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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
SRR6347627	1904	Nair2019phase	GRO-seq	circularization	control	True	1	1
SRR6347628	1905	Nair2019phase	GRO-seq	circularization	experimental	False	1	1
SRR6347629	1906	Nair2019phase	GRO-seq	circularization	control	True	1	1
SRR6347630	1907	Nair2019phase	GRO-seq	circularization	experimental	False	1	1
SRR7550986	1908	Nair2019phase	GRO-seq	circularization	control	True	1	1
SRR7550987	1909	Nair2019phase	GRO-seq	circularization	experimental	False	1	1
SRR7550988	1910	Nair2019phase	GRO-seq	circularization	control	True	3	1
SRR7550989	1911	Nair2019phase	GRO-seq	circularization	experimental	False	2	1
SRR7550990	1912	Nair2019phase	GRO-seq	circularization	control	True	1	1
SRR7550991	1913	Nair2019phase	GRO-seq	circularization	experimental	False	1	1
SRR7550992	1914	Nair2019phase	GRO-seq	circularization	experimental	False	2	1
SRR7550993	1915	Nair2019phase	GRO-seq	circularization	control	False	2	1
SRR7550994	1916	Nair2019phase	GRO-seq	circularization	experimental	False	2	1
SRR7550995	1917	Nair2019phase	GRO-seq	circularization	control	False	3	1
SRR7550996	1918	Nair2019phase	GRO-seq	circularization	experimental	False	3	1
SRR8419429	1919	Nair2019phase	GRO-seq	circularization	control	False	1	1
SRR8419430	1920	Nair2019phase	GRO-seq	circularization	experimental	False	1	1
SRR8419431	1921	Nair2019phase	GRO-seq	circularization	experimental	False	1	1

Cellular details

Sample name	Organism	Sample type	Cell type	Clone/Individual	Strain	Genotype	Construct
SRR6347627	H. sapiens	cell line	MCF7
SRR6347628	H. sapiens	cell line	MCF7
SRR6347629	H. sapiens	cell line	MCF7
SRR6347630	H. sapiens	cell line	MCF7
SRR7550986	H. sapiens	cell line	MCF7
SRR7550987	H. sapiens	cell line	MCF7
SRR7550988	H. sapiens	cell line	MCF7
SRR7550989	H. sapiens	cell line	MCF7
SRR7550990	H. sapiens	cell line	MCF7
SRR7550991	H. sapiens	cell line	MCF7
SRR7550992	H. sapiens	cell line	MCF7
SRR7550993	M. musculus	cell line	RAW264.7
SRR7550994	M. musculus	cell line	RAW264.7
SRR7550995	M. musculus	cell line	RAW264.7
SRR7550996	M. musculus	cell line	RAW264.7
SRR8419429	H. sapiens	cell line	MCF7
SRR8419430	H. sapiens	cell line	MCF7
SRR8419431	H. sapiens	cell line	MCF7

Conditions

Sample name	Condition type	Treatment	Start time	End time	Duration
SRR6347627	vehicle	ethanol	-30 min	0 min	30 min
	treatment	1,6-hexanediol (8.5 percent)	-35 min	-30 min	5 min
SRR6347628	treatment	1,6-hexanediol (8.5 percent)	-35 min	-30 min	5 min
	treatment	17-beta-estradiol (100 nM)	-30 min	0 min	30 min
SRR6347629	vehicle	ethanol	-30 min	0 min	30 min
	treatment	2,5-hexanediol (8.5 percent)	-35 min	-30 min	5 min
SRR6347630	treatment	17-beta-estradiol (100 nM)	-30 min	0 min	30 min
	treatment	2,5-hexanediol (8.5 percent)	-35 min	-30 min	5 min
SRR7550986	vehicle	ethanol	-30 min	0 min	30 min
	treatment	2,5-hexanediol (8 percent)	-35 min	-30 min	5 min
SRR7550987	treatment	2,5-hexanediol (8 percent)	-35 min	-30 min	5 min
	treatment	TNF-alpha (100 nM)	-30 min	0 min	30 min
SRR7550988	vehicle	ethanol	-30 min	0 min	30 min
	treatment	1,6-hexanediol (8 percent)	-35 min	-30 min	5 min
SRR7550989	treatment	1,6-hexanediol (8 percent)	-35 min	-30 min	5 min
	treatment	TNF-alpha (100 nM)	-30 min	0 min	30 min
SRR7550990	treatment	2,5-hexanediol (8 percent)	-5 min	0 min	5 min
	vehicle	ethanol	-845 min	-5 min	14 hr
SRR7550991	treatment	17-beta-estradiol (100 nM)	-845 min	-5 min	14 hr
	treatment	2,5-hexanediol (8.5 percent)	-5 min	0 min	5 min
SRR7550992	treatment	1,6-hexanediol (8.5 percent)	-5 min	0 min	5 min
	treatment	17-beta-estradiol (100 nM)	-845 min	-5 min	14 hr
SRR7550993	treatment	2,5-hexanediol (8.5 percent)	-5 min	0 min	5 min
SRR7550994	treatment	2,5-hexanediol (8.5 percent)	-35 min	-5 min	30 min
	treatment	Kdo2-Lipid A (100 nM)	-5 min	0 min	5 min
SRR7550995	treatment	1,6-hexanediol (8.5 percent)	-5 min	0 min	5 min
SRR7550996	treatment	1,6-hexanediol (8.5 percent)	-35 min	-5 min	30 min
	treatment	Kdo2-Lipid A (100 nM)	-5 min	0 min	5 min
SRR8419429	treatment	ICI 182,780	-3 hr	0 hr	3 hr
SRR8419430	treatment	17-beta-estradiol (100 nM)	-30 min	0 min	30 min
	treatment	2,5-hexanediol (8.5 percent)	-35 min	-30 min	5 min
SRR8419431	treatment	17-beta-estradiol (100 nM)	-905 min	-5 min	15 hr
	treatment	2,5-hexanediol (8.5 percent)	-5 min	0 min	5 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
SRR6347627	75	32,926,479	0.36159	0.8764	3.13484	0.71476	1	2
SRR6347628	75	25,911,237	0.42706	0.8684	3.44284	0.622	1	2
SRR6347629	75	27,142,984	0.39924	0.8838	2.75157	0.64281	1	1
SRR6347630	75	27,722,454	0.32499	0.8605	2.62414	0.71997	1	1
SRR7550986	100	45,128,308	0.38622	0.7948	2.19689	0.69749	1	1
SRR7550987	100	50,117,111	0.43041	0.8015	2.23114	0.66283	1	1
SRR7550988	100	47,641,350	0.73268	0.7241	4.22942	0.301	3	2
SRR7550989	100	51,759,246	0.62945	0.7158	3.55676	0.46393	2	2
SRR7550990	75	55,420,788	0.27842	0.7499	3.22465	0.8287	1	2
SRR7550991	75	54,857,045	0.35602	0.9257	3.47588	0.75177	1	2
SRR7550992	75	51,929,157	0.51497	0.916	5.21846	0.64075	2	3
SRR7550993	100	51,058,234	0.5479	0.7194	2.18554	0.53896	2	1
SRR7550994	100	51,886,244	0.59024	0.7535	2.36488	0.52597	2	2
SRR7550995	100	48,389,393	0.70663	0.6793	3.0304	0.36753	3	2
SRR7550996	100	49,118,375	0.70704	0.6909	2.77494	0.36419	3	1
SRR8419429	75	55,420,788	0.27843	0.7499	3.22465	0.82864	1	2
SRR8419430	75	56,241,983	0.34354	0.9321	3.16202	0.78255	1	2
SRR8419431	75	45,670,350	0.30983	0.7863	3.34495	0.77419	1	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
SRR6347627	35256	14433	14355	6197	24592	8856	10423	5293
SRR6347628	32597	13815	13369	5211	21769	8568	9020	4311
SRR6347629	24380	10099	10163	3728	17580	8081	6779	2939
SRR6347630	26135	11385	10611	3977	18570	8178	7061	3377
SRR7550986	34182	9784	16028	7347	21142	7243	8931	4861
SRR7550987	34588	9272	16526	7553	20887	6814	9061	4818
SRR7550988	30248	10193	14076	3824	14473	6267	5793	2527
SRR7550989	45547	14217	20563	8405	24602	8128	10695	5746
SRR7550990	30678	13094	11983	5088	21156	7801	8448	4307
SRR7550991	32889	14324	12282	5532	21688	7981	8312	4707
SRR7550992	39834	18052	14793	6735	26452	8908	10393	6097
SRR7550993	27755	7384	11778	5935	18640	4946	6866	5117
SRR7550994	21898	4412	10094	5220	14396	3176	5655	4532
SRR7550995	26948	7511	10334	5519	16097	5225	5189	4195
SRR7550996	23622	6277	9371	4879	14293	4530	4648	3856
SRR8419429	30744	13107	12035	5101	21199	7816	8456	4323
SRR8419430	34027	13542	12898	6579	23819	7745	9865	5424
SRR8419431	29817	13551	11527	4242	18366	7743	6769	3424