DBNascent | Samples

SRZ1744506 Sample ID 2617

**Data sources**
Paper identifier	Wang2015molecular
SRP accession	SRP051769
GEO accession	GSE64748
Samples	SRR1744506
	SRR1744507

**Technical details**
QC score	3
Replicate	1
Protocol	GRO-seq
Library prep	ligation
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	58 Mb
Stranded gene read counts	TXT file	914 Kb
Unstranded bidirectional read counts	TXT file	17 Mb
Tfit bidirectional regions	BED file	1 Mb
dREG bidirectional regions	BED file	504 Kb
All data files	ZIP archive

**Cellular details**
Organism	M. musculus
Sample type	cell line
Cell type	ESC
Clone/Individual
Strain
Genotype	Tdg fl/fl
Construct

**Conditions and treatments**
Condition type	Treatment	Start time	End time	Duration
treatment	DRB (100 mM)	-210 min	-30 min	3 hr

**Extended notes**
Pipeline info and software versions
Sample notes
Analysis notes	May needs samtools/1.10 and 60Gb memory for samtools step (that is in my notes but does not match running script, which uses samtools 1.8); One sample required rerun of picardtools; Ran qc redo nextflow

**Sample metrics**
Sample QC score	3
Sample NRO score	1
Raw read length	40
Read depth after trimming	69,193,264
Duplication proportion	0.76692
Proportion reads mapped	0.4902
Exon/intron ratio	1.70677
Unique read proportion	0.25161

**Bidirectionals**
Total # Tfit bidirectionals	16285
# Promoter Tfit bidirectionals	5095
# Intronic Tfit bidirectionals	5780
# Intergenic Tfit bidirectionals	3632
Total # dREG bidirectionals	11703
# Promoter dREG bidirectionals	4238
# Intronic dREG bidirectionals	3432
# Intergenic dREG bidirectionals	3047
Part of Tfit master merge?	True
Part of dREG master merge?	True