DBNascent | Samples

SRR6660277 Sample ID 1540

**Data sources**
Paper identifier	Link2018analysis
SRP accession	SRP131922
GEO accession	GSE109965
Samples	SRR6660277

**Technical details**
QC score	3
Replicate	2
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	40 Mb
Stranded gene read counts	TXT file	905 Kb
Unstranded bidirectional read counts	TXT file	17 Mb
Tfit bidirectional regions	BED file	1 Mb
dREG bidirectional regions	BED file	447 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 PWK/PhJ(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	3
Sample NRO score	1
Raw read length	50
Read depth after trimming	12,683,243
Duplication proportion	0.41497
Proportion reads mapped	0.7261
Exon/intron ratio	1.64898
Unique read proportion	0.57541

**Bidirectionals**
Total # Tfit bidirectionals	14947
# Promoter Tfit bidirectionals	4004
# Intronic Tfit bidirectionals	6224
# Intergenic Tfit bidirectionals	3171
Total # dREG bidirectionals	10376
# Promoter dREG bidirectionals	3695
# Intronic dREG bidirectionals	3593
# Intergenic dREG bidirectionals	2283
Part of Tfit master merge?	False
Part of dREG master merge?	False