DBNascent | Samples

SRR3555069 Sample ID 1208

**Data sources**
Paper identifier	Kim2018pluripotency
SRP accession	SRP075469
GEO accession	GSE81677
Samples	SRR3555069

**Technical details**
QC score	5
Replicate	1
Protocol	PRO-cap
Library prep	ligation
Spike-in	None
Single/Paired end	single
Raw strandedness	forward
Reverse complemented?	False
Mapped strandedness	forward
Timecourse	False
Control/Experimental	control
Wildtype & Untreated?	True
Outlier	No
Unusable	No

**Downloads**
TDF visualization file	TDF file	9 Mb
Stranded gene read counts	TXT file	903 Kb
Unstranded bidirectional read counts	TXT file	17 Mb
Tfit bidirectional regions	BED file	243 Kb
dREG bidirectional regions	BED file	98 Kb
All data files	ZIP archive

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

**Conditions and treatments**
Condition type	Treatment	Start time	End time	Duration
no treatment		None	None	None

**Extended notes**
Pipeline info and software versions
Sample notes	Paper and data indicate ligation library prep, GEO metadata says circularization, no poly-A tail; Not completely clear if there was treatment, but I don't think so
Analysis notes

**Sample metrics**
Sample QC score	5
Sample NRO score	3
Raw read length	51
Read depth after trimming	16,356,331
Duplication proportion	0.90975
Proportion reads mapped	0.2382
Exon/intron ratio	6.36434
Unique read proportion	0.06168

**Bidirectionals**
Total # Tfit bidirectionals	2875
# Promoter Tfit bidirectionals	1438
# Intronic Tfit bidirectionals	759
# Intergenic Tfit bidirectionals	219
Total # dREG bidirectionals	2280
# Promoter dREG bidirectionals	1730
# Intronic dREG bidirectionals	303
# Intergenic dREG bidirectionals	78
Part of Tfit master merge?	True
Part of dREG master merge?	True