DBNascent | Samples

SRR6660292 Sample ID 1543

**Data sources**
Paper identifier	Link2018analysis
SRP accession	SRP131922
GEO accession	GSE109965
Samples	SRR6660292

**Technical details**
QC score	2
Replicate	1
Protocol	GRO-seq
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	110 Mb
Stranded gene read counts	TXT file	915 Kb
Unstranded bidirectional read counts	TXT file	17 Mb
Tfit bidirectional regions	BED file	2 Mb
dREG bidirectional regions	BED file	1009 Kb
All data files	ZIP archive

**Cellular details**
Organism	M. musculus
Sample type	primary cell
Cell type	bone marrow derived macrophage
Clone/Individual
Strain	C57BL/6J mice(f) x SPRET/EiJ(m)
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	2
Sample NRO score	1
Raw read length	35
Read depth after trimming	58,739,930
Duplication proportion	0.53787
Proportion reads mapped	0.6507
Exon/intron ratio	2.33875
Unique read proportion	0.57728

**Bidirectionals**
Total # Tfit bidirectionals	24182
# Promoter Tfit bidirectionals	6918
# Intronic Tfit bidirectionals	9026
# Intergenic Tfit bidirectionals	6536
Total # dREG bidirectionals	23196
# Promoter dREG bidirectionals	5852
# Intronic dREG bidirectionals	9817
# Intergenic dREG bidirectionals	6132
Part of Tfit master merge?	False
Part of dREG master merge?	False