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sw480 fancd2 ko cell line  (ATCC)


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    ATCC sw480 fancd2 ko cell line
    Sw480 Fancd2 Ko Cell Line, supplied by ATCC, used in various techniques. Bioz Stars score: 99/100, based on 7419 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/sw480+fancd2+ko+cell+line/SW480/pmc10897517__mmc4-188-33-60
    Average 99 stars, based on 7419 article reviews
    sw480 fancd2 ko cell line - by Bioz Stars, 2026-11
    99/100 stars

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    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 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 .. 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) Cell Reports Medicine 5, 101376, February 20, 2024 e3 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 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 .. 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) Cell Reports Medicine 5, 101376, February 20, 2024 e3 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 ..

    Software:

    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 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 .. 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) Cell Reports Medicine 5, 101376, February 20, 2024 e3 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 ..

    Homologous Recombination:

    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 ..



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