Key Resources Table

REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
CPSF1	Bethyl Laboratories	A301-580A
GAPDH	Cell Signaling	14C10
H3	Abcam	ab1791
Int3	Bethyl Laboratories	A302-050A
Int11	Abcam	ab75276
RNA Pol II CTD	MBL	MABI0601
RNA Pol II (N-terminus)	Cell Signaling	D8L4Y
RNA Pol II Tyr1-P CTD	Active Motif	61383
U1-70K	Kastner et al. 1992; Tarn and Steitz. 1994	N/A
Xrn2	Bethyl Laboratories	A301-101
Chemicals, Peptides, and Recombinant Proteins
Dynabeads Protein A	Invitrogen	1001D
4-thiouridine	Sigma	T4509
Goat anti-mouse beads	NEB	S1431S
Lipofectamine RNAimax	Invitrogen	13778-150
Micrococcal nuclease	NEB	M0247S
RQ1 DNase	Promega	M610A
Superscript III	Invitrogen	56575
Deposited Data
Raw and analyzed TT-TL-seq data	This paper	GSE152059
Raw and analyzed anti-Pol II ChIP-seq data	This paper	GSE152062
Raw and analyzed anti-Int3 and anti-Int11 data	This paper	GSE159190
Experimental Models: Cell Lines
HEK-293T	Steitz lab	N/A
HEK-293T 2x FLAG-Int11 WT	Xie et al. 2015	N/A
HEK-293T 2x FLAG-Int11 E203Q	Xie et al. 2015	N/A
Drosophila S2 cells	Simon lab	N/A
SK-N-BE(2)C	Steitz lab	N/A
Oligonucleotides
RT-qPCR primers	Table S5	N/A
siRNAs	Table S5	N/A
Northern blot probes	Table S5	N/A
Random primers	Invitrogen	58875
Software and Algorithms
ARTDeco	Roth et al. 2020	N/A
bedtools	Quinlan et al. 2010	N/A
Bowtie2	Langmead et al. 2009	N/A
Cutadapt	Martin 2011	N/A
DESeq2	Love et al. 2014	N/A
DoGFinder	Wiesel et al. 2018	N/A
edger	Robinson et al. 2010	N/A
enrichr	Chen et al. 2013; Kuleshov et al. 2016	N/A
eulerr	Larsson J (2020)	https://github.com/jolars/eulerr
FastUniq	Xu et al. 2012	N/A
ggplot2	Wickham. 2016	N/A
Hisat2	Kim et al. 2015	N/A
HTSeq	Anders et al. 2015	N/A
MACS2	Zhang et al. 2008	N/A
Prism	GraphPad	N/A
samtools	Li et al. 2009	N/A