REAGENT OR RESOURCE	SOURCE	IDENTIFIER
Reagent
APH	Santa Cruz	Cat# sc-201535
Tetracycline (Tet)	Sigma	Cat# 87128
Primers
Random primers	Thermo Fisher	Cat# 48190011
Drosophila positive control primer set	Active motif	Cat# 71037
siRNAs
siLuc (custom siRNA)	Sigma	Sequence (5′-3′) Sense: GAUUAUGUCCGGUUAUGUAUU Antisense: [phos]UACAUAACCGGACAUAAUCUU
siSPT6 (human), SMART pool, ON-TARGETplus	Dharmacon (GE)	L-010540-00-0010
Antibodies
Mouse monoclonal anti-Pol II CTD, Total	MBL international	Cat# MABI0601; RRID: AB_2728735
Mouse monoclonal anti-Pol II CTD, phospho Ser2	MBL international	Cat# MABI0602; RRID: AB_2747403
Mouse monoclonal anti-Pol II CTD, phospho Ser5	MBL international	Cat# MABI0603; RRID: AB_2728736
Rat monoclonal anti-Pol II CTD, phospho Thr4 (6D7)	Active Motif	Cat# 61361; RRID: AB_2750848
Mouse monoclonal anti-Trimethyl Histone H3 (Lys36)	MBL international	Cat# MABI0333; RRID: AB_11126731
Mouse monoclonal anti-Trimethyl Histone H3 (Lys27)	MBL international	Cat# MABI0323; RRID: AB_11123929
Mouse monoclonal anti-Trimethyl Histone H3 (Lys4)	MBL international	Cat# MABI0304; RRID: AB_11123891
Mouse monoclonal anti-Monomethyl Histone H3 (Lys4)	MBL international	Cat# MABI0302; RRID: AB_11126551
Mouse monoclonal anti-H3	MBL international	Cat# MABI0301; RRID: AB_11142498
Rabbit polyclonal anti-Spt6	Novus Biologicals	Cat# NB100-2582; RRID: AB_2196402
Rabbit polyclonal anti-EXOSC3	Novus Biologicals	Cat# NBP2-22261; RRID: AB_2750849
Rabbit polyclonal anti- INTS3	Proteintech	Cat# 16620-1-AP; RRID: AB_2127274
Rabbit monoclonal anti-p57 Kip2 [EP2515Y]	Abcam	Cat# ab75974; RRID: AB_1310535
Rabbit monoclonal anti-p21 Waf1/Cip1 (12D1)	Cell Signaling	Cat# 2947; RRID: AB_823586
Mouse monoclonal anti-phospho Histone H2A.X Ser139, (JBW301)	Millipore	Cat# 05-636; RRID: AB_309864
Mouse monoclonal anti-RNA:DNA hybrids, (S9.6)	Proudfoot Lab	N/A; RRID: AB_2750851
Mouse monoclonal anti-V5 antibody	Thermo Fisher	Cat# R960-25; RRID: AB_2556564
Rabbit polyclonal anti-SETD2 antibody	Abcam	Cat#ab69836; RRID: AB_2185782
Deposited Data
Raw sequencing data	This paper	GEO: GSE110028
Re-analyzed ChIP-seq data	(Stadelmayer et al., 2014)	GEO: GSE60586
Re-analyzed Chromatin and Nucleosplasmic RNA-seq	(Schlackow et al., 2017)	GEO: GSE81662
RDIP-seq data	This paper	GEO: GSE120371
Re-analyzed EdU-seq data	(Macheret and Halazonetis, 2018)	SRA: PRJNA397123
Raw image data	Mendeley	https://doi.org/10.17632/gtgh75y4ct.1
Cell Lines
HeLa (human)	Proudfoot Lab	N/A
U2OS (human)	(Pfister et al., 2014)	Parental and SETD2 KO cells are available from Humphrey Lab by request.
V5-RNase H1 overexpressing HeLa (human)	this study	N/A
Gels
Novex 6% TBE gel, 12 well	Invitrogen	Cat# EC62652BOX
Novex 6% TBE-Urea (TBU) gel, 12 well	Invitrogen	Cat# EC68652BOX
Kits
Dynabeads mRNA Purification kit	Ambion	Cat# 61006
Superscript III first strand synthesis system	Thermo Fisher	Cat# 18080051
SensiMix SYBR Non ROX kit	Bioline	Cat# QT650
Ribo-Zero Gold rRNA removal kit (H/M/R)	Illumina	Cat# MRZG12324
Senescence β-gal staining kit	Cell Signaling	Cat# 9860
Quantitative cellular senescence assay kit (SA- β-gal, Fluorometric)	Cell Biolabs	Cat# CBA-232
NEBNext Ultra II DNA library prep kit for illumina	NEB	Cat# E7645S
NEBNext Ultra II Directional RNA library prep kit for illumina	NEB	Cat# E7760S
NEBNext small RNA library prep kit for Illumina	NEB	Cat# E7300S
QuantSeq 3′mRNA-Seq library prep kit REV for Illumina	LEXOGEN	Cat# SKU016.24.
Software and Algorithms
Cutadapt(v1.9.1)		https://cutadapt.readthedocs.io/en/stable/installation.html
Tophat(v2.1.0)		http://ccb.jhu.edu/software/tophat/index.shtml
Cufflinks(v2.2.0)		http://cole-trapnell-lab.github.io/cufflinks/getting_started/
bedtools (v2.25.0)		https://bedtools.readthedocs.io/en/latest/content/installation.html
Bowtie2 (v2.2.5)		http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
SAMtools (v1.6)		http://www.htslib.org/
Picard (v1.131)		http://broadinstitute.github.io/picard/
Deeptools (v2.5.3)		https://deeptools.readthedocs.io/en/latest/index.html
HTseq (v0.6.1)		https://htseq.readthedocs.io/en/release_0.9.1/#