KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| anti-PCNA | Santa Cruz | sc-56 |
| anti-γH2AX | Millipore | 05-636 |
| anti-phospho-P53 | Cell Signaling | 9286 |
| anti-RAD18 | Cell Signaling | 9040S |
| anti-Tubulin | Abeam | ab6046 |
| anti-GFP | Thermo Fisher | A11122 |
| Anti-rabbit IgG, HRP-linked Antibody | Cell Signaling | 7074 |
| Anti-mouse IgG, HRP-linked Antibody | Cell Signaling | 7076 |
| Goat anti-Mouse IgG (H+L) Highly Cross-Adsorbed Secondary Antibody, Alexa Fluor 647 | Invitrogen | A21236 |
| anti-Pol IV polyclonal | Kim et al., 2001 | N/A |
| anti-RuvC (5G9/3) monoclonal | Santa Cruz | sc-53437 |
| anti-Mouse IgG | Bethyl Laboratories | A90-116D5 |
| anti-Goat IgG | Bethyl Laboratories | A50-100D5 |
| Bacterial and Virus Strains | ||
| E. coli mobile plasmid overexpression library | (Saka et al., 2005) | N/A |
| See Table S7 for all bacterial strains used | ||
| Human cell lines | ||
| MRC5-SV40 | Stephen P. Jackson Lab | N/A |
| HEK293T | ATCC | CRL3216 |
| Plasmid | ||
| See Tables S5 and S7 for all plasmids used | ||
| Chemicals | ||
| GenJet™ In Vitro DNA Transfection Reagent | SignaGen Laboratories | SL100489 |
| Polyethylenimine | Polysciences | 23966 |
| Lipofectamine RNAiMAX Transfection Reagent | Invitrogen | 13778030 |
| N-acetyl cysteine | Sigma | A7250 |
| DNA-PK inhibitor | Tocris Bioscience | NU7441 |
| 6-thioguanine | Sigma | A4882 |
| Critical Commercial assays | ||
| FM® 4-64FX | Thermo Fisher | F34653 |
| DHR123 | Thermo Fisher | D23806 |
| pHrodo® Green AM Intracellular pH indicator | Thermo Fisher | P35373 |
| RNeasy Mini Kit | Qiagen | 74104 |
| RiboZero | Illumina | MRZB12424 |
| TruSeq Stranded mRNA Library Preparation Kit | Illumina | RS-122-2001 |
| qPCR-based Illumina Library Quantification Kit | KAPA Biosystems | KK4828 |
| Dneasy Blood & Tissue kits | Qiagen | 69506 |
| QIAprep Spin Miniprep Kit | Qiagen | 27106 |
| Gateway™ LR Clonase™ II Enzyme mix | Invitrogen | 11791100 |
| SuperScript™ III Reverse Transcriptase | Invitrogen | 18080-093 |
| Q5 High-Fidelity DNA Polymerase | New England Biolabs | M0491S |
| Oligonucleotides | ||
| ON-TARGETplus Non-targeting Pool | Dharmacon | D-001810-10-05 |
| siRAD18 ACUCAGUGUCCAACUUGCU | Sigma | N/A |
| cI forward primer ACCGCGGCGTGGGTAGTAAAGT | (Gutierrez et al., 2013) | N/A |
| cI reverse primer GCCAATCCCCATGGCATCGAGTAAC | (Gutierrez et al., 2013) | N/A |
| Deposited Data | ||
| RNA-Seq data | This paper | ENA: E-MTAB-7361 |
| ChIP-Seq data | This paper | ENA: PRJEB21035 |
| Software and Algorithms | ||
| cBioportal | Gao et al., 2013 | http://www.cbioportal.org/ |
| R programming language | R Development Core Team, 2015. | https://www.R-project.org/ |
| E. coli-to-Cancer Gene-function Atlas (ECGA) | This paper | https://microbialphenotypes.org/wiki/index.php/Special:ECGA |
| R package for progeny clustering: ProgenyClust | CRAN | https://cran.r-project.org/ |
| Trimmomatic | The Usadel lab | http://www.usadellab.org/cms/?page=trimmomatic |
| BWA-MEM | Li, 2013 | N/A |
| deepTools | Bioinformatics Facility at the Max Planck Institute for Immunobiology and Epigenetics, Freiburg | https://deeptools.readthedocs.io/en/develop/ |
| MOSAICS | CRAN | https://cran.r-project.org/ |
| Rockhopper | McClure et al., 2013 | N/A |
| Prism | GraphPad | https://www.graphpad.com/scientific-software/prism/ |
| R programming language | R Development Core Team, 2015. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. | https://www.R-project.org/ |
| FlowJo 10.2 | FLOWJO | https://www.flowjo.com/ |
| STRING 10.0 | (Szklarczyk et al., 2015) | https://string-db.org/ |
| FACSDivaTM | BD Biosciences | http://www.bdbiosciences.com |
| Advanced Imaging collection In Pipeline pilot 8.5 or 9.2 | Biovia-Dassault Systems | N/A |
| Softworx | GE | N/A |
| BLASTp and delta BLAST | NCBI | https://blast.ncbi.nlm.nih.gov/Blast.cgI |
| RNA-sequencing data | The Cancer Genome Atlas | N/A |
| Gene-Set Enrichment Analysis (ssGSEA) using GSVA package | CRAN | https://cran.r-project.org/ |