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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
SRR5195270	13	Agarwal2021kdm1a	Bru-seq	ligation	control	True	1	1
SRR5195271	14	Agarwal2021kdm1a	Bru-seq	ligation	control	True	1	2
SRR5195272	15	Agarwal2021kdm1a	Bru-seq	ligation	control	False	1	1
SRR5195273	16	Agarwal2021kdm1a	Bru-seq	ligation	control	False	1	2
SRR5195274	17	Agarwal2021kdm1a	Bru-seq	ligation	experimental	False	1	1
SRR5195275	18	Agarwal2021kdm1a	Bru-seq	ligation	experimental	False	1	2
SRR5195276	19	Agarwal2021kdm1a	Bru-seq	ligation	experimental	False	1	1
SRR5195277	20	Agarwal2021kdm1a	Bru-seq	ligation	experimental	False	1	2
SRR5195548	21	Agarwal2021kdm1a	GRO-seq	circularization	control	True	1	1
SRR5195549	22	Agarwal2021kdm1a	GRO-seq	circularization	control	True	2	2
SRR5195550	23	Agarwal2021kdm1a	GRO-seq	circularization	experimental	False	2	1
SRR5195551	24	Agarwal2021kdm1a	GRO-seq	circularization	experimental	False	1	2
SRZ5195540	25	Agarwal2021kdm1a	GRO-seq	circularization	control	True	2	1
SRZ5195542	26	Agarwal2021kdm1a	GRO-seq	circularization	control	True	2	2
SRZ5195544	27	Agarwal2021kdm1a	GRO-seq	circularization	experimental	False	2	1
SRZ5195546	28	Agarwal2021kdm1a	GRO-seq	circularization	experimental	False	1	2

Cellular details

Sample name	Organism	Sample type	Cell type	Clone/Individual	Strain	Genotype	Construct
SRR5195270	M. musculus	primary cell	cortical neuron
SRR5195271	M. musculus	primary cell	cortical neuron
SRR5195272	M. musculus	primary cell	cortical neuron			shRNA control (stable)
SRR5195273	M. musculus	primary cell	cortical neuron			shRNA control (stable)
SRR5195274	M. musculus	primary cell	cortical neuron			shRNA Lsd1 A (stable)
SRR5195275	M. musculus	primary cell	cortical neuron			shRNA Lsd1 A (stable)
SRR5195276	M. musculus	primary cell	cortical neuron			shRNA Lsd1 B (stable)
SRR5195277	M. musculus	primary cell	cortical neuron			shRNA Lsd1 B (stable)
SRR5195548	M. musculus	cell line	ESC		129S1/SvImJ x C57BL/6J
SRR5195549	M. musculus	cell line	ESC		129S1/SvImJ x C57BL/6J
SRR5195550	M. musculus	cell line	ESC		129S1/SvImJ x C57BL/6J	Smcx -/-
SRR5195551	M. musculus	cell line	ESC		129S1/SvImJ x C57BL/6J	Smcx -/-
SRZ5195540	M. musculus	cell line	ESC		129P2/OlaHsd
SRZ5195542	M. musculus	cell line	ESC		129P2/OlaHsd
SRZ5195544	M. musculus	cell line	ESC		129P2/OlaHsd	Kdm1a +/gene trap
SRZ5195546	M. musculus	cell line	ESC		129P2/OlaHsd	Kdm1a +/gene trap

Conditions

Sample name	Condition type	Treatment	Start time	End time	Duration
SRR5195270	treatment	bromouridine (2 mM)	-32 min	0 min	32 min
SRR5195271	treatment	bromouridine (2 mM)	-32 min	0 min	32 min
SRR5195272	treatment	bromouridine (2 mM)	-32 min	0 min	32 min
SRR5195273	treatment	bromouridine (2 mM)	-32 min	0 min	32 min
SRR5195274	treatment	bromouridine (2 mM)	-32 min	0 min	32 min
SRR5195275	treatment	bromouridine (2 mM)	-32 min	0 min	32 min
SRR5195276	treatment	bromouridine (2 mM)	-32 min	0 min	32 min
SRR5195277	treatment	bromouridine (2 mM)	-32 min	0 min	32 min
SRR5195548	no treatment		None	None	None
SRR5195549	no treatment		None	None	None
SRR5195550	no treatment		None	None	None
SRR5195551	no treatment		None	None	None
SRZ5195540	no treatment		None	None	None
SRZ5195542	no treatment		None	None	None
SRZ5195544	no treatment		None	None	None
SRZ5195546	no treatment		None	None	None

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
SRR5195270	51	34,475,663	0.32807	0.7654	1.86476	0.71372	1	1
SRR5195271	51	29,858,591	0.314	0.7332	1.88992	0.71019	1	1
SRR5195272	51	30,857,825	0.27331	0.7874	1.84697	0.76358	1	1
SRR5195273	51	36,853,477	0.26983	0.7509	1.80575	0.77041	1	1
SRR5195274	51	46,632,785	0.31274	0.7067	1.72821	0.77109	1	1
SRR5195275	51	34,671,823	0.24511	0.7091	1.82562	0.78603	1	1
SRR5195276	51	33,558,229	0.25659	0.7802	2.06369	0.79254	1	1
SRR5195277	51	41,242,242	0.24707	0.7245	2.02877	0.79684	1	1
SRR5195548	50	45,513,176	0.475	0.5982	2.2973	0.58934	1	1
SRR5195549	50	65,346,215	0.55258	0.6134	2.34	0.52534	2	1
SRR5195550	50	49,055,826	0.54273	0.6054	2.30218	0.57291	2	1
SRR5195551	50	48,393,618	0.49378	0.5919	2.32308	0.57818	1	1
SRZ5195540	50	77,476,522	0.50454	0.7673	3.16276	0.59106	2	2
SRZ5195542	50	84,654,730	0.50981	0.7682	3.16732	0.59282	2	2
SRZ5195544	50	110,334,248	0.50894	0.7437	2.9256	0.60334	2	1
SRZ5195546	50	105,949,297	0.46776	0.7675	2.91843	0.65036	1	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
SRR5195270	6792	2922	2238	325	7025	3085	1731	1105
SRR5195271	6331	2736	2134	244	6055	2758	1440	917
SRR5195272	7394	3224	2464	323	7100	3172	1704	1001
SRR5195273	7291	3137	2437	339	7699	3381	1945	1086
SRR5195274	8592	3538	3044	422	9295	3839	2465	1371
SRR5195275	7174	2969	2410	360	7288	3217	1779	1028
SRR5195276	6722	2694	2300	347	7849	3190	2103	1216
SRR5195277	7096	2771	2419	481	8835	3514	2531	1456
SRR5195548	42195	12813	12684	13403	29723	8281	9075	10340
SRR5195549	44799	14246	13045	14118	33163	8363	10507	11780
SRR5195550	39299	12154	11963	12059	28194	8249	8431	9579
SRR5195551	40483	13401	11776	12079	28811	8344	8738	9566
SRZ5195540	54065	17539	14574	17979	47364	8780	15984	18042
SRZ5195542	55231	17493	14841	18768	49551	8817	16903	19129
SRZ5195544	76165	17208	20302	33925	72196	9229	24064	33697
SRZ5195546	76442	16549	20426	34632	73548	9206	24640	34509