DBNascent | Samples

SRR6660350 Sample ID 1554

**Data sources**
Paper identifier	Link2018analysis
SRP accession	SRP131922
GEO accession	GSE109965
Samples	SRR6660350

**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	13 Mb
Stranded gene read counts	TXT file	900 Kb
Unstranded bidirectional read counts	TXT file	17 Mb
Tfit bidirectional regions	BED file
dREG bidirectional regions	BED file	242 Kb
All data files	ZIP archive

**Cellular details**
Organism	M. musculus
Sample type	primary cell
Cell type	bone marrow derived macrophage
Clone/Individual
Strain	PWK/PhJ
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	7,359,996
Duplication proportion	0.8452
Proportion reads mapped	0.6326
Exon/intron ratio	2.71098
Unique read proportion	0.10717

**Bidirectionals**
Total # Tfit bidirectionals	None
# Promoter Tfit bidirectionals	None
# Intronic Tfit bidirectionals	None
# Intergenic Tfit bidirectionals	None
Total # dREG bidirectionals	5643
# Promoter dREG bidirectionals	2802
# Intronic dREG bidirectionals	1534
# Intergenic dREG bidirectionals	991
Part of Tfit master merge?	False
Part of dREG master merge?	False