KEY RESOURCES TABLE

REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
CHK1	Santa Cruz	sc-8408
CHK1 pS317	Cell Signaling	2344
CHK1 pS345	Cell Signaling	2348
Cyclin A	Cell Signaling	4656
dsDNA	Abcam	ab27156
EME1	Santa Cruz	sc-53275
GAPDH	Millipore	ABS16
GFP	Millipore	MAB2510
γH2AX	Millipore	05-636
HA	Abcam	ab18181
HLTF	Sana Cruz	sc-398357
KAP1 pS824	Bethyl	A300-767A
MUS81	Abcam	ab14387
PCNA	Abcam	ab18197
PCNA	Santa Cruz	sc-56
Rad17	Abcam	ab151513
RECQ1	Bethyl	A300-450A
RNAP II pSer2	Novus Bio	NB100-1805
RPA32	Abcam	ab109084
S9.6	Antibodies Incorporated	Protein A purified from hybridoma S9.6
SETX	Bethyl	A301-105A
SLX4	Bethyl	A302-269A
SLX4	Bethyl	A302-270A
SMARCAL1	Santa Cruz	sc-376377
SRSF1	Bethyl	A302-053A
TopBPl	Bethyl	A300-111A
XPG	Bethyl	A301-484A
ZRANB3	Bethyl	A303-033A
Chemicals, Peptides, and Recombinant Proteins
Pladienolide B	Tocris Biosciences	6070
RNase H	NEB	M0297
Critical Commercial Assays
alamarBlue™ Cell Viability Reagent	Thermo Fischer	DAL1025
Comet Assay Kit	Trevigen	4250-050-K
Click-iT™ EdU Alexa Fluor™ 488 Imaging Kit	Thermo Fischer	C10337
Click-iT™ Plus EdU Alexa Fluor™ 647 Flow Cytometry Assay Kit	Thermo Fischer	C10634
Duolink™ In Situ Detection Reagents Red	Sigma-Aldrich	DUO92008
Oligonucleotides
siRNA	This Study	See List in Methods
Recombinant DNA
Plasmid: EME2	Harvard PlasmID Repository
Software and Algorithms
GraphPad Prism 5	NIH	https://www.graphpad.com/scientific-software/prism/
ImageJ	NIH	https://imagej.nih.gov/ij/
Fiji	(Schindelin et al., 2012)	https://fiji.sc/
NIS element viewer	Nikon	https://www.nikoninstruments.com/Products/Software/NIS-Elements-Advanced-Research/NIS-Elements-Viewer
Quantity One	Bio-rad	http://www.bio-rad.com/en-us/product/quantity-one-1-d-analysis-software?ID=1de9eb3a-1eb5-4edb-82d2-68b91bf360fb
Python 3.7	Python	https://www.python.org/downloads/release/python-370/