DBNascent | Samples

SRZ930712 Sample ID 1173

**Data sources**
Paper identifier	Kaikkonen2013remodeling
SRP accession	SRP026695
GEO accession	GSE48759
Samples	SRR930712
	SRR930713
	SRR930714
	SRR930715
	SRR930716

**Technical details**
QC score	3
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	900 Kb
Unstranded bidirectional read counts	TXT file	17 Mb
Tfit bidirectional regions	BED file	227 Kb
dREG bidirectional regions	BED file	64 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	alpha-amanitin (10 microg/mL)	-5 hr	0 hr	5 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	3
Sample NRO score	2
Raw read length	51
Read depth after trimming	15,050,316
Duplication proportion	0.76527
Proportion reads mapped	0.7045
Exon/intron ratio	2.44619
Unique read proportion	0.23624

**Bidirectionals**
Total # Tfit bidirectionals	2659
# Promoter Tfit bidirectionals	539
# Intronic Tfit bidirectionals	1021
# Intergenic Tfit bidirectionals	175
Total # dREG bidirectionals	1495
# Promoter dREG bidirectionals	362
# Intronic dREG bidirectionals	498
# Intergenic dREG bidirectionals	435
Part of Tfit master merge?	True
Part of dREG master merge?	True