Explore DBNascent | browse or search sample metadata

Downloads

Gene read counts	Bidirectional read counts	Tfit regions	dREG regions
ZIP archive	ZIP archive	ZIP archive	ZIP archive
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
SRR6492219	524	Cuartero2020control	GRO-seq	circularization	control	False	4	1
SRR6492220	525	Cuartero2020control	GRO-seq	circularization	experimental	False	3	1
SRR6492221	526	Cuartero2020control	GRO-seq	circularization	experimental	False	4	1
SRR6492222	527	Cuartero2020control	GRO-seq	circularization	control	False	3	2
SRR6492223	528	Cuartero2020control	GRO-seq	circularization	experimental	False	3	2
SRR6492224	529	Cuartero2020control	GRO-seq	circularization	experimental	False	3	2
SRR6492225	530	Cuartero2020control	GRO-seq	circularization	experimental	False	3	1
SRR6492226	531	Cuartero2020control	GRO-seq	circularization	experimental	False	4	1
SRR6492227	532	Cuartero2020control	GRO-seq	circularization	experimental	False	4	1
SRR6492228	533	Cuartero2020control	GRO-seq	circularization	experimental	False	3	2
SRR6492229	534	Cuartero2020control	GRO-seq	circularization	experimental	False	2	2
SRR6492230	535	Cuartero2020control	GRO-seq	circularization	experimental	False	2	2

Cellular details

Sample name	Organism	Sample type	Cell type	Clone/Individual	Strain	Genotype	Construct
SRR6492219	M. musculus	primary cell	bone marrow derived macrophage			Rad21 +/+; tamoxifen-inducible Cre/+
SRR6492220	M. musculus	primary cell	bone marrow derived macrophage			Rad21 +/+; tamoxifen-inducible Cre/+
SRR6492221	M. musculus	primary cell	bone marrow derived macrophage			Rad21 +/+; tamoxifen-inducible Cre/+
SRR6492222	M. musculus	primary cell	bone marrow derived macrophage			Rad21 +/+; tamoxifen-inducible Cre/+
SRR6492223	M. musculus	primary cell	bone marrow derived macrophage			Rad21 +/+; tamoxifen-inducible Cre/+
SRR6492224	M. musculus	primary cell	bone marrow derived macrophage			Rad21 +/+; tamoxifen-inducible Cre/+
SRR6492225	M. musculus	primary cell	bone marrow derived macrophage			Rad21 fl/fl; tamoxifen-inducible Cre/+
SRR6492226	M. musculus	primary cell	bone marrow derived macrophage			Rad21 fl/fl; tamoxifen-inducible Cre/+
SRR6492227	M. musculus	primary cell	bone marrow derived macrophage			Rad21 fl/fl; tamoxifen-inducible Cre/+
SRR6492228	M. musculus	primary cell	bone marrow derived macrophage			Rad21 fl/fl; tamoxifen-inducible Cre/+
SRR6492229	M. musculus	primary cell	bone marrow derived macrophage			Rad21 fl/fl; tamoxifen-inducible Cre/+
SRR6492230	M. musculus	primary cell	bone marrow derived macrophage			Rad21 fl/fl; tamoxifen-inducible Cre/+

Conditions

Sample name	Condition type	Treatment	Start time	End time	Duration
SRR6492219	treatment	hydroxytamoxifen (200 nM)	-72 hr	0 hr	3 day
SRR6492220	treatment	hydroxytamoxifen (200 nM)	-73 hr	-1 hr	3 day
	treatment	lipopolysaccharide (10 ng/mL)	-1 hr	0 hr	1 hr
SRR6492221	treatment	hydroxytamoxifen (200 nM)	-78 hr	-6 hr	3 day
	treatment	lipopolysaccharide (10 ng/mL)	-6 hr	0 hr	6 hr
SRR6492222	treatment	hydroxytamoxifen (200 nM)	-72 hr	0 hr	3 day
SRR6492223	treatment	hydroxytamoxifen (200 nM)	-73 hr	-1 hr	3 day
	treatment	lipopolysaccharide (10 ng/mL)	-1 hr	0 hr	1 hr
SRR6492224	treatment	hydroxytamoxifen (200 nM)	-78 hr	-6 hr	3 day
	treatment	lipopolysaccharide (10 ng/mL)	-6 hr	0 hr	6 hr
SRR6492225	treatment	hydroxytamoxifen (200 nM)	-72 hr	0 hr	3 day
SRR6492226	treatment	hydroxytamoxifen (200 nM)	-73 hr	-1 hr	3 day
	treatment	lipopolysaccharide (10 ng/mL)	-1 hr	0 hr	1 hr
SRR6492227	treatment	hydroxytamoxifen (200 nM)	-78 hr	-6 hr	3 day
	treatment	lipopolysaccharide (10 ng/mL)	-6 hr	0 hr	6 hr
SRR6492228	treatment	hydroxytamoxifen (200 nM)	-72 hr	0 hr	3 day
SRR6492229	treatment	hydroxytamoxifen (200 nM)	-73 hr	-1 hr	3 day
	treatment	lipopolysaccharide (10 ng/mL)	-1 hr	0 hr	1 hr
SRR6492230	treatment	hydroxytamoxifen (200 nM)	-78 hr	-6 hr	3 day
	treatment	lipopolysaccharide (10 ng/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
SRR6492219	50	87,584,515	0.93719	0.6431	2.08916	0.25791	4	1
SRR6492220	50	37,632,754	0.67568	0.7346	1.72421	0.5484	3	1
SRR6492221	50	92,262,328	0.94171	0.7395	1.89009	0.28119	4	1
SRR6492222	50	63,576,287	0.79778	0.7297	2.05542	0.51907	3	1
SRR6492223	50	50,226,325	0.68906	0.5767	1.81369	0.52978	3	1
SRR6492224	50	66,523,186	0.79601	0.8605	1.49889	0.54467	3	1
SRR6492225	50	39,706,200	0.68443	0.7383	1.83618	0.55846	3	1
SRR6492226	50	59,939,690	0.83271	0.5515	1.54387	0.40219	4	1
SRR6492227	50	116,492,554	0.92145	0.6299	1.8793	0.37652	4	1
SRR6492228	50	58,828,128	0.79006	0.6781	1.86944	0.50788	3	1
SRR6492229	50	52,201,994	0.54896	0.7548	1.72317	0.69149	2	1
SRR6492230	50	43,984,083	0.55858	0.755	1.73785	0.6329	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
SRR6492219	12217	4415	4170	2362	12316	5999	3308	2140
SRR6492220	18855	5540	6926	4895	16432	5322	6156	3916
SRR6492221	11578	3971	4110	2419	10784	5018	3153	1873
SRR6492222	20792	7427	6865	4818	21489	7367	7428	5182
SRR6492223	18594	5698	6763	4619	16979	5501	6305	4074
SRR6492224	18184	5570	6477	4611	18849	6067	7077	4525
SRR6492225	23616	7914	8364	5569	21489	7163	7838	5141
SRR6492226	13484	3647	5282	3375	11291	3966	4088	2613
SRR6492227	15918	4994	5769	3725	14757	5934	4723	3139
SRR6492228	18119	5827	6530	4189	18862	6625	6680	4264
SRR6492229	23943	7101	8888	6238	23113	6190	9592	5863
SRR6492230	25452	7935	8894	6893	24032	6897	9185	6388