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Downloads

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
SRR988329	1450	Li2013ncor	GRO-seq	circularization	control	False	4	1
SRR988330	1451	Li2013ncor	GRO-seq	circularization	control	False	5	2
SRR988331	1452	Li2013ncor	GRO-seq	circularization	control	False	4	3
SRR988332	1453	Li2013ncor	GRO-seq	circularization	control	False	4	4
SRR988333	1454	Li2013ncor	GRO-seq	circularization	control	False	5	5
SRR988334	1455	Li2013ncor	GRO-seq	circularization	experimental	False	5	1
SRR988335	1456	Li2013ncor	GRO-seq	circularization	experimental	False	5	2
SRR988336	1457	Li2013ncor	GRO-seq	circularization	experimental	False	5	3
SRR988337	1458	Li2013ncor	GRO-seq	circularization	experimental	False	5	4
SRR988338	1459	Li2013ncor	GRO-seq	circularization	experimental	False	4	1
SRR988339	1460	Li2013ncor	GRO-seq	circularization	experimental	False	4	2
SRR988340	1461	Li2013ncor	GRO-seq	circularization	experimental	False	5	3
SRR988341	1462	Li2013ncor	GRO-seq	circularization	experimental	False	4	1
SRR988342	1463	Li2013ncor	GRO-seq	circularization	experimental	False	5	2
SRR988343	1464	Li2013ncor	GRO-seq	circularization	experimental	False	4	1
SRR988344	1465	Li2013ncor	GRO-seq	circularization	experimental	False	5	2
SRR988345	1466	Li2013ncor	GRO-seq	circularization	experimental	False	4	1
SRR988346	1467	Li2013ncor	GRO-seq	circularization	experimental	False	5	2

Cellular details

Sample name	Organism	Sample type	Cell type	Clone/Individual	Strain	Genotype	Construct
SRR988329	M. musculus	primary cell	peritoneal macrophage		C57BL/6J	NCoR fl/fl
SRR988330	M. musculus	primary cell	peritoneal macrophage		C57BL/6J	NCoR fl/fl
SRR988331	M. musculus	primary cell	peritoneal macrophage		C57BL/6J	NCoR fl/fl
SRR988332	M. musculus	primary cell	peritoneal macrophage		C57BL/6J	NCoR fl/fl
SRR988333	M. musculus	primary cell	peritoneal macrophage		C57BL/6J	NCoR fl/fl
SRR988334	M. musculus	primary cell	peritoneal macrophage		C57BL/6J	NCoR fl/fl; LysM-Cre +/-
SRR988335	M. musculus	primary cell	peritoneal macrophage		C57BL/6J	NCoR fl/fl; LysM-Cre +/-
SRR988336	M. musculus	primary cell	peritoneal macrophage		C57BL/6J	NCoR fl/fl; LysM-Cre +/-
SRR988337	M. musculus	primary cell	peritoneal macrophage		C57BL/6J	NCoR fl/fl; LysM-Cre +/-
SRR988338	M. musculus	primary cell	peritoneal macrophage		C57BL/6J	NCoR fl/fl
SRR988339	M. musculus	primary cell	peritoneal macrophage		C57BL/6J	NCoR fl/fl
SRR988340	M. musculus	primary cell	peritoneal macrophage		C57BL/6J	NCoR fl/fl
SRR988341	M. musculus	primary cell	peritoneal macrophage		C57BL/6J	NCoR fl/fl; LysM-Cre +/-
SRR988342	M. musculus	primary cell	peritoneal macrophage		C57BL/6J	NCoR fl/fl; LysM-Cre +/-
SRR988343	M. musculus	primary cell	peritoneal macrophage		C57BL/6J	NCoR fl/fl
SRR988344	M. musculus	primary cell	peritoneal macrophage		C57BL/6J	NCoR fl/fl
SRR988345	M. musculus	primary cell	peritoneal macrophage		C57BL/6J	NCoR fl/fl; LysM-Cre +/-
SRR988346	M. musculus	primary cell	peritoneal macrophage		C57BL/6J	NCoR fl/fl; LysM-Cre +/-

Conditions

Sample name	Condition type	Treatment	Start time	End time	Duration
SRR988329	no treatment		None	None	None
SRR988330	no treatment		None	None	None
SRR988331	no treatment		None	None	None
SRR988332	no treatment		None	None	None
SRR988333	no treatment		None	None	None
SRR988334	no treatment		None	None	None
SRR988335	no treatment		None	None	None
SRR988336	no treatment		None	None	None
SRR988337	no treatment		None	None	None
SRR988338	treatment	Kdo2-Lipid A (100 ng/mL)	-1 hr	0 hr	1 hr
SRR988339	treatment	Kdo2-Lipid A (100 ng/mL)	-1 hr	0 hr	1 hr
SRR988340	treatment	Kdo2-Lipid A (100 ng/mL)	-1 hr	0 hr	1 hr
SRR988341	treatment	Kdo2-Lipid A (100 ng/mL)	-1 hr	0 hr	1 hr
SRR988342	treatment	Kdo2-Lipid A (100 ng/mL)	-1 hr	0 hr	1 hr
SRR988343	treatment	Kdo2-Lipid A (100 ng/mL)	-12 hr	0 hr	12 hr
SRR988344	treatment	Kdo2-Lipid A (100 ng/mL)	-12 hr	0 hr	12 hr
SRR988345	treatment	Kdo2-Lipid A (100 ng/mL)	-12 hr	0 hr	12 hr
SRR988346	treatment	Kdo2-Lipid A (100 ng/mL)	-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
SRR988329	34	7,749,271	0.34462	0.7004	2.40909	0.61828	4	1
SRR988330	34	5,293,688	0.34086	0.6317	2.38068	0.60333	5	1
SRR988331	34	8,362,505	0.44436	0.759	2.72756	0.48811	4	1
SRR988332	34	7,467,000	0.37327	0.7381	2.66421	0.59893	4	1
SRR988333	34	5,030,027	0.34092	0.6466	2.5528	0.60901	5	1
SRR988334	34	3,865,881	0.3861	0.7152	2.45255	0.55917	5	1
SRR988335	34	6,135,801	0.40121	0.526	2.37107	0.55142	5	1
SRR988336	34	5,366,044	0.55016	0.5376	2.42424	0.38138	5	1
SRR988337	34	3,925,776	0.48695	0.5486	2.4	0.42252	5	1
SRR988338	34	8,324,380	0.43182	0.6965	2.26688	0.52125	4	1
SRR988339	34	8,226,437	0.57468	0.7057	2.82534	0.33856	4	1
SRR988340	34	6,174,819	0.42266	0.6076	2.32161	0.50741	5	1
SRR988341	34	9,563,252	0.43564	0.7216	2.07692	0.54442	4	1
SRR988342	34	2,689,111	0.28648	0.6221	1.82979	0.60746	5	2
SRR988343	34	8,096,741	0.47326	0.7415	2.90541	0.47165	4	1
SRR988344	34	4,665,668	0.40937	0.6166	2.88652	0.4823	5	1
SRR988345	34	9,849,502	0.51384	0.603	2.69065	0.4655	4	1
SRR988346	34	3,132,719	0.3668	0.6169	2.57447	0.56045	5	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
SRR988329	9009	3975	2846	1054	6028	3266	1426	711
SRR988330	5433	2389	1748	551	2901	1609	670	345
SRR988331	12948	5442	3999	1992	9062	4679	2236	1342
SRR988332	10776	4355	3368	1641	6686	3469	1590	1004
SRR988333	5693	2130	1872	824	2469	1185	620	423
SRR988334	3936	1663	1328	439	1647	903	361	247
SRR988335	4745	1897	1610	533	2083	1095	488	316
SRR988336	3125	1359	999	222	1287	696	254	176
SRR988337	1677	552	654	185	593	200	163	165
SRR988338	7715	3038	2761	1056	5033	2400	1483	680
SRR988339	9816	3915	3395	1511	6911	3415	1951	906
SRR988340	5255	2126	1937	610	3057	1520	860	375
SRR988341	7278	2592	2694	1152	4531	1919	1460	800
SRR988342	1068	229	513	195	531	118	200	184
SRR988343	9327	3814	2990	1364	5820	3029	1429	855
SRR988344	4200	1671	1418	571	1823	905	459	299
SRR988345	10331	4919	3098	1151	7094	4196	1462	734
SRR988346	1830	569	715	259	653	234	199	170