REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Mouse monoclonal anti-RPA32 (RPA ChIP on MEF 4–3 cells)	Millipore	NA19L-100UG; RRID:AB_565123
Mouse IgG2a Isotype Control from murine myeloma antibody (Pre-clear for RPA ChIP on MEF 4–3 cells)	Sigma Aldrich	M5409; RRID:AB_1163691
Bacterial and Virus Strains
R408 Helper Phage	Promega	Cat# P2291
SURE 2 Supercompetent Cells	Agilent Technologies	Cat# 200152
Chemicals, Peptides, and Recombinant Proteins
4-OHT	EMD Chemicals/Calbiochem	579002–5MG
Shield-1	Laboratory of Tom Wandless, Stanford	N/A
ATR45 (ATR inhibitor for MEFs)	Ohio State University (OSU); Charrier et al., 2011	ATR45
VE-822 (ATR inhibitor for MDA-MB-231 cells)	Selleck Chemicals	Cat# S7102
Aphidicolin (for RPA ChIP and BrITL experiments)	Calbiochem	CAS 38966–21-1
Biotin-16-ddUTP	Enzo Life Sciences	ENZ-42813
TdT	Roche	Cat# 03333566001
Polyethylene Glycol (Avg Mol Wt of 8000)	Sigma	Cat# P5413; CAS 25322–68-3
Aphidicolin (for Fork Pausing experiments)	Sigma	Cat#A0781; CAS 38966–21-1
Equilibrated Phenol, pH 8.0, Ultrapure	Affymetrix/Thermo-Fisher	Cat# AAJ75829AN; CAS 108–95-2
γ32P ATP (6000Ci/mmol)	Perkin-Elmer	Cat# BLU002Z001MC
T4 Polynucleotide Kinase	Thermo-Fisher	Cat# 18004010
Recombinant human PCNA	Laboratory of Marietta Lee	Biochemistry 2001 40: 4512–4520
Recombinant yeast RFC	Laboratory of Linda Bloom	The Journal of Biological Chemistry 2012 287: 2203–9
Sequenase 2.0	Affymetrix/Thermo-Fisher	Cat# 70775Y
Exo- Klenow Polymerase	Affymetrix/Thermo-Fisher	Cat# 70057Z
Critical Commercial Assays
NEBNext Library KIt	NEB	E6000S
Dynabeads KilobaseBinder kit	Life Technologies	601–01
Ampure XP Beads purification kit	Beckman Coulter	A63880
Lipofectamine™ 3000 Transfection Reagent	Thermo Fisher Scientific	L3000001
Biotin Chromogenic Detection kit	Thermo Fisher Scientific	K0661
High Prime DNA labeling kit version 10	Roche Diagnostics	REF: 11585592001
Biotin DecaLabel DNA Labeling Kit	Thermo Fisher Scientific	K0651
Dynabeads Protein A for Immunoprecipitation	Invitrogen	100–02D
Deposited Data
RPA ChIP-Seq raw and processed files	This paper	GEO: GSE100790
BrITL raw and processed files	This paper	GEO: GSE115623; GSE115624
Mendeley deposited data	This paper	https://data.mendeley.com/datasets/9gwyx4vxt8/draft?a=7789056e-b4d3–4f8b-9735–992304ad2679
Experimental Models: Cell Lines
MEF 4–3 cells (ATRflox/-Cre-ERT2+)	Smith et al., 2009	N/A
TIM KD MEF 4–3 cells	Smith et al., 2009	N/A
I-PpoI MEF 4–3 cells	This paper	N/A
MDA-MB-231 cells	Andy J. Minn, Univ. of Pennsylvania	N/A
U-2OS osteosarcoma cells	ATCC	HTB-96
Fetal Bovine Serum	GE Life Sciences/Hyclone	Cat. No. SH 30071.03
Oligonucleotides
Primers for BrITL qRT-PCR, see below	This paper	N/A
Oligos used for biophysical studies, see Table S3	Integrated DNA Technology	N/A
dTn gel electrophoresis ladder: 5’-dT15, 5’-dT24, 5’-dT30, 5’-dT57, 5’-dT60, 5’-dT90	Integrated DNA Technology	N/A
G94–43mer, PAGE-Purified 5’-GGA TAA CAA TTT CAC ACA GGA AAC AGC TAT GAC CAT GAT TAC G-3’	Integrated DNA Technologies	N/A
Scrambled and (CAGAGG)105 insert sequences, see below	This paper	N/A
PSH1 probe primer set: Forward: 5’-TTCCAGTGATGGAAGCACCC-3’ Reverse: 5’-CTTGGCTTGGCACACAGAAC-3’	Integrated DNA Technologies	N/A
HFUGW probe primer set (against UBC promoter): Forward: 5’-CATAAGACTCGGCCTTAGAACC-3’ Reverse: 5’-GCCAGAATTTAGCGGACAATTT-3’	Integrated DNA Technologies	N/A
Recombinant DNA
pBabe-ddIPpoI	Addgene, Goldstein et al., 2013	#49052
pMIG Bcl-XL	Addgene	#8790
pGEM-3Zf(-) Vector	Promega	Cat# P2261
pML113, pML114, pML115	Massimo Lopes, Univ. of Zurich	Nature Structural and Molecular Biology 2013 20: 486–494.
Software and Algorithms
Trimmomatic	Bolger et al., 2014	N/A
Fastqc	Leggett et al., 2013	N/A
STAR-2.5.2a Aligner	Dobin et al., 2013	N/A
MACS2 peak-calling	Zhang et al., 2008	N/A
IDR analysis	Landt et al., 2012	N/A
Homer2 motif-finding		N/A
The M-fold Web Server (DNA folding form)	Zuker, 2003	N/A
MISA	Beier et al., 2017	N/A
ImageQuant version 5.2	GE Healthcare	N/A
Other
Illustra Microspin G-50 column	GE Healthcare	Cat# 27–5330-1
Xtreme Gene XP version 8	Roche Diagnostics	REF: 06366236001