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Downloads

Gene read counts	Bidirectional read counts	Tfit regions	dREG regions
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For TDF visualization files please see individual sample downloads or dataset pages for prebuilt ZIP archives.

Technical details

Sample name	Sample ID	Paper identifier	Protocol	Library prep	Control/Experimental	Wildtype & Untreated	QC score	Replicate
SRR579293	559	Danko2013signaling	GRO-seq	ligation	control	True	1	1
SRR579294	560	Danko2013signaling	GRO-seq	ligation	control	True	1	2
SRR579295	561	Danko2013signaling	GRO-seq	ligation	experimental	False	1	1
SRR579296	562	Danko2013signaling	GRO-seq	ligation	experimental	False	2	2
SRR579297	563	Danko2013signaling	GRO-seq	ligation	experimental	False	2	1
SRR579298	564	Danko2013signaling	GRO-seq	ligation	experimental	False	1	2
SRZ579299	565	Danko2013signaling	GRO-seq	circularization	control	True	1	1
SRZ579310	566	Danko2013signaling	GRO-seq	circularization	control	True	3	2
SRZ579319	567	Danko2013signaling	GRO-seq	circularization	control	True	4	3
SRZ579324	568	Danko2013signaling	GRO-seq	circularization	experimental	False	1	1
SRZ579335	569	Danko2013signaling	GRO-seq	circularization	experimental	False	2	2
SRZ579342	570	Danko2013signaling	GRO-seq	circularization	experimental	False	3	3
SRZ579347	571	Danko2013signaling	GRO-seq	circularization	experimental	False	2	1
SRZ579353	572	Danko2013signaling	GRO-seq	circularization	experimental	False	1	2
SRZ579360	573	Danko2013signaling	GRO-seq	circularization	experimental	False	3	1
SRZ579364	574	Danko2013signaling	GRO-seq	circularization	experimental	False	1	2
SRZ579370	575	Danko2013signaling	GRO-seq	circularization	experimental	False	3	3

Cellular details

Sample name	Organism	Sample type	Cell type	Clone/Individual	Strain	Genotype	Construct
SRR579293	H. sapiens	cell line	AC16
SRR579294	H. sapiens	cell line	AC16
SRR579295	H. sapiens	cell line	AC16
SRR579296	H. sapiens	cell line	AC16
SRR579297	H. sapiens	cell line	AC16
SRR579298	H. sapiens	cell line	AC16
SRZ579299	H. sapiens	cell line	MCF7
SRZ579310	H. sapiens	cell line	MCF7
SRZ579319	H. sapiens	cell line	MCF7
SRZ579324	H. sapiens	cell line	MCF7
SRZ579335	H. sapiens	cell line	MCF7
SRZ579342	H. sapiens	cell line	MCF7
SRZ579347	H. sapiens	cell line	MCF7
SRZ579353	H. sapiens	cell line	MCF7
SRZ579360	H. sapiens	cell line	MCF7
SRZ579364	H. sapiens	cell line	MCF7
SRZ579370	H. sapiens	cell line	MCF7

Conditions

Sample name	Condition type	Treatment	Start time	End time	Duration
SRR579293	no treatment		None	None	None
SRR579294	no treatment		None	None	None
SRR579295	treatment	TNF-alpha (25 ng/mL)	-10 min	0 min	10 min
SRR579296	treatment	TNF-alpha (25 ng/mL)	-10 min	0 min	10 min
SRR579297	treatment	TNF-alpha (25 ng/mL)	-30 min	0 min	30 min
SRR579298	treatment	TNF-alpha (25 ng/mL)	-30 min	0 min	30 min
SRZ579299	no treatment		None	None	None
SRZ579310	no treatment		None	None	None
SRZ579319	no treatment		None	None	None
SRZ579324	treatment	17-beta-estradiol (100 nM)	-10 min	0 min	10 min
SRZ579335	treatment	17-beta-estradiol (100 nM)	-10 min	0 min	10 min
SRZ579342	treatment	17-beta-estradiol (100 nM)	-10 min	0 min	10 min
SRZ579347	treatment	17-beta-estradiol (100 nM)	-25 min	0 min	25 min
SRZ579353	treatment	17-beta-estradiol (100 nM)	-25 min	0 min	25 min
SRZ579360	treatment	17-beta-estradiol (100 nM)	-40 min	0 min	40 min
SRZ579364	treatment	17-beta-estradiol (100 nM)	-40 min	0 min	40 min
SRZ579370	treatment	17-beta-estradiol (100 nM)	-40 min	0 min	40 min

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
SRR579293	43	21,543,740	0.29856	0.8315	2.45627	0.74155	1	1
SRR579294	43	23,182,200	0.29562	0.867	2.07443	0.76177	1	1
SRR579295	38	21,095,684	0.33488	0.8221	2.89621	0.70533	1	1
SRR579296	38	17,926,564	0.36843	0.8586	2.70813	0.683	2	1
SRR579297	38	15,902,227	0.33408	0.8235	2.45397	0.69053	2	1
SRR579298	43	21,457,631	0.28897	0.8718	1.78175	0.76133	1	1
SRZ579299	50	40,550,753	0.41003	0.7626	4.05853	0.68875	1	2
SRZ579310	50	26,912,237	0.75662	0.827	2.3266	0.39984	3	1
SRZ579319	50	13,011,410	0.86952	0.7866	2.58967	0.16425	4	1
SRZ579324	50	46,003,041	0.35857	0.8072	3.67191	0.73606	1	2
SRZ579335	50	23,957,980	0.52974	0.8145	2.51052	0.59002	2	1
SRZ579342	50	10,153,847	0.6124	0.8014	2.19375	0.37347	3	1
SRZ579347	50	19,255,335	0.44662	0.8217	3.166	0.59801	2	2
SRZ579353	50	23,258,177	0.4966	0.8363	3.23701	0.59599	1	2
SRZ579360	50	14,786,814	0.42151	0.8078	2.60969	0.59221	3	1
SRZ579364	50	21,231,771	0.36645	0.8377	2.85446	0.6948	1	1
SRZ579370	50	32,454,616	0.76911	0.8309	2.14379	0.45895	3	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
SRR579293	40803	15446	16789	8779	25920	9408	10698	5949
SRR579294	45412	12388	21592	10131	26676	8495	11287	6730
SRR579295	39606	14216	16674	8961	26309	9223	11146	6012
SRR579296	36709	9005	19089	7075	19467	7182	8204	3854
SRR579297	32899	11220	14608	7175	20625	7715	8725	4228
SRR579298	39784	9912	19716	9272	23422	6934	10805	5635
SRZ579299	34727	16314	12728	6700	28320	9875	11609	6506
SRZ579310	18262	7747	7878	2279	13988	8288	4689	1698
SRZ579319	5176	2575	1748	612	4471	3396	1015	428
SRZ579324	42865	17161	15983	10485	34072	9777	14949	8790
SRZ579335	28815	11170	12627	4535	19097	9196	7271	2995
SRZ579342	14232	5687	5709	2327	9752	6371	2836	1151
SRZ579347	26390	12210	10017	4376	18979	9201	7023	2960
SRZ579353	29553	13048	11436	5102	19606	9089	7343	3228
SRZ579360	20081	9691	7692	2806	14850	8388	4988	1889
SRZ579364	28251	13146	10698	4763	20258	9325	7980	3317
SRZ579370	19869	7491	8424	3123	14192	7858	4811	2016