REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Mouse monoclonal anti-SLX4IP (clone G4)	Santa Cruz Biotechnology	Cat#sc-377066; RRID:AB_2752253
Sheep polyclonal anti-SLX4 (BTBD12, sheep S714C)	MRC PPU University of Dundee	Cat#DU16029; RRID:AB_2752254
Rabbit polyclonal anti-SLX4 (BTBD12)	Bethyl Laboratories	Cat#A302-270A, RRID:AB_1850156
Rabbit polyclonal anti-SLX1B (GIYD2)	Proteintech	Cat#21158-1-AP; RRID:AB_2752255
Mouse monoclonal anti-MUS81 (clone MTA30 2G10/3)	Abcam	Cat#ab14387; RRID:AB_301167
Mouse monoclonal anti-ERCC4 (XPF, clone 219)	Thermo Fisher Scientific	Cat#MA5-12054; RRID:AB_10981652
Mouse monoclonal anti-GFP (clones 7.1 and 13.1)	Roche	Cat#11814460001; RRID:AB_390913
Chicken polyclonal anti-GFP	Abcam	Cat#ab13970, RRID:AB_300798
Rabbit polyclonal anti-BLM	Abcam	Cat#ab2179; RRID:AB_2290411
Mouse polyclonal anti-ERCC6L (PICH)	Abcam	Cat# ab88560; RRID:AB_2041158
Mouse monoclonal anti-PML (clone PG-M3)	Santa Cruz Biotechnology	Cat#sc-966; RRID: RRID:AB_628162
Mouse monoclonal anti-RPA32 (clone 9H8)	Abcam	Cat#ab2175; RRID:AB_302873
Mouse monoclonal anti-γH2AX (clone JBW301)	Millipore	Cat#05-63; RRID:AB_309864
Rabbit polyclonal anti-γH2AX	Cell Signaling Technologies	Cat#2577; RRID:AB_2118010
Rabbit polyclonal anti-RAP1	Bethyl Laboratories	Cat#A300-306A; RRID:AB_162721
Rabbit polyclonal anti-DNA2	Abcam	Cat#ab96488, RRID:10677769
Mouse monoclonal anti-α-Tubulin	Sigma-Aldrich	Cat#T6074; RRID:AB_477582
Mouse monoclonal anti-Vinculin	Abcam	Cat#ab11194; RRID:AB_297835
Mouse monoclonal anti-SMARCAL1	Santa Cruz Biotechnology	Cat# sc-376377; RRID:AB_10987841
Rabbit monoclonal anti-ATRX	Santa Cruz Biotechnology	Cat# sc-15408; RRID:AB_2061023
Rabbit monoclonal anti-DAXX	Cell Signaling Technologies	Cat# 4533; RRID:AB_2088778
Mouse monoclonal anti-H3	Abcam	Cat# ab10799; RRID:AB_470239
Rabbit polyclonal anti-histone H3	Abcam	Cat# ab1791; RRID:AB_302613
Rabbit polyclonal anti-pH3 (Ser10)	Cell Signaling Technology	Cat# 9701, RRID:AB_331535
Mouse monoclonal anti-SUMO2/3 (clone 8A2)	Abcam	Cat#ab81371; RRID:AB_1658424
Mouse monoclonal anti-p62/SQSTM1 (clone 3)	BD Biosciences	Cat#610832; RRID:AB_398151
Mouse monoclonal anti-cytochrome C (clone 6H2.B4)	Thermo Fisher Scientific	Cat# 33-8200; RRID:AB_2533141
Goat polyclonal anti-mouse, horseradish peroxidase-conjugated	Dako	Cat#P0447; RRID:AB_2617137
Swine polyclonal anti-rabbit, horseradishperoxidase-conjugated	Dako	Cat#P0399; RRID:AB_2617141
Rabbit polyclonal anti-sheep, horseradishperoxidase-conjugated	Abcam	Cat#ab6747; RRID:AB_955453
Goat anti-chicken IgG (H+L), Alexa Fluor 488 conjugated	Invitrogen	Cat#A11039; RRID:AB_2534096
Goat anti-mouse IgG (H+L), Alexa Fluor 488 conjugated	Invitrogen	Cat#A11001; RRID:AB_2534069
Goat anti-rabbit IgG (H+L), Alexa Fluor 488 conjugated	Invitrogen	Cat#A11008; RRID:AB_143165
Goat anti-rabbit IgG (H+L), Alexa Fluor 546 conjugated	Invitrogen	Cat#A11010; RRID:AB_2534077
Sheep anti-digoxigenin-AP, Fab Fragments	Sigma	Cat#11093274910 RRID: AB_2734716
Biological Samples
Osteosarcoma patient derived xenograft models	Pediatric Preclinical Testing Program; Houghton et al. Pediatric Blood and Cancer. 2007	PMID:17066459
Chemicals, Peptides, and Recombinant Proteins
BrdU	Sigma-Aldrich	Cat#B5002
Camptothecin	Sigma-Aldrich	Cat#C9911
Mitomycin C	Sigma-Aldrich	Cat#M0503-5X2MG
Doxycycline	Sigma-Aldrich	Cat#D3447
Cycloheximide	Sigma-Aldrich	Cat#C4859
Blasticidin	ThermoFisher Scientific	Cat#A1113903
Hygromycin B	ThermoFisher Scientific	Cat#10687010
Mevinolin (lovastatin)	Sigma-Aldrich	Cat#M2147-25MG
RO-3306	Sigma-Aldrich	Cat#SML0569-25MG
Thymidine	Sigma-Aldrich	Cat#T1895-25G
Nocodazole	Sigma-Aldrich	Cat# M1404-2MG
Benzonase	Millipore	Cat#E1014-25KU
4x NuPAGE LDS sample buffer	Invitrogen	Cat#13778150
GFP-Trap_MA	Chromotek	Cat#gtma-20
ProLong Gold antifade with DAPI	Thermo Fisher Scientific	Cat#P36931
TAMRA-TelG 5′-(TTAGGG)3-3′ PNA probe	PNA Bio-synthesis	Cat#F1006
FITC-TelC 5′-(CCCTAA)3-3′ PNA probe	PNA Bio-synthesis	Cat#F1009
Phi29 DNA Polymerase	Thermo FisherScientific	Cat#EP0091
ATP, [γ-32P]- 6000Ci/mmol 10mCi/ml	Perkin Elmer	Cat#NEG502Z250UC
Blocking Reagent	Sigma-Aldrich	Cat#11096176001 ROCHE
Colcemid	Sigma-Aldrich	Cat#0295892001 ROCHE
EDTA-free Complete protease inhibitor cocktail	Roche	Cat#COEDTAF-RO
PhosSTOP phosphatase inhibitor cocktail	Roche	Cat#PHOSS-RO
Exonuclease III	Promega	Cat#M1815
Hoechst 33258	Sigma-Aldrich	Cat#861405
AluI	New England Biolabs	Cat#R0137
MboI	New England Biolabs	Cat#R0147
Phi-29 Polymerase	New England Biolabs	Cat#M0269
CDP-Star	Sigma Aldrich	Cat#11685627001
ULTRAhyb Ultrasensitive Hybridization Buffer	Thermo Fisher	Cat#AM8669
Dharmafect I Transfection Reagent	Dharmacon	Cat#T-2001-03
Lipofectamine RNAiMAX	Invitrogen	Cat#13778150
DIG Oligo 3′ End labeling kit (2nd generation, Roche)	Sigma Aldrich	Cat#03353575910
QiaAMP DNA mini kit	QIAGEN	Cat#51304
RNeasy Mini Kit (250)	QIAGEN	Cat#74106
Kapa RNA HyperPrep kit with Riboerase	Kappa Biosystems	Cat#08098140702
QIAquick PCR purification kit	QIAGEN	Cat#28106
DIG Wash and Block Buffer Set	Sigma Aldrich	Cat# 11585762001
Senescence Cells Histochemical Staining Kit	GE Healthcare	Cat# CS0030-1KT
Human: U2OS	The Francis Crick Institute Cell Services	N/A
Human: WI38VA13	The Francis Crick Institute Cell Services	N/A
Human: HeLa 1.2.11	The Francis Crick Institute Cell Services	N/A
Human: HEK293	The Francis Crick Institute Cell Services	N/A
Human: RPE-1 hTERT	The Francis Crick Institute Cell Services	N/A
Human: U2OS FLP-IN HOST	Gift of Daniel Durocher	N/A
Human: U2OS FLP-IN GFP	This study	N/A
Human: U2OS FLP-IN GFP-SLX4IP WT	This study	N/A
Human: U2OS SLX4IP−/− (clone 2) SLX4IP-pLenti-CMV-Blast-DEST	This study	N/A
Human: U2OS SLX4IP−/− (clone 2) pLenti-CMV-Blast-DEST	This study	N/A
Human: HOS	Boston University	N/A
Human: HeLa	Boston University	N/A
Human: MG63	Boston University	N/A
Human: SJSA1	Boston University	N/A
Human: G292	Boston University	N/A
Human: SAOS2	Boston University	N/A
Human: HUO9	Boston University	N/A
Human: NOS1	Boston University	N/A
Human: NY	Boston University	N/A
Human: CAL72	Boston University	N/A
Human: CAL78	Boston University	N/A
Human: HUO3N1	Boston University	N/A
Human: hFOB1.19	Boston University	N/A
Deposited Data
RNA sequencing data, GEO Series accession number GGSE124768	This study	Gene Expression Omnibus/NCBI GEO: GSE124768https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE124768
Experimental Models: Organisms/Strains
Mouse: CB17SC-F scid−/− female mice	Taconic	CB17SC-F RF
Oligonucleotides
ON-TARGET plus Non-targeting Pool	Dharmacon	D-001810-10
ON-TARGET plus SMARTpool human SLX4	Dharmacon	L-014895-00
ON-TARGET plus SMARTpool human SLX1A	Dharmacon	L-034933-01
ON-TARGET plus SMARTpool human MUS81	Dharmacon	L-016143-01
ON-TARGET plus SMARTpool human ERCC4	Dharmacon	L-019946-00
ON-TARGET plus SMARTpool human BLM	Dharmacon	L-007287-00
ON-TARGET plus SMARTpool human DNA2	Dharmacon	L-026431-01
siGENOME SMARTpool human TRF2	Dharmacon	M-003546-00
TelG probe (TTAGGG)4	This study	N/A
TelC probe (CCCTAA)4	This study	N/A
Alu probe 5′-GTAATCCCAGCACTTTGG-3′	This study	N/A
Recombinant DNA
EGFP-C1-GFP-BLM	Addgene	Cat#80070;RRID:Addgene_80070
pcDNA5-FRT/TO-GFP	Gift from Daniel Durocher	DD982
pcDNA5-FRT/TO-GFP-SLX4-FL	Gift from John Rouse, Wilson et al., 2013	PMID:23994477
pcDNA5-FRT/TO-GFP-SLX4-WT (1-669)	This study	N/A
pcDNA5-FRT/TO-GFP-SLX4-A (1-200)	This study	N/A
pcDNA5-FRT/TO-GFP-SLX4-B (201-400)	This study	N/A
pcDNA5-FRT/TO-GFP-SLX4-C (401-669)	This study	N/A
pcDNA5-FRT/TO-GFP-SLX4-MLR (409-555)	This study	N/A
pET-SUMO-SLX4IP	This study	N/A
pcDNA5-FRT/TO-GFP-SLX4IP-FL	This study	N/A
pcDNA5-FRT/TO-GFP-SLX4IP-A (1-120)	This study	N/A
pcDNA5-FRT/TO-GFP-SLX4IP-B (121-230)	This study	N/A
pcDNA5-FRT/TO-GFP-SLX4IP-C (231-408)	This study	N/A
pcDNA5-FRT/TO-GFP-SLX4IP-ΔA (121-408)	This study	N/A
pcDNA5-FRT/TO-GFP-SLX4IP-ΔB (Δ121-230)	This study	N/A
pcDNA5-FRT/TO-GFP-SLX4IP-ΔC (1-231)	This study	N/A
px335-U6-Chimeric_BB-CBh-hSpCas9n(D10A)	Addgene	Cat#:42335;RRID:Addgene_42335
px335-C20A	This study	N/A
px335-C20B	This study	N/A
pLentiCRISPRv2	Addgene	Cat#:52961;RRID:Addgene_52961
pLentiCRISPRv2_SLX4IP_A	This study	N/A
pLentiCRISPRv2_SLX4IP_B	This study	N/A
pLenti-CMV-Blast-DEST	Addgene	Cat#17451; RRID:Addgene_17451
SLX4IP-pLenti-CMV-Blast	This study	N/A
His-SUMO3	Guervilly et al., 2015	PMID:25533188
FHA-SLX4 WT	Guervilly et al., 2015	PMID:25533188
FHA-SLX4 SIM∗	Guervilly et al., 2015	PMID:25533188
Software and Algorithms
Adobe Photoshop CS5.1	Adobe	http://www.adobe.com/es/products/photoshop.html
Prism 7	GraphPad Software	https://www.graphpad.com/
Fiji	NIH	https://imagej.net/Fiji/Downloads
Volocity 6.3	PerkinElmer	http://cellularimaging.perkinelmer.com/downloads/detail.php?id=14
FV10-ASW 4.2	Olympus	https://www.olympus-lifescience.com/en/support/downloads/#!dlOpen=%23detail847249651
FV31S-SW	Olympus	https://www.olympus-lifescience.com/en/support/downloads/
Cell Profiler	Broad Institute	http://cellprofiler.org/releases/
Image Lab 5.2.1	Bio-Rad Laboratories	http://www.bio-rad.com/en-uk/product/image-lab-software?ID=KRE6P5E8Z
FlowJo v10	FlowJo	https://www.flowjo.com/solutions/flowjo/downloads
FastQC	N/A	https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
Salmon	N/A	https://github.com/COMBINE-lab/Salmon
ggplot2 package	N/A	https://cran.r-project.org/web/packages/ggplot2/index.html
GXCapture	GT Vision	https://www.gtvision.co.uk/GX-Capture-Camera-Control-Image-Capture-Storage-Annotation-Enhancement-Analysis-FREE
Other
SLX4IP CRISPR target sequence C20A 5′-GATCTTCATATCTTGCCACA AGG-3′	This study	N/A
SLX4IP CRISPR target sequence C20B 5′-CCA TTAATGTCTTTCAGTGTGGG-3′	This study	N/A
SLX4IP CRISPR target sequence SLX4IPA 5′-GATCTTCATATCTTGCCACA-3′	This study	N/A
SLX4IP CRISPR target sequence SLX4IPB 5′-TGGGAATTTTGCTGTCCTCG-3′	This study	N/A