| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Mouse monoclonal antibody anti-H2AX-phospho-serine139 (anti-γH2AX) IgG1κ, clone JBW301, use at 1:500 dilution | Merck Sigma-Aldrich | Cat# 05-636-I; RRID:AB_2755003 |
| Mouse monoclonal antibody anti-p53 Binding Protein 1 (anti-53BP1) IgG1, clone BP13, use at 1:750 dilution | Merck Sigma-Aldrich | Cat# MAB3802; RRID:AB_2206767 |
| Mouse monoclonal anti-Tubulin, clone DMA1, ascites fluid, use at 1:1000 dilution | Merck Sigma-Aldrich | Cat# T-9026; RRID:AB_477593) |
| Donkey anti-Mouse IgG (H + L) Alexa Fluor 647 conjugated, use at 1:500 dilution | Thermo Fisher Scientific | Cat# A-31571; RRID: AB_162542 |
| Peroxidase-AffiniPure Goat Anti-Mouse IgG (H + L), use at 1:10 000 dilution | Jackson ImmunoResearch Labs | Cat# 115-035-003; RRID: AB_10015289 |
| Chemicals, peptides, and recombinant proteins | ||
| Phosphate-buffered saline (PBS) tablets | EUROMEDEX | Cat# EU1-2052-100 |
| (S)-(+)-Camptothecin (CPT) | Merck Sigma-Aldrich | Cat# C9911-100 mg; CAS: 7689-03-4 |
| Dimethyl sulfoxide (DMSO) | Merck Sigma-Aldrich | Cat# D8418-100 mL; CAS: 67-68-5 |
| 5′-Ethylene-2′-deoxyuridine (EdU) | Thermo Fisher Scientific | Cat# A10044 |
| PIPES | Merck Sigma-Aldrich | Cat# P1851; CAS: 5625-37-6 |
| Sucrose | Merck Sigma-Aldrich | Cat# S0389; CAS: 57-50-1 |
| TritonTM X-100 | Merck Sigma-Aldrich | Cat# 1.08603.1000; CAS: 9036-19-5 |
| MgCl2 1 M | Thermo Fisher Scientific | Cat# AM9530G |
| NaCl | Merck Sigma-Aldrich | Cat# 31434-1KG-M; CAS: 7647-14-5 |
| Tris-HCl 1 M, pH 7.5 | Thermo Fisher Scientific | Cat# 15567027 |
| Tris-HCl 0.5 M, pH 8.5 | Thermo Fisher Scientific | Cat# J62131.AP |
| cOmpleteTM, Mini, EDTA-free Protease Inhibitor Cocktail, Roche | Merck Sigma-Aldrich | Cat# 4693159001 |
| Paraformaldehyde (PFA), 16% (v/v) solution | Electron Microscopy Sciences | Cat# EM-15710 |
| Bovine serum albumin (BSA), standard grade | Interchim | Cat# UPQ84170; CAS: 9048-46-8 |
| (+) Sodium L-ascorbate | Merck Sigma-Aldrich | Cat# A4034; CAS: 134-03-2 |
| Copper (II) sulfate, anhydrous, 98%, Alfa Aesar | Thermo Fisher Scientific | Cat# A13986.30; CAS: 7758-98-7 |
| Alexa Fluor 488 Azide (Alexa Fluor 488 5-Carboxamido-(6-Azidohexanyl), Bis(Triethylammonium Salt)), 5-isomer) | Thermo Fisher Scientific | Cat# A10266 |
| 4′,6-Diamidine-2′-phenylindole dihydrochloride (DAPI) | Merck Sigma-Aldrich | Cat# D9542-5MG; CAS: 28718-90-3 |
| 1,4-Diazobicyclo-[2.2.2]-octane (DABCO) | Merck Sigma-Aldrich | Cat# D27802-25G; CAS: 280-57-9 |
| Glycerol, anhydrous, ≥99.5% (GC) | Honeywell | Cat# 49770; CAS: 56-81-5 |
| Mowiol® 4-88 | Merck Sigma-Aldrich | Cat# 813381-50G |
| UltraPure™ DNase/RNase-Free Distilled water | Thermo Fisher Scientific | Cat# 10977-035 |
| Accutase | Biowest | Cat# L0950 |
| LipofectamineTM RNAiMAX | Thermo Fisher Scientific | Cat# 13778075 |
| Deposited data | ||
| Raw and analyzed images | This paper | Zenodo DOI (https://doi.org/10.5281/zenodo.8014997) |
| Fiji-script to convert files to TIF images (00_Convert Files to TIF) | This paper, adapted from the script (Export_Images_Folder.ijm) from Olivier Burri, EPFL | https://gist.github.com/lacan/16e12482b52f539795e49cb2122060cc |
| Fiji-script (01_Shading-Dark correction_v2.ijm) | This paper | Zenodo DOI (https://doi.org/10.5281/zenodo.8014997 |
| Fiji-script (02_StarDist-QIBC_v12.ijm) | This paper | Zenodo DOI (https://doi.org/10.5281/zenodo.8014997 |
| Canava (SpotFire) for QIBC multivariate representations | This paper | Zenodo DOI (https://doi.org/10.5281/zenodo.8014997 |
| Step-by-step Fiji-script tutorials and video | This paper | Zenodo DOI (https://doi.org/10.5281/zenodo.8014997 |
| Experimental models: Cell lines | ||
| U-2 OS | RRID: CVCL_0042 | |
| Oligonucleotides | ||
| Non-targeting Pool siRNA (siCTL) | Dharmacon | Cat# D-001810-10-05 |
| ON-TARGET plus Smart pool Human TP53BP1 siRNA (si53BP1) | Dharmacon | Cat# L-003548-00-0010 |
| Software and algorithms | ||
| MetaMorph Microscopy Automation and Image Analysis Software (Version 7.10.4.407) | Molecular Devices | RRID:SCR_002368 |
| Scan slide interface for MataMorph | Gataca Systems® | nD-SCAN |
| Fiji (ImageJ version > 1.53d)ji | RRID:SCR_002285 https://imagej.net/software/fiji/downloads | |
| Fiji plugin for StarDist - Object Detection with Star-convex Shapes15 |
https://github.com/StarDist/StarDist https://imagej.net/StarDist |
|
| Fiji plugin for CSBDeep (Require to use StarDist) | https://github.com/CSBDeep/CSBDeep_fiji | |
| SpotFire (Desktop Version 11.4.2) | Tipco | RRID:SCR_008858 |
| Prism (Version v9.4.0) | GraphPad | RRID:SCR_005375 |
| Other | ||
| CO2 incubator, temperature 37°C, 5% CO2, 95% humidity, HeraCell 150 | Thermo Fisher Scientific | Cat# 51026282 |
| DMEM with 4,5 g/L of glucose | Biowest | Cat# L0101-500 |
| Fetal bovine serum (FBS) | Thermo Fisher Scientific | Cat# 10270 |
| 2 mM L-glutamine | EUROBIO | Cat# CSTGLU00-0U |
| 10 UI/mL Penicillin, 100 μg/mL Streptomycin | EUROBIO | Cat# CABPES01-0U |
| Accutase | Biowest | Cat# L0950 |
| Automated cell counter TC20 | Bio-Rad | Cat# 1450102 |
| Cell counting dual-chamber slide | Bio-Rad | Cat# 1450003 |
| 6-well tissue culture plates | TPP | Cat# 9206 |
| Conical tubes, 15 mL and 50 mL | TPP | Cat# 191015 and 19050 |
| Pipets P1000, P200, P20, P10 | Gilson | |
| Vacuum pump | Rocker | Cat# 169300-22 |
| Round coverslip, 22 mm diameter, #1½ (0.16–0.19 mm) | Electron Microscopy Sciences | Cat# EM-72224-01 |
| GSR D1® gamma irradiator | Gamma-Service Medical GmbH | |
| Humidity chamber | StainTray M920 | Cat# 631-1923 |
| Microscopy slides Epredia™ SuperFrost Plus™ Adhesion slides | Thermo Fisher Scientific | Cat# 10149870 |
| Autofluorescent plastics slides | Chroma | Cat# 92001 |
| Transparent nail polish | Mavala | colorless N°43 |
| NuPAGE Novex 4%–12% Bis-Tris pre-cast gels | Thermo Fisher Scientific | Cat# NW04120BOX |
| NuPAGE Transfer Buffer | Thermo Fisher Scientific | Cat# NP0006 |
| Nitrocellulose membrane | Amersham Protran | Cat# 10600001 |
| Widefield inverted microscope DMI6000B with Adaptive Focus Control system | Leica Microsystems | Cat# 11888945 |
| HC PL APO 40×/0,95 CORR objective | Leica Microsystems | Cat# 506414 |
| Lumen 200S Fluorescence Illumination System | Prior Scientific | Cat# L200S |
| Motorized scanning stage for DMI6000B | Märzhäuser | Cat# SCAN IM 127x83 |
| Two fast filter wheel Lambda 10-3, one for excitation and one for emission | Sutter Instrument® | Cat# LB10-3 |
| Quad Sedat D/F/Cy3/Cy5 band dichroic mirror | Semrock®/AHF analysentechnik AG | Cat# F66-988 |
| Band-pass filter for DAPI excitation AT350/50× | Chroma Technology/AHF analysentechnik AG | Cat# F34-000SG |
| Band-pass filter for FITC excitation ET490/20× | Chroma Technology/AHF analysentechnik AG | Cat# F49-490SG |
| Band-pass filter for CY3 excitation ET555/25× | Chroma Technology/AHF analysentechnik AG | Cat# F49-555SG |
| Band-pass filter for CY5 excitation ET645/30× | Chroma Technology/AHF analysentechnik AG | Cat# F49-645SG |
| Band-pass filter for DAPI emission ET455/50m | Chroma Technology/AHF analysentechnik AG | Cat# F47-456 |
| Band-pass filter for FITC emission ET525/36m | Chroma Technology/AHF analysentechnik AG | Cat# F47-526 |
| Band-pass filter for CY3 emission ET605/52m | Chroma Technology/AHF analysentechnik AG | Cat# F47-606 |
| Band-pass filter for CY5 emission ET705/72m | Chroma Technology/AHF analysentechnik AG | Cat# F47-705 |
| ORCA-Fusion Digital sCMOS camera | Hamamatsu® | Cat# C14440-20UP |
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