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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
SRR1648886	2087	Puc2015ligand	GRO-seq	circularization	control	False	3	1
SRR1648887	2088	Puc2015ligand	GRO-seq	circularization	experimental	False	2	1
SRR1648888	2089	Puc2015ligand	GRO-seq	circularization	experimental	False	2	1
SRR1648889	2090	Puc2015ligand	GRO-seq	circularization	experimental	False	2	1
SRR1648890	2091	Puc2015ligand	GRO-seq	circularization	control	False	3	2
SRR1648891	2092	Puc2015ligand	GRO-seq	circularization	experimental	False	3	2
SRR1648892	2093	Puc2015ligand	GRO-seq	circularization	experimental	False	2	1
SRR1648893	2094	Puc2015ligand	GRO-seq	circularization	experimental	False	2	1
SRR1648894	2095	Puc2015ligand	GRO-seq	circularization	experimental	False	2	1
SRR1648895	2096	Puc2015ligand	GRO-seq	circularization	experimental	False	2	1
SRR1648900	2097	Puc2015ligand	GRO-seq	circularization	experimental	False	2	2
SRR1648901	2098	Puc2015ligand	GRO-seq	circularization	experimental	False	3	2
SRR1648909	2101	Puc2015ligand	GRO-seq	circularization	control	False	3	4
SRR1648910	2102	Puc2015ligand	GRO-seq	circularization	experimental	False	3	4
SRR1648911	2103	Puc2015ligand	GRO-seq	circularization	experimental	False	3	2
SRR1648912	2104	Puc2015ligand	GRO-seq	circularization	experimental	False	2	2
SRZ1648896	2105	Puc2015ligand	GRO-seq	circularization	control	False	2	3
SRZ1648898	2106	Puc2015ligand	GRO-seq	circularization	experimental	False	3	3
SRR1648904	2099	Puc2015ligand	PRO-cap	ligation	control	True	5	1
SRR1648905	2100	Puc2015ligand	PRO-cap	ligation	experimental	False	4	1

Cellular details

Sample name	Organism	Sample type	Cell type	Clone/Individual	Strain	Genotype	Construct
SRR1648886	H. sapiens	cell line	LNCaP				siRNA control
SRR1648887	H. sapiens	cell line	LNCaP				siRNA control
SRR1648888	H. sapiens	cell line	LNCaP				siRNA Top1
SRR1648889	H. sapiens	cell line	LNCaP				siRNA Top1
SRR1648890	H. sapiens	cell line	LNCaP				siRNA control
SRR1648891	H. sapiens	cell line	LNCaP				siRNA control
SRR1648892	H. sapiens	cell line	LNCaP				siRNA Mre11
SRR1648893	H. sapiens	cell line	LNCaP				siRNA Mre11
SRR1648894	H. sapiens	cell line	LNCaP				siRNA Nkx3-1
SRR1648895	H. sapiens	cell line	LNCaP				siRNA Nkx3-1
SRR1648900	H. sapiens	cell line	LNCaP				siRNA Mre11
SRR1648901	H. sapiens	cell line	LNCaP				siRNA Mre11
SRR1648909	H. sapiens	cell line	LNCaP				siRNA control
SRR1648910	H. sapiens	cell line	LNCaP				siRNA control
SRR1648911	H. sapiens	cell line	LNCaP				siRNA Top1
SRR1648912	H. sapiens	cell line	LNCaP				siRNA Top1
SRZ1648896	H. sapiens	cell line	LNCaP				siRNA control
SRZ1648898	H. sapiens	cell line	LNCaP				siRNA control
SRR1648904	H. sapiens	cell line	LNCaP
SRR1648905	H. sapiens	cell line	LNCaP

Conditions

Sample name	Condition type	Treatment	Start time	End time	Duration
SRR1648886	vehicle	ethanol	-1 hr	0 hr	1 hr
SRR1648887	treatment	dihydrotestosterone (100 nM)	-1 hr	0 hr	1 hr
SRR1648888	vehicle	ethanol	-1 hr	0 hr	1 hr
SRR1648889	treatment	dihydrotestosterone (100 nM)	-1 hr	0 hr	1 hr
SRR1648890	vehicle	ethanol	-1 hr	0 hr	1 hr
SRR1648891	treatment	dihydrotestosterone (100 nM)	-1 hr	0 hr	1 hr
SRR1648892	vehicle	ethanol	-1 hr	0 hr	1 hr
SRR1648893	treatment	dihydrotestosterone (100 nM)	-1 hr	0 hr	1 hr
SRR1648894	vehicle	ethanol	-1 hr	0 hr	1 hr
SRR1648895	treatment	dihydrotestosterone (100 nM)	-1 hr	0 hr	1 hr
SRR1648900	vehicle	ethanol	-1 hr	0 hr	1 hr
SRR1648901	treatment	dihydrotestosterone (100 nM)	-1 hr	0 hr	1 hr
SRR1648909	vehicle	ethanol	-1 hr	0 hr	1 hr
SRR1648910	treatment	dihydrotestosterone (100 nM)	-1 hr	0 hr	1 hr
SRR1648911	vehicle	ethanol	-1 hr	0 hr	1 hr
SRR1648912	treatment	dihydrotestosterone (100 nM)	-1 hr	0 hr	1 hr
SRZ1648896	vehicle	ethanol	-1 hr	0 hr	1 hr
SRZ1648898	treatment	dihydrotestosterone (100 nM)	-1 hr	0 hr	1 hr
SRR1648904	vehicle	ethanol	-1 hr	0 hr	1 hr
SRR1648905	treatment	dihydrotestosterone (100 nM)	-1 hr	0 hr	1 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
SRR1648886	50	26,659,401	0.67115	0.9387	2.37705	0.38123	3	1
SRR1648887	50	31,414,743	0.63774	0.9411	2.29958	0.3999	2	1
SRR1648888	50	28,258,592	0.62822	0.9456	2.36252	0.39939	2	1
SRR1648889	50	27,473,271	0.63156	0.944	2.24649	0.4001	2	1
SRR1648890	50	24,915,818	0.65042	0.901	2.50898	0.36882	3	1
SRR1648891	50	25,906,620	0.65403	0.9008	2.63301	0.36383	3	1
SRR1648892	50	22,385,772	0.63909	0.9301	2.7666	0.37766	2	1
SRR1648893	50	27,778,062	0.62782	0.8923	2.59619	0.39352	2	1
SRR1648894	50	23,791,530	0.61112	0.9438	2.32975	0.40962	2	1
SRR1648895	50	22,685,121	0.57457	0.9458	2.25569	0.4446	2	1
SRR1648900	50	36,984,484	0.64589	0.8715	2.42308	0.44789	2	1
SRR1648901	50	25,971,988	0.65317	0.886	2.69216	0.37531	3	1
SRR1648909	50	45,264,120	0.66772	0.9443	3.02527	0.36216	3	2
SRR1648910	50	46,758,232	0.68455	0.9472	2.99671	0.34517	3	1
SRR1648911	50	41,117,646	0.65668	0.9385	3.00238	0.36946	3	2
SRR1648912	50	37,114,660	0.62521	0.948	2.89212	0.40059	2	1
SRZ1648896	50	44,432,835	0.62618	0.8598	2.39626	0.45687	2	1
SRZ1648898	50	62,856,466	0.66707	0.9041	2.44597	0.41622	3	1
SRR1648904	51	8,581,255	0.6013	0.2351	6.60377	0.15958	5	3
SRR1648905	51	19,377,453	0.59388	0.2857	5.23529	0.304	4	3

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
SRR1648886	12966	6600	4718	1563	10292	6152	3206	1306
SRR1648887	16400	8154	6085	2185	12708	7091	4234	1771
SRR1648888	14652	7472	5347	1727	10843	6312	3467	1389
SRR1648889	13443	7101	4806	1435	10163	6083	3096	1287
SRR1648890	12580	6843	4562	1247	9414	6018	2684	1094
SRR1648891	12240	6860	4316	1090	9284	5983	2628	1011
SRR1648892	11082	6197	3723	981	7545	4907	2073	821
SRR1648893	13369	7551	4607	1230	9792	6210	2856	1065
SRR1648894	13455	7153	4861	1501	9970	6057	3074	1180
SRR1648895	12874	6829	4633	1448	9840	6021	2976	1187
SRR1648900	18298	8257	7372	2678	14172	7151	5048	2271
SRR1648901	16936	8404	6439	2170	12803	7550	4118	1650
SRR1648909	20210	9885	7211	2890	14277	7245	4854	2330
SRR1648910	18791	9081	6734	2616	13753	7092	4736	2110
SRR1648911	19227	9004	7031	2865	13423	6665	4623	2310
SRR1648912	17446	8084	6418	2582	12764	6390	4440	2114
SRZ1648896	23210	10165	9139	4004	18984	8416	7288	3483
SRZ1648898	26675	12290	9771	4759	21881	8936	8869	4273
SRR1648904	8119	5041	2766	588	8121	6342	1992	404
SRR1648905	14847	7330	5959	1731	13157	8874	4060	1018