REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Rabbit polyclonal anti-pSer137-Pfn1	Previous Paper (Shao et al., 2008)	N/A
Mouse monoclonal anti-pSer784-VCP, clone (3E4)	This Paper	N/A
Rabbit monoclonal anti-GFP	Cell Signaling Technology	Cat#2956; RRID: AB_1196615
Mouse monoclonal anti-VCP	Santa Cruz	Cat#sc-57492; RRID: AB_793927
		Cat#sc-136273; RRID: AB_2214651
Mouse monoclonal anti-actin	Santa Cruz	Cat#sc-47778; RRID: AB_626632
Mouse monoclonal anti-GAPDH	Santa Cruz	Cat#sc-365062; RRID: AB_10847862
Rabbit monoclonal anti-Histone H3	Cell Signaling Technology	Cat#4499; RRID: AB_10544537
Rabbit monoclonal anti-γH2AX	Cell Signaling Technology	Cat#9718; RRID: AB_2118009
Mouse monoclonal anti-Ku70	Santa Cruz	Cat#sc-17789; RRID: AB_628454
Mouse monoclonal anti-ATM	Santa Cruz	Cat#sc-377293
Rabbit monoclonal anti-pSer1981-ATM	Cell Signaling Technology	Cat#5883; RRID: AB_10835213
Rabbit polyclonal anti-pSer428-ATR	Cell Signaling Technology	Cat#2853; RRID: AB_2290281
Mouse monoclonal anti-Chk2	Cell Signaling Technology	Cat#3440; RRID: AB_2229490
Rabbit monoclonal anti-pThr68-Chk2	Cell Signaling Technology	Cat#2197; RRID: AB_2080501
Rabbit monoclonal anti-pSer345-Chk1	Cell Signaling Technology	Cat#2348; RRID: AB_331212
Rabbit monoclonal anti-NBS1	Cell Signaling Technology	Cat#14956; RRID: AB_2798660
Rabbit polyclonal anti-pSer343-NBS1	Cell Signaling Technology	Cat#3001; RRID: AB_10829154
Rabbit polyclonal anti-K48-ubiquitin	Cell Signaling Technology	Cat#4289; RRID: AB_10557239
Rat monoclonal anti-FLAG tag	BioLegend	Cat#637301; RRID: AB_1134266
Rabbit polyclonal anti-NPL4	Bethyl Laboratories	Cat#A304-102A; RRID: AB_2621351
Rabbit polyclonal anti-UFD1	Bethyl Laboratories	Cat#A301-875A; RRID: AB_1309801
Mouse monoclonal anti-CHOP	Cell Signaling Technology	Cat#2895; RRID: AB_2089254
Rabbit monoclonal anti-BiP	Cell Signaling Technology	Cat#3177; RRID: AB_2119845
Rabbit monoclonal anti-phospho-ATM/ATR substrate motif	Cell Signaling Technology	Cat# 6966, RRID: AB_10949894
Rabbit monoclonal anti-Pfn1	Cell Signaling Technology	Cat#3246; RRID: AB_2163185
Mouse monoclonal anti-BRCA1	Santa Cruz	Cat#sc-6954; RRID: AB_626761
Mouse monoclonal Anti-Human 53BP1(Clone19)	BD Biosciences	Cat#612522; RRID: AB_2206766
Mouse anti-tubulin	Sigma	Cat#T9026; RRID: AB_477593
Rabbit polyclonal anti-PELP1	Bethyl Laboratories	Cat# A300-180A
Rabbit monoclonal anti-ATR	Cell Signaling Technology	Cat# 13934; RRID: AB_2798347
Mouse monoclonal anti-HIF1 alpha	Cell Signaling Technology	Cat# 79233; RRID: AB_2799924
Rabbit monoclonal anti-K48-linked polyubiquitin	Cell Signaling Technology	Cat# 8081; RRID: AB_10859893
Mouse monoclonal anti-pSer1981-ATM	Rockland	Cat# 200-301-400; RRID: AB_217868
Bacterial and Virus Strains
Stbl2 competent cells	Thermo Fisher	Cat#: 10268019
Stbl3 competent cells	Thermo Fisher	Cat#: C737303
DH5 alpha competent cells	Thermo Fisher	Cat#: 18258012
XL10-Gold ultracompetent cells	Agilent	Cat#: 200314
Chemicals, Peptides, and Recombinant Proteins
Etoposide	Selleckchem	Cat#S1225; CAS:33419-42-0
KU55933	Selleckchem	Cat#S1092; CAS:587871-26-9
Niraparib	Selleckchem	Cat#S7625; CAS:038915-73-9
Olaparib	Selleckchem	Cat#S1060; CAS:763113-22-0
Cisplatin	Selleckchem	Cat#S1166; CAS:15663-27-1
Gemcitabine	Selleckchem	Cat#S1714; CAS:95058-81-4
Hydroxyurea	Sigma	Cat#H8627; CAS:27-07-1
5-Fluoracil	Sigma	Cat#F6627; CAS:51-21-8
SN38	Sigma	Cat#H1065; CAS:86639-52-3
NMS-873	Selleckchem	Cat#S7285; CAS:1418013-75-8
MG-132	Selleckchem	Cat# S2619; CAS:133407-82-6
Critical Commercial Assays
ImmPACT DAB kit	Vectorlabs	Cat#SK-4105
Single Cell Gel Electrophoresis Assay	Trevigen	Cat#4250-050-K
Experimental Models: Cell Lines
Human: T47D	ATCC	HTB-133
Human: HCC1806	ATCC	CRL-2335
Human: HeLa	ATCC	CCL-2
Human: HEK293T	ATCC	CRL-11268
Human: U2OS	ATCC	HTB-96
Human: MDA-MB-231	ATCC	HTB-26
Human: BT549	ATCC	HTB-122
Oligonucleotides
shLuc: ATATCCGAGTGTAGTAAACATT	This Paper	N/A
shPfn1#1: GTGGTTTGATCAACAAGAA	(Diamond et al., 2015)	N/A
shPfn1#2: TACGTGAATGGGCTGACACTT	(Diamond et al., 2015)	N/A
The primers for VCP S784A: sense TGGAGCTGGCCCCGCTCAGGGCAGTGGA	This Paper	N/A
The primer for VCP S784D: sense TGGAGCTGGCCCCGATCAGGGCAGTGGA	This Paper	N/A
The primers for VCP S784A: antisense TCCACTGCCCTGAGCGGGGCCAGCTCCA	This Paper	N/A
The primer for VCP S784D: antisense TCCACTGCCCTGATCGGGGCCAGCTCCA	This Paper	N/A
shVCP#1: CCTGATGTGAAGTACGGCAAA	This Paper	N/A
shVCP#2: AGGGAGGTAGATATTGGAATT	This Paper	N/A
Recombinant DNA
VCP(WT)-GFP (shVCP#1,Resistant)	This Paper	N/A
VCP(WT)-GFP (shVCP#2,Resistant)	This Paper	N/A
VCP(WT)-EGFP	Addgene	Cat#23971; RRID: Addgene_23971
pEGFP-C1	Clontech (discontinued)	https://www.addgene.org/vector-database/2487/
pFLRu-NYFP-FH	Feng et al., 2010	N/A
VCP(WT)-FLAG	This Paper	N/A
VCP(S784A)-EGFP	This Paper	N/A
VCP(S784D)-EGFP	This Paper	N/A
VCP(S326A)-EGFP	This paper	N/A
VCP(S652A)-EGFP	This paper	N/A
VCP(S746A,S748A)-EGFP	This paper	N/A
pFLRu-FH vector	(Feng et al., 2010)	N/A
VCP(S664A)-EGFP	This paper	N/A
VCP(S784A)-FLAG	This paper	N/A
VCP(S784D)-FLAG	This paper	N/A
VCP(S784A)-GFP (shVCP#1,Resistant)	This paper	N/A
VCP(S784A)-GFP (shVCP#2,Resistant)	This paper	N/A
VCP(S784D)-GFP (shVCP#1,Resistant)	This paper	N/A
VCP(S784D)-GFP (shVCP#2, Resistant)	This paper	N/A
Software and Algorithms
R software	The R foundation	N/A
SPSS version 23	IBM corporation	N/A
ImageJ with the OpenComet plugin	(Gyori et al., 2014)	http://www.cometbio.org/index.html
GraphPad Prism 7	GraphPad software	N/A
Cellsens software	Olympus Lifescience	N/A
Other
SignalStain Boost IHC Detection Reagent, mouse	Cell Signaling Technology	Cat#: 8125
SignalStain Boost IHC Detection Reagent, rabbit	Cell Signaling Technology	Cat#: 8114
RIPA lysis buffer	Cell Signaling Technology	Cat#: 9806
HiTrap protein G column	GE healthcare	cat#: 17040403
Mouse monoclonal anti-FLAG M2 affinity gel	Sigma	Cat#: A2220