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Gene read counts	Bidirectional read counts	Tfit regions	dREG regions
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Technical details

Sample name	Sample ID	Paper identifier	Protocol	Library prep	Control/Experimental	QC score	Replicate	Outlier?
SRR1661564	793	Fong2014pre	GRO-seq	ligation	control	5	1	No
SRR1661565	794	Fong2014pre	GRO-seq	ligation	control	4	1	No
SRR1661566	795	Fong2014pre	GRO-seq	ligation	control	4	1	No
SRR1661567	796	Fong2014pre	GRO-seq	ligation	control	4	1	No
SRR1661568	797	Fong2014pre	GRO-seq	ligation	experimental	5	1	No
SRR1661569	798	Fong2014pre	GRO-seq	ligation	experimental	5	1	No
SRR1661570	799	Fong2014pre	GRO-seq	ligation	experimental	5	1	No
SRR1661571	800	Fong2014pre	GRO-seq	ligation	experimental	5	1	No
SRR1661572	801	Fong2014pre	GRO-seq	ligation	experimental	5	1	No
SRR1661573	802	Fong2014pre	GRO-seq	ligation	experimental	5	1	No
SRR1661574	803	Fong2014pre	GRO-seq	ligation	experimental	5	1	No
SRR1661575	804	Fong2014pre	GRO-seq	ligation	experimental	5	1	No
SRR1661576	805	Fong2014pre	GRO-seq	ligation	experimental	4	1	No
SRR1661577	806	Fong2014pre	GRO-seq	ligation	experimental	4	1	No
SRR1661578	807	Fong2014pre	GRO-seq	ligation	experimental	5	1	No
SRR1661579	808	Fong2014pre	GRO-seq	ligation	experimental	5	1	No

Cellular details

Sample name	Organism	Sample type	Cell type	Clone/Individual	Strain	Genotype	Construct
SRR1661564	H. sapiens	cell line	HEK293 Flp-In			alpha-amanitin resistant, dox-inducible Rpb1 N792D (Flp knock-in)
SRR1661565	H. sapiens	cell line	HEK293 Flp-In			alpha-amanitin resistant, dox-inducible Rpb1 N792D (Flp knock-in)
SRR1661566	H. sapiens	cell line	HEK293 Flp-In			alpha-amanitin resistant, dox-inducible Rpb1 N792D (Flp knock-in)
SRR1661567	H. sapiens	cell line	HEK293 Flp-In			alpha-amanitin resistant, dox-inducible Rpb1 N792D (Flp knock-in)
SRR1661568	H. sapiens	cell line	HEK293 Flp-In			alpha-amanitin resistant, dox-inducible Rpb1 N792D/R749H (Flp knock-in)
SRR1661569	H. sapiens	cell line	HEK293 Flp-In			alpha-amanitin resistant, dox-inducible Rpb1 N792D/R749H (Flp knock-in)
SRR1661570	H. sapiens	cell line	HEK293 Flp-In			alpha-amanitin resistant, dox-inducible Rpb1 N792D/R749H (Flp knock-in)
SRR1661571	H. sapiens	cell line	HEK293 Flp-In			alpha-amanitin resistant, dox-inducible Rpb1 N792D/R749H (Flp knock-in)
SRR1661572	H. sapiens	cell line	HEK293 Flp-In			alpha-amanitin resistant, dox-inducible Rpb1 N792D/H1108Y (Flp knock-in)
SRR1661573	H. sapiens	cell line	HEK293 Flp-In			alpha-amanitin resistant, dox-inducible Rpb1 N792D/H1108Y (Flp knock-in)
SRR1661574	H. sapiens	cell line	HEK293 Flp-In			alpha-amanitin resistant, dox-inducible Rpb1 N792D/H1108Y (Flp knock-in)
SRR1661575	H. sapiens	cell line	HEK293 Flp-In			alpha-amanitin resistant, dox-inducible Rpb1 N792D/H1108Y (Flp knock-in)
SRR1661576	H. sapiens	cell line	HEK293 Flp-In			alpha-amanitin resistant, dox-inducible Rpb1 N792D/E1126G (Flp knock-in)
SRR1661577	H. sapiens	cell line	HEK293 Flp-In			alpha-amanitin resistant, dox-inducible Rpb1 N792D/E1126G (Flp knock-in)
SRR1661578	H. sapiens	cell line	HEK293 Flp-In			alpha-amanitin resistant, dox-inducible Rpb1 N792D/E1126G (Flp knock-in)
SRR1661579	H. sapiens	cell line	HEK293 Flp-In			alpha-amanitin resistant, dox-inducible Rpb1 N792D/E1126G (Flp knock-in)

Conditions

Sample name	Condition type	Treatment	Start time	End time	Duration
SRR1661564	treatment	alpha-amanitin (2.5 microg/mL)	-45 hr	-3 hr	42 hr
	treatment	doxycycline (2 microg/mL)	-59 hr	-45 hr	14 hr
SRR1661565	treatment	DRB (100 microM)	-3 hr	0 hr	3 hr
	treatment	alpha-amanitin (2.5 microg/mL)	-45 hr	-3 hr	42 hr
	treatment	doxycycline (2 microg/mL)	-59 hr	-45 hr	14 hr
SRR1661566	treatment	DRB (100 microM)	-190 min	-10 min	3 hr
	treatment	alpha-amanitin (2.5 microg/mL)	-2710 min	-190 min	42 hr
	treatment	doxycycline (2 microg/mL)	-3550 min	-2710 min	14 hr
SRR1661567	treatment	DRB (100 microM)	-200 min	-20 min	3 hr
	treatment	alpha-amanitin (2.5 microg/mL)	-2720 min	-200 min	42 hr
	treatment	doxycycline (2 microg/mL)	-3560 min	-2720 min	14 hr
SRR1661568	treatment	alpha-amanitin (2.5 microg/mL)	-45 hr	-3 hr	42 hr
	treatment	doxycycline (2 microg/mL)	-59 hr	-45 hr	14 hr
SRR1661569	treatment	DRB (100 microM)	-3 hr	0 hr	3 hr
	treatment	alpha-amanitin (2.5 microg/mL)	-45 hr	-3 hr	42 hr
	treatment	doxycycline (2 microg/mL)	-59 hr	-45 hr	14 hr
SRR1661570	treatment	DRB (100 microM)	-190 min	-10 min	3 hr
	treatment	alpha-amanitin (2.5 microg/mL)	-2710 min	-190 min	42 hr
	treatment	doxycycline (2 microg/mL)	-3550 min	-2710 min	14 hr
SRR1661571	treatment	DRB (100 microM)	-200 min	-20 min	3 hr
	treatment	alpha-amanitin (2.5 microg/mL)	-2720 min	-200 min	42 hr
	treatment	doxycycline (2 microg/mL)	-3560 min	-2720 min	14 hr
SRR1661572	treatment	alpha-amanitin (2.5 microg/mL)	-45 hr	-3 hr	42 hr
	treatment	doxycycline (2 microg/mL)	-59 hr	-45 hr	14 hr
SRR1661573	treatment	DRB (100 microM)	-3 hr	0 hr	3 hr
	treatment	alpha-amanitin (2.5 microg/mL)	-45 hr	-3 hr	42 hr
	treatment	doxycycline (2 microg/mL)	-59 hr	-45 hr	14 hr
SRR1661574	treatment	DRB (100 microM)	-190 min	-10 min	3 hr
	treatment	alpha-amanitin (2.5 microg/mL)	-2710 min	-190 min	42 hr
	treatment	doxycycline (2 microg/mL)	-3550 min	-2710 min	14 hr
SRR1661575	treatment	DRB (100 microM)	-200 min	-20 min	3 hr
	treatment	alpha-amanitin (2.5 microg/mL)	-2720 min	-200 min	42 hr
	treatment	doxycycline (2 microg/mL)	-3560 min	-2720 min	14 hr
SRR1661576	treatment	alpha-amanitin (2.5 microg/mL)	-45 hr	-3 hr	42 hr
	treatment	doxycycline (2 microg/mL)	-59 hr	-45 hr	14 hr
SRR1661577	treatment	DRB (100 microM)	-3 hr	0 hr	3 hr
	treatment	alpha-amanitin (2.5 microg/mL)	-45 hr	-3 hr	42 hr
	treatment	doxycycline (2 microg/mL)	-59 hr	-45 hr	14 hr
SRR1661578	treatment	DRB (100 microM)	-190 min	-10 min	3 hr
	treatment	alpha-amanitin (2.5 microg/mL)	-2710 min	-190 min	42 hr
	treatment	doxycycline (2 microg/mL)	-3550 min	-2710 min	14 hr
SRR1661579	treatment	DRB (100 microM)	-200 min	-20 min	3 hr
	treatment	alpha-amanitin (2.5 microg/mL)	-2720 min	-200 min	42 hr
	treatment	doxycycline (2 microg/mL)	-3560 min	-2720 min	14 hr

Sample metrics

Sample name	Raw read length	Trim read depth	Duplication proportion	Proportion reads mapped	Exon/intron ratio	Unique read proportion	Sample QC score	Sample NRO score
SRR1661564	38	5,669,326	0.66851	0.5945	2.11688	0.27941	5	1
SRR1661565	38	13,307,153	0.80681	0.6611	3.76033	0.18641	4	2
SRR1661566	38	7,731,274	0.70896	0.5636	2.21111	0.25575	4	1
SRR1661567	38	6,846,560	0.66792	0.6429	2.36957	0.29575	4	1
SRR1661568	40	8,507,336	0.79936	0.3488	1.53846	0.15823	5	1
SRR1661569	40	6,541,340	0.81693	0.3363	1.8	0.11765	5	1
SRR1661570	40	9,122,147	0.80651	0.4358	1.98305	0.165	5	1
SRR1661571	40	4,659,630	0.78206	0.2379	1.38095	0.09753	5	2
SRR1661572	40	4,454,837	0.81041	0.4191	1.56522	0.1326	5	1
SRR1661573	40	4,125,732	0.83004	0.5761	2.22222	0.12415	5	1
SRR1661574	40	5,515,773	0.85696	0.5436	2.28125	0.11021	5	1
SRR1661575	40	3,855,230	0.82596	0.5573	1.69231	0.12337	5	1
SRR1661576	40	8,236,212	0.75304	0.6017	3.02532	0.22777	4	2
SRR1661577	40	8,098,585	0.81869	0.625	3.30508	0.16198	4	2
SRR1661578	40	5,756,620	0.72425	0.4165	2.55814	0.21817	5	1
SRR1661579	40	6,778,957	0.72988	0.4837	2.59259	0.2333	5	1

Bidirectionals

Sample name	Tfit total bidirs	Tfit promoter bidirs	Tfit intronic bidirs	Tfit intergenic bidirs	dREG total bidirs	dREG promoter bidirs	dREG intronic bidirs	dREG intergenic bidirs
SRR1661564	4690	2665	1880	232	1080	681	257	187
SRR1661565	12569	7612	4849	732	10551	6883	3088	713
SRR1661566	3036	1595	1244	240	1181	651	304	268
SRR1661567	2407	1291	969	205	1151	605	275	305
SRR1661568	344	168	165	51	362	128	80	165
SRR1661569	1487	1066	438	79	1068	859	167	104
SRR1661570	1709	809	773	141	552	244	148	190
SRR1661571	135	85	63	20	155	61	25	71
SRR1661572	221	122	104	48	263	98	50	122
SRR1661573	456	299	170	48	341	130	79	146
SRR1661574	700	431	306	59	449	196	126	165
SRR1661575	266	142	134	46	312	117	66	144
SRR1661576	893	438	342	98	716	279	228	262
SRR1661577	4696	2551	1946	227	1771	1027	517	208
SRR1661578	529	270	233	66	454	181	124	175
SRR1661579	613	295	264	91	629	223	184	265