REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Mouse monoclonal anti-HA	Thermo Fisher	26183, RRID: AB_10978021
Rabbit polyclonal anti-U2AF35	Bethyl	A302-079A, RRID: AB_1604295
Mouse monoclonal anti-U2AF65	Sigma-Aldrich	U4758, RRID: AB_262122
Mouse monoclonal anti-β-Actin	Sigma-Aldrich	A2228, RRID: AB_476697
Mouse monoclonal anti-γ-H2AX	EMD Millipore	05-636, RRID: AB_309864
Rabbit polyclonal anti-H2AX	Bethyl	A300-083A, RRID: AB_203289
Rabbit polyclonal anti-phospho-Chk1 (Ser345)	Cell Signaling	2348, RRID: AB_331212
Rabbit polyclonal anti-Chk1	Bethyl	A300-298A, RRID: AB_309459
Mouse monoclonal anti-phospho-ATM (Ser1981)	Rockland	200-301-400, RRID: AB_217868
Rabbit polyclonal anti-ATM	Bethyl	A300-299A, RRID: AB_263415
Rabbit polyclonal anti-phospho-Chk2 (Thr68)	Cell Signaling	2661, RRID: AB_331479
Rabbit polyclonal anti-Chk2	Bethyl	A300-620A, RRID: AB_513590
Rabbit polyclonal anti-phospho-RPA32 (Ser4/Ser8)	Bethyl	A300-245A, RRID: AB_210547
Rabbit polyclonal anti-RPA32	Bethyl	A300-244A, RRID: AB_185548
Rabbit polyclonal anti-V5	Santa Cruz	sc-83849-R, RRID: AB_2019669
Rabbit polyclonal anti-CDK9	Cell Signaling	2316, RRID: AB_2291505
Mouse monoclonal anti-BrdU	BD	BDB555627
Rat monoclonal anti-BrdU	Thermo Fisher	MA1-82718, RRID: AB_927213
Rabbit polyclonal anti-HEXIM1 (for IP)	Bethyl	A303-111A, RRID: AB_10893099
Rabbit polyclonal anti-HEXIM1 (for WB)	Bethyl	A303-113A, RRID: AB_10892626
Rabbit polyclonal anti-phospho-RNA polymerase II CTD repeat (Ser2)	Abcam	ab5095, RRID: AB_304749
Mouse monoclonal S9.6 antibody	Kerafast	ENH001, RRID: AB_2687463
Chemicals, Peptides, and Recombinant Proteins
SIGMAFAST Protease Inhibitor Cocktail Tablet	Sigma-Aldrich	S8830-2TAB
Glycogen	Thermo Fisher	FERR0561
Formaldehyde	Sigma-Aldrich	252549-100ML
Pierce Anti-HA Magnetic Beads	Thermo Fisher	88836
Protein A/G Magnetic Beads	Thermo Fisher	PI88802
Proteinase K	NEB	P8107S
RiboLock RNase Inhibitor	Thermo Fisher	FEREO0382
RNase A	Thermo Fisher	EN0531
Phi29 DNA Polymerase	NEB	M0269S
Klenow Fragment (3′-5′ exo-)	NEB	M0212S
T4 DNA Ligase	NEB	M0202S
FastStart Universal SYBR Green Master (Rox) 2X	Roche	4913850001
BrdU	Sigma-Aldrich	B7166-5MG
RQ1 RNase-Free DNase	Promega	M6101
Antarctic Phosphatase	NEB	M0289S
BrdU Antibody Conjugated Agarose Beads	Santa Cruz	sc-32323 AC
T4 Polynucleotide Kinase	NEB	M0201S
E. coli Poly (A) Polymerase	NEB	M0276S
SuperScript III First-Strand Synthesis System	Thermo Fisher	18080051
Exonuclease I	NEB	M0293S
Circligase II	Epicentre	CL9021K
APE1	NEB	M0282S
Phusion High-Fidelity DNA Polymerase	NEB	M0530S
SYBR Gold Nucleic Acid Gel Stain	Thermo Fisher	S11494
IdU	ACROS Organics	AC122350010
CIdU	Sigma-Aldrich	C6891-100MG
IL-3	PeproTech	200-03
Anti-mouse CD117 MicroBeads	Miltenyi Biotech	130-091-224
Fluoromount-G Mounting Medium	Southern Biotech	0100-01
DAPI	Thermo Fisher	D1306
HA Peptide	GenScript	RP11735-1
Critical Commercial Assays
FITC Annexin V Apoptosis Detection Kit I	BD	556547
PureLink PCR Micro Kit	Thermo Fisher	K310050
PureLink Quick Gel Extraction Kit	Thermo Fisher	K210012
Deposited Data
Sequencing data of R-ChIP experiments	This study	GSE97183
Sequencing data of GRO-seq experiments	This study	GSE97183
Experimental Models: Cell Lines
Human: HEK293T cells	Laboratory of Steve Dowdy	N/A
Human: MDS-L cells	Laboratory of Daniel Starczynowski	N/A
Mouse: MEFs	This study	N/A
Oligonucleotides
Primers for qRT-PCR and ChIP-qPCR experiments	This study	See Table S1
Software and Algorithms
ImageJ	N/A	https://imagej.nih.gov/ij/download.html
Bowtie2	(Langmead and Salzberg, 2012)	http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
Samtools	(Li et al., 2009)	http://samtools.sourceforge.net/
Bedtools	(Quinlan and Hall, 2010)	http://bedtools.readthedocs.io/en/latest/
R	N/A	https://www.r-project.org/
MACS2	(Feng et al., 2012)	https://github.com/taoliu/MACS
Step One Software v2.3	Thermo Fisher	https://www.thermofisher.com/us/en/home/technical-resources/software-downloads/StepOne-and-StepOnePlus-Real-Time-PCR-System.html