DBNascent | Samples

SRR1342251 Sample ID 887

**Data sources**
Paper identifier	Gardini2014integrator
SRP accession	SRP015419
GEO accession	GSE40632
Samples	SRR1342251

**Technical details**
QC score	1
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	140 Mb
Stranded gene read counts	TXT file	1 Mb
Unstranded bidirectional read counts	TXT file	21 Mb
Tfit bidirectional regions	BED file	4 Mb
dREG bidirectional regions	BED file	1 Mb
All data files	ZIP archive

**Cellular details**
Organism	H. sapiens
Sample type	cell line
Cell type	HeLa
Clone/Individual
Strain
Genotype
Construct	dox-inducible shRNA Ints11

**Conditions and treatments**
Condition type	Treatment	Start time	End time	Duration
treatment	EGF (100 ng/mL)	-30 min	0 min	30 min
treatment	doxycycline (1 microg/mL)	-96 hr	0 hr	4 day
treatment	serum starvation (0.5% FBS)	-24 hr	0 hr	1 day

**Extended notes**
Pipeline info and software versions
Sample notes	Treatment times don't match between GEO and paper - used paper
Analysis notes	Ran qc redo nextflow

**Sample metrics**
Sample QC score	1
Sample NRO score	2
Raw read length	25
Read depth after trimming	45,226,834
Duplication proportion	0.39701
Proportion reads mapped	0.825
Exon/intron ratio	2.97944
Unique read proportion	0.70464

**Bidirectionals**
Total # Tfit bidirectionals	48176
# Promoter Tfit bidirectionals	14801
# Intronic Tfit bidirectionals	20035
# Intergenic Tfit bidirectionals	12274
Total # dREG bidirectionals	31099
# Promoter dREG bidirectionals	8691
# Intronic dREG bidirectionals	14573
# Intergenic dREG bidirectionals	7656
Part of Tfit master merge?	True
Part of dREG master merge?	True