DBNascent | Samples

SRR988340 Sample ID 1461

**Data sources**
Paper identifier	Li2013ncor
SRP accession	SRP029986
GEO accession	GSE50944
Samples	SRR988340

**Technical details**
QC score	5
Replicate	3
Protocol	GRO-seq
Library prep	circularization
Spike-in	None
Single/Paired end	single
Raw strandedness	forward
Reverse complemented?	False
Mapped strandedness	forward
Timecourse	True
Control/Experimental	experimental
Wildtype & Untreated?	False
Outlier	No
Unusable	No

**Downloads**
TDF visualization file	TDF file	21 Mb
Stranded gene read counts	TXT file	898 Kb
Unstranded bidirectional read counts	TXT file	17 Mb
Tfit bidirectional regions	BED file	442 Kb
dREG bidirectional regions	BED file	132 Kb
All data files	ZIP archive

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

**Extended notes**
Pipeline info and software versions
Sample notes	replicate info not clear, but implies biological in paper
Analysis notes	Ran qc redo nextflow; Originally labeled and processed as technical replicates, but paper implies biological - kept tech rep processed data just in case but removed SRZ labels from metadata

**Sample metrics**
Sample QC score	5
Sample NRO score	1
Raw read length	34
Read depth after trimming	6,174,819
Duplication proportion	0.42266
Proportion reads mapped	0.6076
Exon/intron ratio	2.32161
Unique read proportion	0.50741

**Bidirectionals**
Total # Tfit bidirectionals	5255
# Promoter Tfit bidirectionals	2126
# Intronic Tfit bidirectionals	1937
# Intergenic Tfit bidirectionals	610
Total # dREG bidirectionals	3057
# Promoter dREG bidirectionals	1520
# Intronic dREG bidirectionals	860
# Intergenic dREG bidirectionals	375
Part of Tfit master merge?	True
Part of dREG master merge?	True