_10859369 Phospho-NF-kB p65 (Ser536) (93H1) Rabbit mAb #3033 Cell Signaling Technology Cat# 3033, RRID:AB_331284 Phospho-IkBa (Ser32) (14D4) Rabbit mAb #2859 Cell Signaling Technology Cat# 2859, RRID:AB_561111 (Continued on next page) 18 iScience 26, 106169, March 17, 2023
Chromatin Immunoprecipitation:
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Bethyl is a verified supplier 