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Technical details

Sample name	Sample ID	Paper identifier	Protocol	Library prep	Control/Experimental	Wildtype & Untreated	QC score	Replicate
SRR10063517	1571	Linnakuosmanen2020nrf2	GRO-seq	circularization	control	True	2	1
SRR10063518	1572	Linnakuosmanen2020nrf2	GRO-seq	circularization	control	True	4	2
SRR10063519	1573	Linnakuosmanen2020nrf2	GRO-seq	circularization	experimental	False	2	1
SRR10063520	1574	Linnakuosmanen2020nrf2	GRO-seq	circularization	experimental	False	4	2
SRR10063521	1575	Linnakuosmanen2020nrf2	GRO-seq	circularization	experimental	False	3	1
SRR10063522	1576	Linnakuosmanen2020nrf2	GRO-seq	circularization	experimental	False	3	2
SRR10063523	1577	Linnakuosmanen2020nrf2	GRO-seq	circularization	experimental	False	2	1
SRR10063524	1578	Linnakuosmanen2020nrf2	GRO-seq	circularization	experimental	False	2	2
SRR10063525	1579	Linnakuosmanen2020nrf2	GRO-seq	circularization	control	True	2	1
SRR10063526	1580	Linnakuosmanen2020nrf2	GRO-seq	circularization	control	True	2	2
SRR10063527	1581	Linnakuosmanen2020nrf2	GRO-seq	circularization	experimental	False	3	1
SRR10063528	1582	Linnakuosmanen2020nrf2	GRO-seq	circularization	experimental	False	2	2
SRR10063529	1583	Linnakuosmanen2020nrf2	GRO-seq	circularization	experimental	False	3	3
SRR10063530	1584	Linnakuosmanen2020nrf2	GRO-seq	circularization	experimental	False	4	1
SRR10063531	1585	Linnakuosmanen2020nrf2	GRO-seq	circularization	experimental	False	3	2
SRR10063532	1586	Linnakuosmanen2020nrf2	GRO-seq	circularization	experimental	False	3	3
SRR10063533	1587	Linnakuosmanen2020nrf2	GRO-seq	circularization	experimental	False	4	1
SRR10063534	1588	Linnakuosmanen2020nrf2	GRO-seq	circularization	experimental	False	2	2
SRR10063535	1589	Linnakuosmanen2020nrf2	GRO-seq	circularization	experimental	False	3	3
SRR10063536	1590	Linnakuosmanen2020nrf2	GRO-seq	circularization	control	True	3	1
SRR10063537	1591	Linnakuosmanen2020nrf2	GRO-seq	circularization	control	True	2	2
SRR10063540	1592	Linnakuosmanen2020nrf2	GRO-seq	circularization	experimental	False	2	1
SRR10063541	1593	Linnakuosmanen2020nrf2	GRO-seq	circularization	experimental	False	4	2
SRR10063544	1594	Linnakuosmanen2020nrf2	GRO-seq	circularization	control	True	2	1
SRR10063545	1595	Linnakuosmanen2020nrf2	GRO-seq	circularization	control	True	2	2
SRR10063548	1596	Linnakuosmanen2020nrf2	GRO-seq	circularization	experimental	False	2	1
SRR11849645	1597	Linnakuosmanen2020nrf2	GRO-seq	circularization	experimental	False	2	1
SRR11849646	1598	Linnakuosmanen2020nrf2	GRO-seq	circularization	experimental	False	3	1
SRR11849647	1599	Linnakuosmanen2020nrf2	GRO-seq	circularization	experimental	False	1	1
SRR11849648	1600	Linnakuosmanen2020nrf2	GRO-seq	circularization	experimental	False	2	1

Cellular details

Sample name	Organism	Sample type	Cell type	Clone/Individual	Strain	Genotype	Construct
SRR10063517	H. sapiens	primary cell	HAEC
SRR10063518	H. sapiens	primary cell	HAEC
SRR10063519	H. sapiens	primary cell	HAEC
SRR10063520	H. sapiens	primary cell	HAEC
SRR10063521	H. sapiens	primary cell	HAEC
SRR10063522	H. sapiens	primary cell	HAEC
SRR10063523	H. sapiens	primary cell	HAEC
SRR10063524	H. sapiens	primary cell	HAEC
SRR10063525	H. sapiens	primary cell	HUVEC
SRR10063526	H. sapiens	primary cell	HUVEC
SRR10063527	H. sapiens	primary cell	HUVEC
SRR10063528	H. sapiens	primary cell	HUVEC
SRR10063529	H. sapiens	primary cell	HUVEC
SRR10063530	H. sapiens	primary cell	HUVEC
SRR10063531	H. sapiens	primary cell	HUVEC
SRR10063532	H. sapiens	primary cell	HUVEC
SRR10063533	H. sapiens	primary cell	HUVEC
SRR10063534	H. sapiens	primary cell	HUVEC
SRR10063535	H. sapiens	primary cell	HUVEC
SRR10063536	H. sapiens	primary cell	HASM
SRR10063537	H. sapiens	primary cell	HASM
SRR10063540	H. sapiens	primary cell	HASM
SRR10063541	H. sapiens	primary cell	HASM
SRR10063544	H. sapiens	primary cell	CD14+ macrophage
SRR10063545	H. sapiens	primary cell	CD14+ macrophage
SRR10063548	H. sapiens	primary cell	CD14+ macrophage
SRR11849645	H. sapiens	primary cell	HUVEC
SRR11849646	H. sapiens	primary cell	HUVEC
SRR11849647	H. sapiens	primary cell	HUVEC
SRR11849648	H. sapiens	primary cell	HUVEC

Conditions

Sample name	Condition type	Treatment	Start time	End time	Duration
SRR10063517	vehicle	growth media	-6 hr	0 hr	6 hr
SRR10063518	vehicle	growth media	-6 hr	0 hr	6 hr
SRR10063519	treatment	hypoxia (1 percent O2, 5 percent CO2)	-6 hr	0 hr	6 hr
SRR10063520	treatment	hypoxia (1 percent O2, 5 percent CO2)	-6 hr	0 hr	6 hr
SRR10063521	treatment	oxPAPC (30 g/m)	-6 hr	0 hr	6 hr
SRR10063522	treatment	oxPAPC (30 g/m)	-6 hr	0 hr	6 hr
SRR10063523	treatment	hypoxia (1 percent O2, 5 percent CO2)	-6 hr	0 hr	6 hr
	treatment	oxPAPC (30 g/m)	-6 hr	0 hr	6 hr
SRR10063524	treatment	hypoxia (1 percent O2, 5 percent CO2)	-6 hr	0 hr	6 hr
	treatment	oxPAPC (30 g/mL)	-6 hr	0 hr	6 hr
SRR10063525	vehicle	growth media	-6 hr	0 hr	6 hr
SRR10063526	vehicle	growth media	-6 hr	0 hr	6 hr
SRR10063527	treatment	hypoxia (1 percent O2, 5 percent CO2)	-6 hr	0 hr	6 hr
SRR10063528	treatment	hypoxia (1 percent O2, 5 percent CO2)	-6 hr	0 hr	6 hr
SRR10063529	treatment	hypoxia (1 percent O2, 5 percent CO2)	-6 hr	0 hr	6 hr
SRR10063530	treatment	oxPAPC (30 g/mL)	-6 hr	0 hr	6 hr
SRR10063531	treatment	oxPAPC (30 g/mL)	-6 hr	0 hr	6 hr
SRR10063532	treatment	oxPAPC (30 g/mL)	-6 hr	0 hr	6 hr
SRR10063533	treatment	hypoxia (1 percent O2, 5 percent CO2)	-6 hr	0 hr	6 hr
	treatment	oxPAPC (30 g/mL)	-6 hr	0 hr	6 hr
SRR10063534	treatment	hypoxia (1 percent O2, 5 percent CO2)	-6 hr	0 hr	6 hr
	treatment	oxPAPC (30 g/mL)	-6 hr	0 hr	6 hr
SRR10063535	treatment	hypoxia (1 percent O2, 5 percent CO2)	-6 hr	0 hr	6 hr
	treatment	oxPAPC (30 g/mL)	-6 hr	0 hr	6 hr
SRR10063536	vehicle	growth media	-6 hr	0 hr	6 hr
SRR10063537	vehicle	growth media	-6 hr	0 hr	6 hr
SRR10063540	treatment	oxPAPC (30 g/mL)	-6 hr	0 hr	6 hr
SRR10063541	treatment	oxPAPC (30 g/mL)	-6 hr	0 hr	6 hr
SRR10063544	vehicle	growth media	-6 hr	0 hr	6 hr
SRR10063545	vehicle	growth media	-6 hr	0 hr	6 hr
SRR10063548	treatment	oxPAPC (30 g/mL)	-6 hr	0 hr	6 hr
SRR11849645	vehicle	methanol (0.06 percent)	-2 hr	0 hr	2 hr
SRR11849646	vehicle	methanol (0.06 percent)	-12 hr	0 hr	12 hr
SRR11849647	treatment	nitro-octadec-9-enoic acid (3 microM)	-2 hr	0 hr	2 hr
SRR11849648	treatment	nitro-octadec-9-enoic acid (3 microM)	-12 hr	0 hr	12 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
SRR10063517	51	19,245,214	0.39985	0.929	2.08135	0.67422	2	1
SRR10063518	51	9,137,200	0.29636	0.9063	2.24832	0.69366	4	1
SRR10063519	51	18,164,866	0.41404	0.929	2.47766	0.62809	2	1
SRR10063520	51	8,193,993	0.28348	0.9323	2.05724	0.69725	4	1
SRR10063521	51	14,620,388	0.3448	0.9336	2.2434	0.68974	3	1
SRR10063522	51	10,556,526	0.29455	0.9347	1.97625	0.70488	3	1
SRR10063523	51	15,866,759	0.47878	0.934	2.1277	0.58899	2	1
SRR10063524	51	15,623,116	0.37652	0.935	2.15	0.66788	2	1
SRR10063525	51	18,940,314	0.26906	0.9377	2.14919	0.77536	2	1
SRR10063526	51	15,014,124	0.30982	0.931	1.65025	0.72477	2	1
SRR10063527	51	14,960,294	0.52181	0.9481	2.24532	0.55732	3	1
SRR10063528	51	16,581,884	0.41971	0.9216	2.65666	0.61553	2	1
SRR10063529	51	13,235,585	0.37746	0.9116	2.40781	0.64506	3	1
SRR10063530	51	99,426,506	0.85094	0.9477	2.08428	0.53541	4	1
SRR10063531	51	14,378,965	0.35749	0.8778	2.36056	0.67322	3	1
SRR10063532	51	12,410,810	0.31954	0.9229	2.44444	0.69199	3	1
SRR10063533	51	51,447,099	0.88385	0.9371	3.19855	0.33682	4	2
SRR10063534	51	15,524,855	0.33976	0.9323	2.39177	0.69699	2	1
SRR10063535	51	14,252,269	0.34599	0.9514	1.93841	0.69758	3	1
SRR10063536	51	13,629,383	0.41237	0.9445	1.75723	0.63162	3	1
SRR10063537	51	22,586,729	0.62234	0.9181	2.85854	0.51604	2	1
SRR10063540	51	16,536,302	0.44707	0.9311	1.93464	0.62373	2	1
SRR10063541	51	7,344,502	0.89651	0.816	4.62411	0.07569	4	2
SRR10063544	51	19,383,130	0.43467	0.9332	2.53846	0.66922	2	1
SRR10063545	51	26,314,900	0.54436	0.8502	2.61305	0.61938	2	1
SRR10063548	51	18,268,565	0.46955	0.8735	2.55195	0.58623	2	1
SRR11849645	48	18,318,861	0.35128	0.9162	2.81624	0.71427	2	1
SRR11849646	48	17,057,196	0.68528	0.9093	2.56386	0.42761	3	1
SRR11849647	48	20,657,216	0.49822	0.9227	2.3285	0.63466	1	1
SRR11849648	48	17,980,978	0.42878	0.9146	2.57456	0.66294	2	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
SRR10063517	29370	10722	12443	6288	20957	8156	8616	4459
SRR10063518	23836	10367	9644	4242	16297	8443	5769	2601
SRR10063519	28277	11357	11478	6050	23607	9857	9710	4685
SRR10063520	16920	7118	7266	2731	12498	6968	4267	1723
SRR10063521	21763	8937	9381	3660	16351	7632	6643	2513
SRR10063522	24022	10024	9996	4341	17005	8302	6399	2803
SRR10063523	20936	8336	8896	4027	19165	8951	7609	3404
SRR10063524	24420	10063	10407	4344	19741	8910	7992	3321
SRR10063525	31398	11242	12973	7359	23388	8421	9766	5195
SRR10063526	27612	8357	12242	6634	17323	6695	6773	4051
SRR10063527	17990	7226	7628	3197	15301	8017	5706	2218
SRR10063528	29163	11706	12018	6053	23069	9903	9428	4353
SRR10063529	26326	8751	11312	6424	20710	8979	8184	4264
SRR10063530	29945	10858	12821	6128	26861	8607	12128	5913
SRR10063531	22581	9260	9621	3963	16676	7717	6602	2653
SRR10063532	24194	9750	10433	4389	16625	7625	6485	2753
SRR10063533	17081	7215	7421	2355	16636	8866	6110	2141
SRR10063534	29977	10479	12737	7081	25150	9766	10665	5403
SRR10063535	26643	8602	11443	6671	22834	8835	9437	5178
SRR10063536	24280	8833	9982	4967	14845	6963	5547	2639
SRR10063537	26567	11542	10535	4667	19342	9168	7320	3202
SRR10063540	24542	9118	10601	4459	16017	7204	6647	2573
SRR10063541	3151	1774	1072	202	3178	2494	763	174
SRR10063544	30198	11417	11929	6475	22372	8383	9202	4859
SRR10063545	27926	11329	10840	5722	22961	8971	9436	4827
SRR10063548	26396	10258	10753	5061	19268	8058	7771	3601
SRR11849645	16537	6290	7290	2949	13077	5867	5063	2238
SRR11849646	8807	3634	3797	1104	7219	4223	2370	853
SRR11849647	15255	5254	7014	2795	12367	5223	5087	2169
SRR11849648	16553	6240	7381	3004	14458	6714	5597	2378