REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
BrdU Mouse monoclonal	BD Biosciences	Cat# 347580; RRID:AB_10015219
Phospho-Histone H2A.X (Ser139) Mouse monoclonal	Millipore	Cat#05-636; RRID:AB_309864
Phospho-Histone H2A.X (Ser139) Rabbit polyclonal	Cell Signaling	Cat# 2577; RRID:AB_2118010
RPA70/RPA1 Rabbit polyclonal	Cell Signaling	Cat# 2267; RRID:AB_2180506
P97/VCP Rabbit polyclonal	Proteintech	Cat# 10736-1-AP; RRID:AB_2214635
53BP1 Rabbit polyclonal	Cell Signaling	Cat# 4937; RRID:AB_10694558
RAD51 Mouse monoclonal	Santa Cruz	Cat# 398587; RRID:AB_2756353
RAD52 Mouse monoclonal	Santa Cruz	Cat# 365341; RRID:AB_10851346
RAD50 Mouse monoclonal	Abcam	Cat# 89; RRID:AB_2176935
MRE11 Rabbit polyclonal	Abcam	Cat# 33125; RRID:AB_776530
MRE11 Mouse monoclonal	Abcam	Cat# ab214; RRID:AB_302859
L3MBTL1 Rabbit polyclonal	Abcam	Cat# ab51880; RRID:AB_873913
MAD2B Mouse monoclonal	BD Biosciences	Cat# 612266; RRID:AB_399583
NBS1 Mouse monoclonal	BD Biosciences	Cat# 611870; RRID:AB_399350
Vinculin Mouse monoclonal	Abcam	Cat# ab18058; RRID:AB_444215
Lamin A/C Mouse monoclonal	Cell Signaling	Cat# 4777; RRID:AB_10545756
Histone H2B Rabbit monoclonal	Cell Signaling	Cat# 12364; RRID:AB_2714167
Alexa Fluor 488 Rabbit polyclonal	Thermo Fisher Scientific	Cat# A-11034; RRID:AB_2576217
Alexa Fluor 488 Mouse polyclonal	Thermo Fisher Scientific	Cat# A-21202; RRID:AB_141607
Alexa Fluor 568 Rabbit polyclonal	Thermo Fisher Scientific	Cat# A-11011; RRID:AB_143157
Alexa Fluor 568 Mouse polyclonal	Thermo Fisher Scientific	Cat# A-10037; RRID:AB_2534013
RPA32/RPA2 (phospho S4+S8) rabbit polyclonal	Abcam	Cat# ab87277; RRID:AB_1952482
KU80 Mouse monoclonal	Abcam	Cat# 119935; RRID:AB_10899161
Lamin B1 Rabbit polyclonal	Thermo Fisher Scientific	Cat# PA5-19468; RRID:AB_10985414
Mouse 800 secondary	LI-COR	Cat# 925-32210; RRID:AB_2687825
Rabbit 680 secondary	LI-COR	Cat# 925-68021; RRID:AB_2713919
β-actin Mouse monoclonal	Thermo Fisher Scientific	Cat# AM4302; RRID:AB_437394
β-actin Rabbit (13E5) monoclonal	Cell Signaling	Cat# 4970; RRID:AB_2223172
Control Rabbit IgG	Non-commercial	Kristijan Ramadan Lab
Rabbit IgG (HRP conjugated) Goat polyclonal	Sigma-Aldrich	Cat# A9169; RRID:AB_258434
Mouse IgG (HRP conjugated) Rabbit polyclonal	Sigma-Aldrich	Cat# A9044; RRID:AB_258431
Biological samples
Bladder cancer human tumor samples (HGT1)	Oxford Radcliffe Biobank	http://orb.ndcls.ox.ac.uk
Chemicals, peptides, and recombinant proteins
BrdU	Sigma-Aldrich	Cat# B5002
EdU	Thermo Fisher Scientific	Cat# A10044
Cycloheximide	Sigma-Aldrich	Cat# C1988
Benzonase	Millipore	Cat# 71205
Doxycycline	PanReac AppliChem	Cat# A2951,0025
Hoechst 3325	Sigma-Aldrich	Cat# 23491-45-4
RNase A (10 mg/mL)	Thermo Fisher Scientific	Cat# EN0531
ProLong Diamond antifade with DAPI	Thermo Fisher Scientific	Cat# P36962
cOmplete, Mini, EDTA-free Protease Inhibitor Cocktail	Roche	Cat# 11836170001
Intercept® (PBS) Blocking Buffer	LI-COR	Cat# 927-70001
Sequencing Grade Modified Trypsin	Promega	Cat# V5111
BSA	Sigma-Aldrich	Cat# 9048-46-8
Fisher Bioreagents Phosphatase Inhibitor Cocktail I	Thermo Fisher Scientific	Cat# 12821650
Pierce Protease Inhibitor Mini Tablets, EDTA-free	Thermo Fisher Scientific	Cat# A32955
Hoechst 33342	Thermo Fisher Scientific	Cat# H3570
Lipofectamine RNAiMAX	Thermo Fisher Scientific	Cat# 13778-150
QIAGEN maxiprep kit	QIAGEN	Cat# 12362
FuGENE Transfection Reagent	Promega	Cat# E2311
jetPRIME Transfection Reagent	Polyplus-transfection	Cat# 114-01
Opti-MEM reduced serum medium	Thermo Fisher Scientific	Cat# 11058021
CB-5083	MedChem Express	Cat# HY-12861
Mirin	Sigma-Aldrich	Cat# M9948
PFM01	Tocris	Cat# 6222
PFM39	Sigma-Aldrich	Cat# SML1839
DMSO	Sigma-Aldrich	Cat# D2650
Methyl cellulose	Thermo Fisher Scientific	Cat# 155496
NEM	Sigma-Aldrich	Cat# EE3876-25G
Tween-20	Sigma-Aldrich	Cat# P7949
Tween-80	Sigma-Aldrich	Cat# 9005-65-6
Puromycin	GIBCO	Cat# A11138-03
G-418	Sigma-Aldrich	Cat# 108321-42-2
Gefitinib	Sigma-Aldrich	Cat# SML1657
Matrigel	BD Biosciences	Cat# 356237
PBS	GIBCO	Cat# 10010023
20X Transfer buffer	Bio-Rad	Cat# 10026938
10X Running buffer	Bio-Rad	Cat# 1610772
Laemmli 2X concentrate	Sigma-Aldrich	Cat# S3401
Antibody diluent	LI-COR	Cat# 927-75001
Hydroxyurea (HU)	Sigma	Cat# H8627
Triton X-100	Sigma-Aldrich	Cat# T8787
HEPES	Sigma-Aldrich	Cat# H4034
Sucrose	Sigma-Aldrich	Cat# S0389
MgCl2	Thermo Fisher Scientific	Cat# AM9530G
NaCl	Sigma-Aldrich	Cat# S5150
EDTA	Thermo Fisher Scientific	Cat# 15575020
Tris hydrochloride	Sigma-Aldrich	Cat# 1185-53-1
Formaldehyde 36% (39% w/v)	VWR	Cat# 50-00-0
Click-IT EdU Alexa Fluor 647 imaging kit	Thermo Fisher Scientific	Cat# C10340
Pierce Anti-HA Magnetic Beads	Thermo Fisher Scientific	Cat# 88836
Dynabeads Protein A	Thermo Fisher Scientific	Cat# 10002D
Portein A magnetic beads	NEB	Cat# S1425S
Dynabeads Protein G	Thermo Fisher Scientific	Cat# 10003D
Strep-Tactin® Sepharose® 50% suspension beads	IBA Life Sciences	Cat# 2-1201-010
MagStrep “type3” XT beads	IBA Life Sciences	Cat# 2-4090-002
Deposited data
ProteomeXchange Consortium	PRIDE	PXD016279
Experimental models: cell lines
Human: T-24	German Collection of Microorganisms and Cell Cultures (DSMZ)	DSMZ No 376
Human: RT112	German Collection of Microorganisms and Cell Cultures (DSMZ)	DSMZ No 418
Human: HEK293	ATCC	Cat# 300192/p777_HEK293
Human: HeLa	ATCC	Cat# CCL-2
Human: DR-GFP U2OS	Laboratory of Dr Timothy Humphrey (Ahrabi et al., 2016)	N/A
Human: SA-GFP U2OS	Laboratory of Dr. Pavel Janscak (Paliwal et al., 2014)	N/A
HEK293 Flp-In T-REx (p97-E578Q-cSSH)	Laboratory of Prof Kristijan Ramadan (Meerang et al., 2011)	N/A
RT112 (shMRE11)	Laboratory of Prof Anne E Kiltie (Na et al., 2021)	N/A
Experimental models: organisms/strains
CD-1 nude mice (Female)	Charles River Laboratories	Strain Code: 086 (Homozygous)
Oligonucleotides
siRNA_Control (proprietary sequence)	QIAGEN	Cat# 1027280
siRNA_RAD51 (5′- AAGGGAATTAGTGAAGCCAAA-3′)	QIAGEN	Cat# SI02663682
siRNA_RAD52 (5′-AAGGATGGTTCATATCATGAA-3′)	QIAGEN	Cat# SI03035123
siRNA_MRE11 (5′GAGCAUAACUCCAUAAGUA(dT)(dT)-3′)	Thermo Fisher Scientific	Cat# 10620310
siRNA_XRCC5/siKU80 (5′-GCAUGGAUGUGAUUCAACA-3′)	Dharmacon	Cat# 7520
siRNA_VCP_7 (5′-UUCUGUUUGAGAAUGGCUGUU-3′)	Thermo Fisher Scientific	Cat# 10620310
siRNA_VCP_7 (5′-AACAGCCAUUCUCAAACAGAA-3′)	QIAGEN	N/A
siRNA_L3MBT1_5 (5′-AAGCGAGUAUAAGCC-3′)	Microsynth	N/A
siRNA_L3MBT1_7 (5′-CCAGGCAGUCACUCA-3′)	Micorynth	N/A
Recombinant DNA
pcDNA3.3 N-term HA-MRE11	Laboratory of Anne E Kiltie (Nicholson et al., 2017)	N/A
pcDNA5-p97-EQ-Myc-Strep	Laboratory of Hemmo Meyer or Kristijan Ramadan (Meerang et al., 2011)	N/A
Software and algorithms
Prism 8	GraphPad Software	https://www.graphpad.com
Fiji	NIH	https://imagej.net/Fiji/Downloads
FlowJo v10	FlowJo	https://www.flowjo.com/solutions/flowjo/downloads
Image Studio Lite 5.2	LI-COR	https://www.licor.com/bio/image-studio-lite/download
UCSC Xena	University of California, Santa Cruz	https://www.biorxiv.org/content/10.1101/326470v6
Proteome Discoverer Software	Thermo Fisher Scientific	https://thermo.flexnetoperations.com/control/thmo/login
MASCOT 2.3	Matrix Science Inc	http://www.matrixscience.com/
PRIDE	Wellcome Genome Campus, Hinxton, Cambridgeshire	https://www.ebi.ac.uk/pride/archive/