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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	Wildtype & Untreated	QC score	Replicate
SRR7879124	2266	Sheridan2019widespread	Bru-seq	ligation	experimental	False	2	1
SRR7879125	2267	Sheridan2019widespread	Bru-seq	ligation	experimental	False	2	2
SRR7879126	2268	Sheridan2019widespread	Bru-seq	ligation	experimental	False	3	1
SRR7879127	2269	Sheridan2019widespread	Bru-seq	ligation	experimental	False	1	2
SRR7879128	2270	Sheridan2019widespread	Bru-seq	ligation	experimental	False	3	1
SRR7879129	2271	Sheridan2019widespread	Bru-seq	ligation	experimental	False	3	2
SRR7879130	2272	Sheridan2019widespread	Bru-seq	ligation	control	False	4	1
SRR7879131	2273	Sheridan2019widespread	Bru-seq	ligation	control	False	1	1
SRR7879132	2274	Sheridan2019widespread	Bru-seq	ligation	experimental	False	3	1
SRR7879133	2275	Sheridan2019widespread	Bru-seq	ligation	experimental	False	3	1
SRR7879134	2276	Sheridan2019widespread	Bru-seq	ligation	experimental	False	3	1
SRR7879135	2277	Sheridan2019widespread	Bru-seq	ligation	experimental	False	3	1
SRR7879136	2278	Sheridan2019widespread	Bru-seq	ligation	experimental	False	4	1
SRR7879137	2279	Sheridan2019widespread	Bru-seq	ligation	experimental	False	4	1
SRZ7879154	2280	Sheridan2019widespread	GRO-seq	ligation	experimental	False	4	1
SRZ7879156	2281	Sheridan2019widespread	GRO-seq	ligation	experimental	False	4	2
SRZ7879158	2282	Sheridan2019widespread	GRO-seq	ligation	control	False	4	1
SRZ7879160	2283	Sheridan2019widespread	GRO-seq	ligation	control	False	4	2
SRZ7879168	2284	Sheridan2019widespread	NET-seq	ligation	experimental	False	3	1
SRZ7879172	2285	Sheridan2019widespread	NET-seq	ligation	experimental	False	2	2
SRZ7879175	2286	Sheridan2019widespread	NET-seq	ligation	control	False	4	1
SRZ7879179	2287	Sheridan2019widespread	NET-seq	ligation	control	False	3	2

Cellular details

Sample name	Organism	Sample type	Cell type	Clone/Individual	Strain	Genotype	Construct
SRR7879124	H. sapiens	cell line	HEK293T Flp-In			dox-inducible TFIIS D282A, E283A (Flp knock-in)
SRR7879125	H. sapiens	cell line	HEK293T Flp-In			dox-inducible TFIIS D282A, E283A (Flp knock-in)
SRR7879126	H. sapiens	cell line	HEK293T Flp-In			dox-inducible TFIIS D282A, E283A (Flp knock-in)
SRR7879127	H. sapiens	cell line	HEK293T Flp-In			dox-inducible TFIIS D282A, E283A (Flp knock-in)
SRR7879128	H. sapiens	cell line	HEK293T Flp-In			dox-inducible TFIIS D282A, E283A (Flp knock-in)
SRR7879129	H. sapiens	cell line	HEK293T Flp-In			dox-inducible TFIIS D282A, E283A (Flp knock-in)
SRR7879130	H. sapiens	cell line	HEK293T Flp-In			dox-inducible TFIIS D282A, E283A (Flp knock-in)
SRR7879131	H. sapiens	cell line	HEK293T Flp-In			dox-inducible TFIIS D282A, E283A (Flp knock-in)
SRR7879132	H. sapiens	cell line	HEK293T Flp-In			dox-inducible TFIIS D282A, E283A (Flp knock-in)
SRR7879133	H. sapiens	cell line	HEK293T Flp-In			dox-inducible TFIIS D282A, E283A (Flp knock-in)
SRR7879134	H. sapiens	cell line	HEK293T Flp-In			dox-inducible TFIIS D282A, E283A (Flp knock-in)
SRR7879135	H. sapiens	cell line	HEK293T Flp-In			dox-inducible TFIIS D282A, E283A (Flp knock-in)
SRR7879136	H. sapiens	cell line	HEK293T Flp-In			dox-inducible TFIIS D282A, E283A (Flp knock-in)
SRR7879137	H. sapiens	cell line	HEK293T Flp-In			dox-inducible TFIIS D282A, E283A (Flp knock-in)
SRZ7879154	H. sapiens	cell line	HEK293T Flp-In			dox-inducible TFIIS D282A, E283A (Flp knock-in)
SRZ7879156	H. sapiens	cell line	HEK293T Flp-In			dox-inducible TFIIS D282A, E283A (Flp knock-in)
SRZ7879158	H. sapiens	cell line	HEK293T Flp-In			dox-inducible TFIIS D282A, E283A (Flp knock-in)
SRZ7879160	H. sapiens	cell line	HEK293T Flp-In			dox-inducible TFIIS D282A, E283A (Flp knock-in)
SRZ7879168	H. sapiens	cell line	HEK293T Flp-In			dox-inducible TFIIS D282A, E283A (Flp knock-in)
SRZ7879172	H. sapiens	cell line	HEK293T Flp-In			dox-inducible TFIIS D282A, E283A (Flp knock-in)
SRZ7879175	H. sapiens	cell line	HEK293T Flp-In			dox-inducible TFIIS D282A, E283A (Flp knock-in)
SRZ7879179	H. sapiens	cell line	HEK293T Flp-In			dox-inducible TFIIS D282A, E283A (Flp knock-in)

Conditions

Sample name	Condition type	Treatment	Start time	End time	Duration
SRR7879124	treatment	bromouridine (2 mM)	-30 min	0 min	30 min
	treatment	dimethyloxalylglycine (2 mM)	-16 hr	0 hr	16 hr
	treatment	doxycycline (2 microg/mL)	-40 hr	-16 hr	1 day
SRR7879125	treatment	bromouridine (2 mM)	-30 min	0 min	30 min
	treatment	dimethyloxalylglycine (2 mM)	-16 hr	0 hr	16 hr
	treatment	doxycycline (2 microg/mL)	-40 hr	-16 hr	1 day
SRR7879126	treatment	bromouridine (2 mM)	-30 min	0 min	30 min
	treatment	doxycycline (2 microg/mL)	-1 day	0 day	1 day
SRR7879127	treatment	bromouridine (2 mM)	-30 min	0 min	30 min
	treatment	doxycycline (2 microg/mL)	-1 day	0 day	1 day
SRR7879128	treatment	bromouridine (2 mM)	-30 min	0 min	30 min
	treatment	dimethyloxalylglycine (2 mM)	-16 hr	0 hr	16 hr
	vehicle	water	-40 hr	-16 hr	1 day
SRR7879129	treatment	bromouridine (2 mM)	-30 min	0 min	30 min
	treatment	dimethyloxalylglycine (2 mM)	-16 hr	0 hr	16 hr
	vehicle	water	-40 hr	-16 hr	1 day
SRR7879130	treatment	bromouridine (2 mM)	-30 min	0 min	30 min
	vehicle	water	-1 day	0 day	1 day
SRR7879131	treatment	bromouridine (2 mM)	-30 min	0 min	30 min
	vehicle	water	-1 day	0 day	1 day
SRR7879132	treatment	DRB (100 microM)	-190 min	-10 min	3 hr
	treatment	bromouridine (2 mM)	-10 min	0 min	10 min
	treatment	doxycycline (2 microg/mL)	-1630 min	-190 min	1 day
SRR7879133	treatment	DRB (100 microM)	-200 min	-20 min	3 hr
	treatment	bromouridine (2 mM)	-20 min	0 min	20 min
	treatment	doxycycline (2 microg/mL)	-1640 min	-200 min	1 day
SRR7879134	treatment	DRB (100 microM)	-185 min	-5 min	3 hr
	treatment	bromouridine (2 mM)	-5 min	0 min	5 min
	treatment	doxycycline (2 microg/mL)	-1625 min	-185 min	1 day
SRR7879135	treatment	DRB (100 microM)	-190 min	-10 min	3 hr
	treatment	bromouridine (2 mM)	-10 min	0 min	10 min
	vehicle	water	-1630 min	-190 min	1 day
SRR7879136	treatment	DRB (100 microM)	-200 min	-20 min	3 hr
	treatment	bromouridine (2 mM)	-20 min	0 min	20 min
	vehicle	water	-1640 min	-200 min	1 day
SRR7879137	treatment	DRB (100 microM)	-185 min	-5 min	3 hr
	treatment	bromouridine (2 mM)	-5 min	0 min	5 min
	vehicle	water	-1625 min	-185 min	1 day
SRZ7879154	treatment	doxycycline (2 microg/mL)	-1 day	0 day	1 day
SRZ7879156	treatment	doxycycline (2 microg/mL)	-1 day	0 day	1 day
SRZ7879158	no treatment		None	None	None
SRZ7879160	no treatment		None	None	None
SRZ7879168	treatment	doxycycline (2 microg/mL)	-1 day	0 day	1 day
SRZ7879172	treatment	doxycycline (2 microg/mL)	-1 day	0 day	1 day
SRZ7879175	no treatment		None	None	None
SRZ7879179	no treatment		None	None	None

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
SRR7879124	151	18,432,482	0.30763	0.9304	2.02895	0.74383	2	1
SRR7879125	151	16,879,551	0.20847	0.9629	1.77146	0.81273	2	1
SRR7879126	151	11,779,898	0.2824	0.956	1.8602	0.72267	3	1
SRR7879127	151	27,514,232	0.27806	0.9594	2.08499	0.78285	1	1
SRR7879128	151	10,208,030	0.27187	0.882	1.89451	0.70699	3	1
SRR7879129	151	13,027,136	0.19022	0.9639	1.48907	0.8129	3	1
SRR7879130	151	9,744,821	0.37657	0.9591	1.98837	0.60997	4	1
SRR7879131	151	26,708,147	0.28871	0.9634	1.95136	0.77544	1	1
SRR7879132	51	11,194,457	0.42546	0.9488	2.66334	0.57612	3	1
SRR7879133	51	12,576,345	0.32468	0.9486	3.24105	0.69007	3	2
SRR7879134	51	10,268,976	0.53522	0.9482	5.75097	0.45923	3	3
SRR7879135	51	10,768,145	0.34398	0.9384	2.36036	0.65322	3	1
SRR7879136	51	9,368,207	0.27259	0.9399	2.18689	0.71175	4	1
SRR7879137	51	8,348,245	0.49902	0.9482	5.38158	0.47849	4	3
SRZ7879154	51	21,603,771	0.87191	0.8998	4.11187	0.23202	4	2
SRZ7879156	151	34,097,578	0.88567	0.8787	3.50891	0.19891	4	2
SRZ7879158	51	23,253,314	0.81423	0.8889	4.52038	0.28083	4	2
SRZ7879160	151	30,458,510	0.84612	0.8807	3.87724	0.20302	4	2
SRZ7879168	151	42,594,458	0.73952	0.7629	3.29534	0.4914	3	2
SRZ7879172	151	23,866,660	0.60844	0.7531	4.28774	0.49701	2	2
SRZ7879175	151	39,622,391	0.85445	0.7834	3.40296	0.31868	4	2
SRZ7879179	151	29,897,175	0.65928	0.7442	4.68541	0.48774	3	2

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
SRR7879124	16833	6426	6602	2387	8421	4028	2596	1375
SRR7879125	10142	3771	4723	657	4944	2488	1770	385
SRR7879126	5628	2007	2745	257	2666	1488	837	210
SRR7879127	10489	4249	4712	622	8019	3780	2709	596
SRR7879128	12045	3636	4937	2226	4627	1938	1398	1161
SRR7879129	5839	1695	3091	427	2564	1192	1050	238
SRR7879130	5256	1863	2494	278	2027	1125	631	238
SRR7879131	9121	3552	4093	663	7004	3290	2500	560
SRR7879132	20049	7315	9063	1152	7919	3958	2631	597
SRR7879133	7970	2221	3498	669	5698	2264	2284	560
SRR7879134	23238	8800	10661	866	7576	3796	2442	604
SRR7879135	18095	6941	7805	1334	8156	3802	2909	686
SRR7879136	7312	2597	3307	545	4498	1917	1797	432
SRR7879137	22596	8519	10176	918	7433	3677	2396	545
SRZ7879154	20256	7925	9412	1591	7600	4069	2533	799
SRZ7879156	24421	10050	11145	1632	9500	5246	2988	943
SRZ7879158	29392	12502	12554	2569	13914	6794	4711	1566
SRZ7879160	26148	11122	11271	2135	12617	6661	3975	1330
SRZ7879168	31661	12292	14016	3733	18513	8577	7118	2505
SRZ7879172	31484	14150	12947	3508	18062	8979	6342	2328
SRZ7879175	21070	9389	8681	1754	13636	7067	4949	1296
SRZ7879179	31656	14268	12790	3634	18691	9059	6624	2422