DBNascent | Samples

SRZ942413 Sample ID 2150

**Data sources**
Paper identifier	Saponaro2014recql5
SRP	SRP028170
Samples	SRR942413
	SRR942414

**Technical details**
QC score	3
Replicate	1
Protocol	GRO-seq
Library prep	not noted in GEO or publication
Spike-in	None
Single/Paired end	single
Timecourse	True
Control/Experimental	experimental
Outlier	No
Unusable	No

**Downloads**
TDF visualization file	TDF file	105 Mb
Stranded gene read counts	TXT file	1 Mb
Unstranded bidirectional read counts	TXT file	21 Mb
Tfit bidirectional regions	BED file	2 Mb
dREG bidirectional regions	BED file	618 Kb
All data files	ZIP archive

**Cellular details**
Organism	H. sapiens
Sample type	cell line
Cell type	HEK293T
Clone/Individual	clone 15
Strain
Genotype	shRNA Recql5 endogenous (stable); dox-inducible Recql5 exogenous (stable)
Construct

**Conditions and treatments**
Condition type	Treatment	Start time	End time	Duration
treatment	DRB (100 microM)	-250 min	-40 min	210 min
treatment	doxycycline withdrawal	-6010 min	0 min	6010 min

**Extended notes**
Pipeline info and software versions
Sample notes	Treatments incorrect in GEO as doxycycline instead of DRB, but paper methods are clear; Cells treated with 0.2 ng/mL doxycycline until 4 days before extraction, then some depleted; Clones not assumed to be replicates but could be treated as such
Analysis notes	Ran qc redo nextflow

**Sample metrics**
Sample QC score	3
Sample NRO score	2
Raw read length	36
Read depth after trimming	62,645,354
Duplication proportion	0.72044
Proportion reads mapped	0.8874
Exon/intron ratio	3.81641
Unique read proportion	0.3574

**Bidirectionals**
Total # Tfit bidirectionals	27404
# Promoter Tfit bidirectionals	5887
# Intronic Tfit bidirectionals	15485
# Intergenic Tfit bidirectionals	3119
Total # dREG bidirectionals	14329
# Promoter dREG bidirectionals	4409
# Intronic dREG bidirectionals	6266
# Intergenic dREG bidirectionals	2385
Part of Tfit master merge?	True
Part of dREG master merge?	True