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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
SRR6780909	585	Danko2018dynamic	PRO-seq	ligation	control	True	1	3
SRR6780910	586	Danko2018dynamic	PRO-seq	ligation	experimental	False	1	3
SRZ4012415	596	Danko2018dynamic	PRO-seq	ligation	control	True	4	4
SRZ4012417	597	Danko2018dynamic	PRO-seq	ligation	control	True	3	1
SRZ4012420	598	Danko2018dynamic	PRO-seq	ligation	experimental	False	4	1
SRZ4012423	599	Danko2018dynamic	PRO-seq	ligation	control	True	2	2
SRZ4012426	600	Danko2018dynamic	PRO-seq	ligation	experimental	False	3	2
SRR4012429	581	Danko2018dynamic	PRO-seq	ligation	control	True	3	1
SRR4012413	579	Danko2018dynamic	PRO-seq	ligation	control	True	1	3
SRR4012414	580	Danko2018dynamic	PRO-seq	ligation	experimental	False	1	3
SRZ4012404	592	Danko2018dynamic	PRO-seq	ligation	control	True	3	1
SRZ4012406	593	Danko2018dynamic	PRO-seq	ligation	experimental	False	3	1
SRZ4012408	594	Danko2018dynamic	PRO-seq	ligation	control	True	1	2
SRZ4012410	595	Danko2018dynamic	PRO-seq	ligation	experimental	False	2	2
SRR4012430	582	Danko2018dynamic	PRO-seq	ligation	control	True	2	1
SRR4012393	578	Danko2018dynamic	PRO-seq	ligation	experimental	False	3	1
SRR6780907	583	Danko2018dynamic	PRO-seq	ligation	control	True	1	4
SRR6780908	584	Danko2018dynamic	PRO-seq	ligation	experimental	False	1	4
SRZ4012390	587	Danko2018dynamic	PRO-seq	ligation	control	True	2	1
SRZ4012394	588	Danko2018dynamic	PRO-seq	ligation	experimental	False	3	2
SRZ4012396	589	Danko2018dynamic	PRO-seq	ligation	control	True	3	2
SRZ4012400	590	Danko2018dynamic	PRO-seq	ligation	control	True	3	3
SRZ4012402	591	Danko2018dynamic	PRO-seq	ligation	experimental	False	5	3

Cellular details

Sample name	Organism	Sample type	Cell type	Clone/Individual	Strain	Genotype	Construct
SRR6780909	M. mulatta	primary cell	CD4+ T cell	individual 4
SRR6780910	M. mulatta	primary cell	CD4+ T cell	individual 4
SRZ4012415	M. mulatta	primary cell	CD4+ T cell	individual 1
SRZ4012417	M. mulatta	primary cell	CD4+ T cell	individual 2
SRZ4012420	M. mulatta	primary cell	CD4+ T cell	individual 2
SRZ4012423	M. mulatta	primary cell	CD4+ T cell	individual 3
SRZ4012426	M. mulatta	primary cell	CD4+ T cell	individual 3
SRR4012429	M. musculus	primary cell	CD4+ T cell
SRR4012413	P. troglodytes	primary cell	CD4+ T cell	individual 5
SRR4012414	P. troglodytes	primary cell	CD4+ T cell	individual 5
SRZ4012404	P. troglodytes	primary cell	CD4+ T cell	individual 3
SRZ4012406	P. troglodytes	primary cell	CD4+ T cell	individual 3
SRZ4012408	P. troglodytes	primary cell	CD4+ T cell	individual 4
SRZ4012410	P. troglodytes	primary cell	CD4+ T cell	individual 4
SRR4012430	R. norvegicus	primary cell	CD4+ T cell
SRR4012393	H. sapiens	primary cell	CD4+ T cell	individual 1
SRR6780907	H. sapiens	primary cell	CD4+ T cell	individual 4
SRR6780908	H. sapiens	primary cell	CD4+ T cell	individual 4
SRZ4012390	H. sapiens	primary cell	CD4+ T cell	individual 1
SRZ4012394	H. sapiens	primary cell	CD4+ T cell	individual 2
SRZ4012396	H. sapiens	primary cell	CD4+ T cell	individual 2
SRZ4012400	H. sapiens	primary cell	CD4+ T cell	individual 3
SRZ4012402	H. sapiens	primary cell	CD4+ T cell	individual 3

Conditions

Sample name	Condition type	Treatment	Start time	End time	Duration
SRR6780909	vehicle	ethanol	-30 min	0 min	30 min
	vehicle	DMSO	-30 min	0 min	30 min
SRR6780910	treatment	ionomycin (1 mM)	-30 min	0 min	30 min
	treatment	phorbol 12-myristate 13-acetate (25 ng/mL)	-30 min	0 min	30 min
SRZ4012415	vehicle	ethanol	-30 min	0 min	30 min
	vehicle	DMSO	-30 min	0 min	30 min
SRZ4012417	vehicle	ethanol	-30 min	0 min	30 min
	vehicle	DMSO	-30 min	0 min	30 min
SRZ4012420	treatment	ionomycin (1 mM)	-30 min	0 min	30 min
	treatment	phorbol 12-myristate 13-acetate (25 ng/mL)	-30 min	0 min	30 min
SRZ4012423	vehicle	ethanol	-30 min	0 min	30 min
	vehicle	DMSO	-30 min	0 min	30 min
SRZ4012426	treatment	ionomycin (1 mM)	-30 min	0 min	30 min
	treatment	phorbol 12-myristate 13-acetate (25 ng/mL)	-30 min	0 min	30 min
SRR4012429	vehicle	ethanol	-30 min	0 min	30 min
	vehicle	DMSO	-30 min	0 min	30 min
SRR4012413	vehicle	ethanol	-30 min	0 min	30 min
	vehicle	DMSO	-30 min	0 min	30 min
SRR4012414	treatment	ionomycin (1 mM)	-30 min	0 min	30 min
	treatment	phorbol 12-myristate 13-acetate (25 ng/mL)	-30 min	0 min	30 min
SRZ4012404	vehicle	ethanol	-30 min	0 min	30 min
	vehicle	DMSO	-30 min	0 min	30 min
SRZ4012406	treatment	ionomycin (1 mM)	-30 min	0 min	30 min
	treatment	phorbol 12-myristate 13-acetate (25 ng/mL)	-30 min	0 min	30 min
SRZ4012408	vehicle	ethanol	-30 min	0 min	30 min
	vehicle	DMSO	-30 min	0 min	30 min
SRZ4012410	treatment	ionomycin (1 mM)	-30 min	0 min	30 min
	treatment	phorbol 12-myristate 13-acetate (25 ng/mL)	-30 min	0 min	30 min
SRR4012430	vehicle	ethanol	-30 min	0 min	30 min
	vehicle	DMSO	-30 min	0 min	30 min
SRR4012393	treatment	ionomycin (1 mM)	-30 min	0 min	30 min
	treatment	phorbol 12-myristate 13-acetate (25 ng/mL)	-30 min	0 min	30 min
SRR6780907	vehicle	ethanol	-30 min	0 min	30 min
	vehicle	DMSO	-30 min	0 min	30 min
SRR6780908	treatment	ionomycin (1 mM)	-30 min	0 min	30 min
	treatment	phorbol 12-myristate 13-acetate (25 ng/mL)	-30 min	0 min	30 min
SRZ4012390	vehicle	ethanol	-30 min	0 min	30 min
	vehicle	DMSO	-30 min	0 min	30 min
SRZ4012394	treatment	ionomycin (1 mM)	-30 min	0 min	30 min
	treatment	phorbol 12-myristate 13-acetate (25 ng/mL)	-30 min	0 min	30 min
SRZ4012396	vehicle	ethanol	-30 min	0 min	30 min
	vehicle	DMSO	-30 min	0 min	30 min
SRZ4012400	vehicle	ethanol	-30 min	0 min	30 min
	vehicle	DMSO	-30 min	0 min	30 min
SRZ4012402	treatment	ionomycin (1 mM)	-30 min	0 min	30 min
	treatment	phorbol 12-myristate 13-acetate (25 ng/mL)	-30 min	0 min	30 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
SRR6780909	76	52,324,699	0.43764	0.5662	4.13801	0.74852	1	2
SRR6780910	76	45,929,943	0.49687	0.6283	3.99949	0.68815	1	2
SRZ4012415	51	10,342,444	0.60709	0.7665	3.88153	0.34136	4	2
SRZ4012417	50	67,864,406	0.7522	0.7977	3.26514	0.51104	3	2
SRZ4012420	50	57,762,688	0.84016	0.8121	3.83259	0.34137	4	2
SRZ4012423	51	63,476,083	0.63327	0.7905	2.7567	0.64163	2	1
SRZ4012426	51	55,010,357	0.74047	0.7994	2.74224	0.49252	3	1
SRR4012429	75	83,156,952	0.68335	0.8875	4.21663	0.66397	3	2
SRR4012413	76	55,486,603	0.39849	0.7663	4.50903	0.77176	1	2
SRR4012414	76	61,694,790	0.48523	0.8114	4.12716	0.71756	1	2
SRZ4012404	50	49,135,905	0.72233	0.8119	4.66709	0.50113	3	2
SRZ4012406	50	54,407,057	0.77907	0.8158	4.8537	0.43952	3	2
SRZ4012408	51	46,974,080	0.47791	0.8169	3.33534	0.71875	1	2
SRZ4012410	51	37,859,436	0.51131	0.8105	3.30061	0.6498	2	2
SRR4012430	75	83,866,198	0.53076	0.9009	4.27166	0.7276	2	2
SRR4012393	50	41,815,250	0.65702	0.853	3.66547	0.55491	3	2
SRR6780907	76	46,128,670	0.37878	0.5294	4.30578	0.75351	1	2
SRR6780908	76	43,233,899	0.42604	0.6114	3.71289	0.71333	1	2
SRZ4012390	50	39,388,204	0.53566	0.8429	3.77957	0.63181	2	2
SRZ4012394	50	78,323,360	0.79467	0.8116	4.27758	0.4718	3	2
SRZ4012396	51	38,678,020	0.71888	0.8137	3.70183	0.48559	3	2
SRZ4012400	51	16,263,064	0.75617	0.8229	5.01931	0.29171	3	3
SRZ4012402	51	4,151,452	0.69147	0.826	3.9403	0.14475	5	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
SRR6780909	None	None	None	None	None	None	None	None
SRR6780910	None	None	None	None	None	None	None	None
SRZ4012415	None	None	None	None	None	None	None	None
SRZ4012417	None	None	None	None	None	None	None	None
SRZ4012420	None	None	None	None	None	None	None	None
SRZ4012423	None	None	None	None	None	None	None	None
SRZ4012426	None	None	None	None	None	None	None	None
SRR4012429	27235	9847	9784	5406	25761	4734	11485	6361
SRR4012413	None	None	None	None	None	None	None	None
SRR4012414	None	None	None	None	None	None	None	None
SRZ4012404	None	None	None	None	None	None	None	None
SRZ4012406	None	None	None	None	None	None	None	None
SRZ4012408	None	None	None	None	None	None	None	None
SRZ4012410	None	None	None	None	None	None	None	None
SRR4012430	None	None	None	None	None	None	None	None
SRR4012393	20082	7019	9571	3174	16058	6486	7209	2552
SRR6780907	28835	15478	10008	3758	16802	7389	6537	2137
SRR6780908	21842	10670	8421	3056	14453	6845	5871	1699
SRZ4012390	25468	10086	11254	3949	20434	8109	8879	3303
SRZ4012394	20455	7933	9259	3013	16646	6716	7180	2661
SRZ4012396	23266	9661	10082	3453	18315	8063	7431	2767
SRZ4012400	15660	7405	6169	1773	12432	6873	4222	1363
SRZ4012402	4277	1903	1812	487	2691	1536	991	293