Reagent or resource	Reference or source	Identifier or catalog number
Experimental model
Jurkat T cells, clone E6‐1	ATCC	TIB‐152
Antibodies
Anti‐histone H3 rabbit polyclonal	Abcam	ab1791
Anti‐acetyl‐histone H3 rabbit polyclonal	Millipore	06‐599
Anti‐NF‐κB p65 rabbit monoclonal	Cell Signaling Technology	8242
Anti‐RNPII N‐20 rabbit polyclonal	Santa Cruz Biotech	sc‐899
Anti‐ser5‐p RNPII rabbit polyclonal	Abcam	ab5131
Anti‐ser2‐p RNPII rabbit polyclonal	Abcam	ab5095
Anti‐NELF‐E H‐140 rabbit polyclonal	Santa Cruz Biotech	sc‐32912
Anti‐acetyl‐histone H3 rabbit monoclonal	Cell Signaling Technology	8173
Anti‐RNPII NTD rabbit monoclonal	Cell Signaling Technology	14958
Anti‐ser5‐p RNPII rabbit monoclonal	Cell Signaling Technology	13523
Anti‐TNF mouse monoclonal	eBioscience	14‐7348‐81
Anti‐mouse IgG goat polyclonal, conjugated with Alexa Fluor 647	Thermo Fisher Scientific	A‐21235
Chemicals, peptides, and other reagents
Roswell Park Memorial Institute 1640 medium (RPMI)	Thermo Fisher Scientific	11875119
Fetal bovine serum (FBS)	Atlanta Biologicals	S11150
Penicillin‐Streptomycin	Thermo Fisher Scientific	15140122
Human tumor necrosis factor‐alpha (TNF)	PeproTech	300‐01A
A‐485	Structural Genomics Consortium	6387
JQ1	Tocris	4499
Brefeldin A	BioLegend	420601
Sodium chloride (NaCl)	Thermo Fisher Scientific	7647‐14‐5
Tris‐EDTA, pH 8.0	Thermo Fisher Scientific	AM9858
Cell‐tak	Corning	354240
Lab‐Tek #1.0 8‐well chambered coverglass	Thermo Fisher Scientific	155411
μ‐Slide 8‐well glass bottom coverslip	Ibidi	80827
70% Ethanol, RNase‐Free	Thermo Fisher Scientific	15420665
20× saline‐sodium citrate (SSC)	Thermo Fisher Scientific	AM9763
Formamide	Thermo Fisher Scientific	AM9342
50% Dextran Sulfate	Amresco	E516
VectaShield	Vector Labs	H‐1000
37% formaldehyde	Sigma‐Aldrich	818708
10× Phosphate Buffered Saline (PBS)	Thermo Fisher Scientific	AM9625
Tween‐20	Thermo Fisher Scientific	9005‐64‐5
Bovine Serum Albumin (BSA)	Sigma	B4287
Hoechst 33342	Thermo Fisher Scientific	H21492
cOmpleteTM protease inhibitor cocktail	Roche	11836170001
PureProteome protein G magnetic beads	Millipore	LSKMAGG10
Salmon sperm DNA solution	Thermo Fisher Scientific	15632011
RNAse, DNAse‐free	Roche	11119915001
Proteinase K	New England BioLabs	P8107S
EDTA	American Bio	AB00502‐01000
Lithium Chloride (LiCl)	Sigma‐Aldrich	7447‐41‐8
IPEGAL CA630	Sigma‐Aldrich	I8896
Glycine	American Bio	AB00730‐01000
Agarose	Lonza	50074
20% SDS solution	American Bio	AB01922‐00500
Deoxycholic acid	Millipore	302‐95‐4
SYBR safe	Invitrogen	S33102
Actinomycin‐D	Millipore	114666
Sodium bicarbonate (NaHCO3)	Alfa Aesar	144‐55‐8
Triton X‐100	American Bio	AB02025‐00500
SYBR Green supermix	Bio‐Rad	1725271
Oligonucleotides
Primers for RT–qPCR and ChIP‐qPCR	Yale School of Medicine Keck Oligonucleotide Synthesis	Sequences available in Dataset EV2
smFISH probes	Biosearch Technologies	Sequences available in Dataset EV2
Commercial Kits
Upstate EZ‐Magna ChIP	Millipore	17‐10086
QIAQuick PCR purification kit	Qiagen	28104
RNeasy mini kit	Qiagen	74104
BD Cytofix/Cytoperm	BD Biosciences	554714
Software and algorithms
MATLAB 2016b, 2019b	MathWorks
FISH‐quant	Mueller et al (2013) and Tsarnov et al (2016)
Mathematica 12	Wolfram
Prism 7	GraphPad
FlowJo	FlowJo, LLC
NFsim	Sneddon et al (2011)