DBNascent | Samples

SRZ930701 Sample ID 1171

**Data sources**
Paper identifier	Kaikkonen2013remodeling
SRP accession	SRP026695
GEO accession	GSE48759
Samples	SRR930701
	SRR930702
	SRR930703
	SRR930704
	SRR930705
	SRR930706

**Technical details**
QC score	4
Replicate	1
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	23 Mb
Stranded gene read counts	TXT file	904 Kb
Unstranded bidirectional read counts	TXT file	17 Mb
Tfit bidirectional regions	BED file	573 Kb
dREG bidirectional regions	BED file	174 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
treatment	actinomycin D (5 microg/mL)	-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	4
Sample NRO score	2
Raw read length	51
Read depth after trimming	21,591,056
Duplication proportion	0.83501
Proportion reads mapped	0.7317
Exon/intron ratio	3.58041
Unique read proportion	0.18549

**Bidirectionals**
Total # Tfit bidirectionals	6793
# Promoter Tfit bidirectionals	2782
# Intronic Tfit bidirectionals	2347
# Intergenic Tfit bidirectionals	155
Total # dREG bidirectionals	4035
# Promoter dREG bidirectionals	1910
# Intronic dREG bidirectionals	1084
# Intergenic dREG bidirectionals	401
Part of Tfit master merge?	True
Part of dREG master merge?	True