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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
SRR10502417	260	Birkenheuer2020rna	PRO-seq	ligation	experimental	False	2	1
SRR10502418	261	Birkenheuer2020rna	PRO-seq	ligation	experimental	False	1	2
SRR10502419	262	Birkenheuer2020rna	PRO-seq	ligation	experimental	False	3	1
SRR10502420	263	Birkenheuer2020rna	PRO-seq	ligation	experimental	False	2	2
SRR10502421	264	Birkenheuer2020rna	PRO-seq	ligation	experimental	False	3	1
SRR10502422	265	Birkenheuer2020rna	PRO-seq	ligation	experimental	False	3	2
SRR8957130	266	Birkenheuer2020rna	PRO-seq	ligation	control	False	1	1
SRR8957131	267	Birkenheuer2020rna	PRO-seq	ligation	control	False	1	2
SRR8957132	268	Birkenheuer2020rna	PRO-seq	ligation	control	False	1	3
SRR8957133	269	Birkenheuer2020rna	PRO-seq	ligation	control	False	1	4
SRR8957134	270	Birkenheuer2020rna	PRO-seq	ligation	control	False	2	5
SRR8957135	271	Birkenheuer2020rna	PRO-seq	ligation	control	False	1	6
SRR8957136	272	Birkenheuer2020rna	PRO-seq	ligation	control	False	3	1
SRR8957137	273	Birkenheuer2020rna	PRO-seq	ligation	control	False	1	2
SRR8957138	274	Birkenheuer2020rna	PRO-seq	ligation	control	False	1	3
SRR8957139	275	Birkenheuer2020rna	PRO-seq	ligation	experimental	False	1	1
SRR8957140	276	Birkenheuer2020rna	PRO-seq	ligation	experimental	False	1	2
SRR8957141	277	Birkenheuer2020rna	PRO-seq	ligation	experimental	False	1	3
SRR8957142	278	Birkenheuer2020rna	PRO-seq	ligation	experimental	False	2	1
SRR8957143	279	Birkenheuer2020rna	PRO-seq	ligation	experimental	False	2	2

Cellular details

Sample name	Organism	Sample type	Cell type	Clone/Individual	Strain	Genotype	Construct
SRR10502417	H. sapiens	cell line	HEp2
SRR10502418	H. sapiens	cell line	HEp2
SRR10502419	H. sapiens	cell line	HEp2
SRR10502420	H. sapiens	cell line	HEp2
SRR10502421	H. sapiens	cell line	HEp2
SRR10502422	H. sapiens	cell line	HEp2
SRR8957130	H. sapiens	cell line	HEp2
SRR8957131	H. sapiens	cell line	HEp2
SRR8957132	H. sapiens	cell line	HEp2
SRR8957133	H. sapiens	cell line	HEp2
SRR8957134	H. sapiens	cell line	HEp2
SRR8957135	H. sapiens	cell line	HEp2
SRR8957136	H. sapiens	cell line	HEp2
SRR8957137	H. sapiens	cell line	HEp2
SRR8957138	H. sapiens	cell line	HEp2
SRR8957139	H. sapiens	cell line	HEp2
SRR8957140	H. sapiens	cell line	HEp2
SRR8957141	H. sapiens	cell line	HEp2
SRR8957142	H. sapiens	cell line	HEp2
SRR8957143	H. sapiens	cell line	HEp2

Conditions

Sample name	Condition type	Treatment	Start time	End time	Duration
SRR10502417	treatment	HSV-1 (MOI 5)	-6 hr	-5 hr	1 hr
	treatment	acyclovir (10 microM)	-5 hr	0 hr	5 hr
SRR10502418	treatment	HSV-1 (MOI 5)	-6 hr	-5 hr	1 hr
	treatment	acyclovir (10 microM)	-5 hr	0 hr	5 hr
SRR10502419	treatment	HSV-1 (MOI 5)	-6 hr	-5 hr	1 hr
	vehicle	DMSO (0.01%)	-6 hr	0 hr	6 hr
SRR10502420	treatment	HSV-1 (MOI 5)	-6 hr	-5 hr	1 hr
	vehicle	DMSO (0.01%)	-6 hr	0 hr	6 hr
SRR10502421	treatment	HSV-1 (MOI 5)	-6 hr	-5 hr	1 hr
	treatment	flavopiridol (450 nM)	-6 hr	0 hr	6 hr
SRR10502422	treatment	HSV-1 (MOI 5)	-6 hr	-5 hr	1 hr
	treatment	flavopiridol (450 nM)	-6 hr	0 hr	6 hr
SRR8957130	treatment	HSV-1 (MOI 5)	-3 hr	-2 hr	1 hr
SRR8957131	treatment	HSV-1 (MOI 5)	-3 hr	-2 hr	1 hr
SRR8957132	treatment	HSV-1 (MOI 5)	-3 hr	-2 hr	1 hr
SRR8957133	treatment	HSV-1 (MOI 5)	-3 hr	-2 hr	1 hr
SRR8957134	treatment	HSV-1 (MOI 5)	-3 hr	-2 hr	1 hr
SRR8957135	treatment	HSV-1 (MOI 5)	-3 hr	-2 hr	1 hr
SRR8957136	treatment	HSV-1 (MOI 5)	-6 hr	-5 hr	1 hr
SRR8957137	treatment	HSV-1 (MOI 5)	-6 hr	-5 hr	1 hr
SRR8957138	treatment	HSV-1 (MOI 5)	-6 hr	-5 hr	1 hr
SRR8957139	treatment	HSV-1 (MOI 5)	-3 hr	-2 hr	1 hr
	treatment	cycloheximide (10 microM)	-4 hr	0 hr	4 hr
SRR8957140	treatment	HSV-1 (MOI 5)	-3 hr	-2 hr	1 hr
	treatment	cycloheximide (10 microM)	-4 hr	0 hr	4 hr
SRR8957141	treatment	HSV-1 (MOI 5)	-3 hr	-2 hr	1 hr
	treatment	cycloheximide (10 microM)	-4 hr	0 hr	4 hr
SRR8957142	treatment	HSV-1 (MOI 5)	-6 hr	-5 hr	1 hr
	treatment	phosphonoacetic acid (200 microg/mL)	-6 hr	0 hr	6 hr
SRR8957143	treatment	HSV-1 (MOI 5)	-6 hr	-5 hr	1 hr
	treatment	phosphonoacetic acid (200 microg/mL)	-6 hr	0 hr	6 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
SRR10502417	35	26,912,039	0.38589	0.5882	4.08354	0.63097	2	2
SRR10502418	35	31,900,579	0.39335	0.6302	4.19653	0.63762	1	2
SRR10502419	35	23,150,442	0.57943	0.4204	4.1129	0.41229	3	2
SRR10502420	35	28,298,160	0.57378	0.4378	4.35537	0.43208	2	2
SRR10502421	35	27,309,578	0.76584	0.6715	14.3402	0.28009	3	5
SRR10502422	35	27,752,690	0.75783	0.6909	13.6377	0.29042	3	5
SRR8957130	76	44,178,047	0.48622	0.7345	3.87163	0.56088	1	2
SRR8957131	76	51,489,131	0.46293	0.6652	4.12757	0.61031	1	2
SRR8957132	76	58,104,266	0.43299	0.8038	4.1245	0.64995	1	2
SRR8957133	76	41,621,743	0.44267	0.8107	4.20455	0.62209	1	2
SRR8957134	76	27,463,984	0.54007	0.7867	4.63227	0.48485	2	2
SRR8957135	76	41,905,543	0.45565	0.7775	4.3399	0.60567	1	2
SRR8957136	75	83,391,126	0.65058	0.4153	3.94199	0.47324	3	2
SRR8957137	75	48,552,704	0.47033	0.3774	4.05118	0.59154	1	2
SRR8957138	75	43,683,688	0.49299	0.6144	4.21363	0.60077	1	2
SRR8957139	76	35,890,733	0.39414	0.8296	4.6197	0.67422	1	2
SRR8957140	76	41,992,910	0.40788	0.8449	4.22339	0.66829	1	2
SRR8957141	76	39,811,416	0.41571	0.8243	4.50818	0.65923	1	2
SRR8957142	75	84,132,172	0.53758	0.8539	4.9267	0.649	2	2
SRR8957143	75	52,176,855	0.5528	0.8573	4.53231	0.59096	2	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
SRR10502417	20119	6401	8502	4473	9232	4340	3056	1880
SRR10502418	23749	7250	10110	5375	11295	5156	3931	2244
SRR10502419	17340	7789	6884	2348	9676	5841	2992	1095
SRR10502420	22237	8936	9348	3495	12172	6426	4389	1572
SRR10502421	24836	9356	10782	4951	20228	8669	8268	3539
SRR10502422	26329	9887	11551	5118	21043	8847	8764	3540
SRR8957130	30231	12945	11874	4956	18299	6566	7158	3540
SRR8957131	20106	7798	8567	3105	12779	5132	4718	2551
SRR8957132	37928	15587	13928	8083	25785	6601	10948	6435
SRR8957133	34684	13676	14013	6846	23772	7118	10354	5231
SRR8957134	26304	11684	10677	3873	16990	7257	6591	2804
SRR8957135	33381	13086	13498	6612	23216	7041	10093	4988
SRR8957136	26354	11141	10967	3830	17359	7650	6710	2831
SRR8957137	25362	11091	10427	3715	16537	7853	6096	2489
SRR8957138	33028	13628	13266	6030	21530	8215	8819	4144
SRR8957139	35772	13732	14502	8043	26723	6992	12242	6271
SRR8957140	34759	13463	14021	7630	26435	6881	12151	6242
SRR8957141	35133	13358	14328	7742	26458	7027	12223	6103
SRR8957142	48015	16613	18202	12569	32588	7364	14488	8975
SRR8957143	40605	15276	15778	9062	26129	7961	11325	5989