DBNascent | Samples

SRZ930695 Sample ID 1170

**Data sources**
Paper identifier	Kaikkonen2013remodeling
SRP accession	SRP026695
GEO accession	GSE48759
Samples	SRR930695
	SRR930696
	SRR930697
	SRR930698
	SRR930699
	SRR930700

**Technical details**
QC score	2
Replicate	2
Protocol	GRO-seq
Library prep	circularization
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	45 Mb
Stranded gene read counts	TXT file	909 Kb
Unstranded bidirectional read counts	TXT file	17 Mb
Tfit bidirectional regions	BED file	991 Kb
dREG bidirectional regions	BED file	426 Kb
All data files	ZIP archive

**Cellular details**
Organism	M. musculus
Sample type	primary cell
Cell type	peritoneal macrophage
Clone/Individual
Strain	C57BL/6
Genotype
Construct

**Conditions and treatments**
Condition type	Treatment	Start time	End time	Duration
treatment	Kdo2-Lipid A (100 ng/mL)	-1 hr	0 hr	1 hr
vehicle	DMSO	-2 hr	0 hr	2 hr
treatment	serum starvation (0.5% FBS)	-15 hr	0 hr	15 hr

**Extended notes**
Pipeline info and software versions
Sample notes	Replicate information unclear
Analysis notes	Ran qc redo nextflow

**Sample metrics**
Sample QC score	2
Sample NRO score	1
Raw read length	51
Read depth after trimming	22,088,798
Duplication proportion	0.63512
Proportion reads mapped	0.7515
Exon/intron ratio	2.4797
Unique read proportion	0.41471

**Bidirectionals**
Total # Tfit bidirectionals	11645
# Promoter Tfit bidirectionals	5155
# Intronic Tfit bidirectionals	3759
# Intergenic Tfit bidirectionals	1400
Total # dREG bidirectionals	9888
# Promoter dREG bidirectionals	4741
# Intronic dREG bidirectionals	2721
# Intergenic dREG bidirectionals	1306
Part of Tfit master merge?	True
Part of dREG master merge?	True