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Sample Details

SRR6660401 Sample ID 1563

**Data sources**
Paper identifier	Link2018analysis
SRP accession	SRP131922
GEO accession	GSE109965
Samples	SRR6660401

**Technical details**
QC score	4
Replicate	1
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	control
Wildtype & Untreated?	True
Outlier	No
Unusable	No

**Downloads**
TDF visualization file	TDF file	13 Mb
Stranded gene read counts	TXT file	903 Kb
Unstranded bidirectional read counts	TXT file	17 Mb
dREG bidirectional regions	BED file	419 Kb
All data files	ZIP archive

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

**Conditions and treatments**
Condition type	Treatment	Start time	End time	Duration
no treatment		None	None	None

**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	2
Raw read length	20
Read depth after trimming	11,229,961
Duplication proportion	0.882
Proportion reads mapped	0.6046
Exon/intron ratio	3.98618
Unique read proportion	0.09887

**Bidirectionals**
Total # Tfit bidirectionals	None
# Promoter Tfit bidirectionals	None
# Intronic Tfit bidirectionals	None
# Intergenic Tfit bidirectionals	None
Total # dREG bidirectionals	9767
# Promoter dREG bidirectionals	4641
# Intronic dREG bidirectionals	2758
# Intergenic dREG bidirectionals	1739
Part of Tfit master merge?	False
Part of dREG master merge?	False