DBNascent | Samples

SRR6660159 Sample ID 1528

**Data sources**
Paper identifier	Link2018analysis
SRP accession	SRP131922
GEO accession	GSE109965
Samples	SRR6660159

**Technical details**
QC score	4
Replicate	2
Protocol	GRO-cap
Library prep	ligation
Spike-in	None
Single/Paired end	single
Raw strandedness	forward
Reverse complemented?	False
Mapped strandedness	forward
Timecourse	False
Control/Experimental	experimental
Wildtype & Untreated?	False
Outlier	No
Unusable	No

**Downloads**
TDF visualization file	TDF file	14 Mb
Stranded gene read counts	TXT file	903 Kb
Unstranded bidirectional read counts	TXT file	17 Mb
Tfit bidirectional regions	BED file	351 Kb
dREG bidirectional regions	BED file	240 Kb
All data files	ZIP archive

**Cellular details**
Organism	M. musculus
Sample type	primary cell
Cell type	bone marrow derived macrophage
Clone/Individual
Strain	BALB/cJ
Genotype
Construct

**Conditions and treatments**
Condition type	Treatment	Start time	End time	Duration
treatment	Kdo2-Lipid A (10 ng/mL)	-1 hr	0 hr	1 hr

**Extended notes**
Pipeline info and software versions
Sample notes
Analysis notes	needs samtools/1.10 and 60Gb memory for samtools step; Major adapter contamination for some libraries and some very low/no read depth samples; Ran qc redo nextflow

**Sample metrics**
Sample QC score	4
Sample NRO score	1
Raw read length	20
Read depth after trimming	14,779,578
Duplication proportion	0.91522
Proportion reads mapped	0.6237
Exon/intron ratio	2.45672
Unique read proportion	0.08595

**Bidirectionals**
Total # Tfit bidirectionals	4115
# Promoter Tfit bidirectionals	1440
# Intronic Tfit bidirectionals	1393
# Intergenic Tfit bidirectionals	648
Total # dREG bidirectionals	5578
# Promoter dREG bidirectionals	2890
# Intronic dREG bidirectionals	1304
# Intergenic dREG bidirectionals	844
Part of Tfit master merge?	False
Part of dREG master merge?	False