REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
S9.6	Home-made	N/A
BRCA2	Merck Millipore	RRID:AB_2067762
Beta-Actin	Sigma	RRID:AB_476744
RNase H1	Santa Cruz	Cat#: sc-292711
8-oxoguanine	Merck Millipore	RRID:AB_94925
Chemicals, peptides, and recombinant proteins
CM-H2DCFDA	ThermoFisher	Cat#: C6827
MitoSOX red	ThermoFisher	Cat#: M36008
N-Acetyl cysteine	Sigma	Cat#: A9165
H2O2	Sigma	Cat#: H1009
Etomoxir	Sigma	Cat#: E1905
37% formaldehyde solution	Sigma	Cat#: F8775
RNase H	NEB	Cat#: M0297L
RNaseIII	NEB	Cat#: M0245S
RNaseT1	ThermoScientific	Cat#: EN0541
DAPI	Sigma	Cat#: D9542
cOmplete, EDTA-free Protease Inhibitor Cocktail	Roche	Cat#: 11873580001
Critical commercial assays
JetPRIME Transfection Reagent	Polyplus Transfections	Cat#: 114-07
Click-iT EdU Alexa Fluor® 488 Imaging Kit	ThermoFisher Scientific	Cat#: C10086
Experimental models: cell lines
HeLa Kyoto	From the laboratory of Jonathan Pines, Institute of Cancer Research, London	N/A
EUFA423	From the European Fanconi Anemia Registry, VU University Medical Center, Amsterdam, the Netherlands	N/A
EUFA423 B2	Hattori et al., 2011	N/A
Pdx1Cre; KrasG12D/+; Trp53R270H/+; Brca2Wt/Wt or Brca2Tr/Δ11	Skoulidis et al., 2010	N/A
Oligonucleotides
Negative Control (si)RNA	QIAGEN	Cat#: 1027310
BRCA2 (ON-TARGET plus SMARTpool)	Dharmacon	Cat#: L-003462-00
PRPF8 (ON-TARGET plus SMARTpool)	Dharmacon	Cat#: L-012252-00
SETX (si)RNA	QIAGEN	Cat#: SI05052236 and SI04183942
OGG1 (ON-TARGET plus SMARTpool	Dharmacon	Cat#: L-005147-00
D-loop_Fwd CTTTCATGGGGAAGCAGATTTG	Sigma	N/A
D-loop_Rev GCATGGGGAGGGGGTTTTG	Sigma	N/A
ND1_Fwd TCTCCACCCTTATCACAACA	Sigma	N/A
ND1_Rev GACTAGTTCGGACTCCCCTT	Sigma	N/A
OriL_Fwd CCCACAAACACTTAGTTAACAGCT	Sigma	N/A
OriL_Rev GGCCTCTTTTTACCAGCTCC	Sigma	N/A
Mt-CD1_Fwd AACCACAGTTTCATGCCCATC	Sigma	N/A
Mt-CD1_Rev TGTTAGTAAGGGTGGGGAAGC	Sigma	N/A
Mt-CD2_Fwd ACCCTATAGCACCCCCTCTAC	Sigma	N/A
Mt-CD2_Rev CTTGTCAGGGAGGTAGCGATG	Sigma	N/A
HPRT_Fwd TGACACTGGCAAAACAATGCA	Sigma	N/A
HPRT_Rev GGTCCTTTTCACCAGCAAGCT	Sigma	N/A
GAPDH_Fwd CTCCTGTTCGACAGTCAGC	Sigma	N/A
GAPDH_Rev TTCAGGCCGTCCCTAGC	Sigma	N/A
BRCA2 CRISPR/Cas9 KO (CTGTCTACCTG ACCAATCGA; ATGTAGCACGCATTCACATA; CGATTACCTGTGTACCCTTT)	Santa Cruz	Cat#: sc-400700
Software and algorithms
Prism version 5	GraphPad	https://www.graphpad.com/scientific-software/prism/
Fiji	(https://fiji.sc/)	N/A