DBNascent | Samples

SRR3004199 Sample ID 2407

**Data sources**
Paper identifier	Sumida2018ultra
SRP accession	SRP067415
GEO accession	GSE76043
Samples	SRR3004199

**Technical details**
QC score	5
Replicate	1
Protocol	EU-seq
Library prep	ligation
Spike-in	None
Single/Paired end	paired
Raw strandedness	read1 reverse
Reverse complemented?	False
Mapped strandedness	read1 reverse
Timecourse	False
Control/Experimental	control
Wildtype & Untreated?	False
Outlier	No
Unusable	No

**Downloads**
TDF visualization file	TDF file	31 Mb
Stranded gene read counts	TXT file	1 Mb
Unstranded bidirectional read counts	TXT file	21 Mb
Tfit bidirectional regions	BED file	735 Kb
dREG bidirectional regions	BED file	76 Kb
All data files	ZIP archive

**Cellular details**
Organism	H. sapiens
Sample type	cell line
Cell type	HCT116
Clone/Individual
Strain
Genotype
Construct

**Conditions and treatments**
Condition type	Treatment	Start time	End time	Duration
treatment	ethynyl uridine (200 microM)	-1 hr	0 hr	1 hr

**Extended notes**
Pipeline info and software versions
Sample notes	protocol/treatment are the click-IT EU nascent RNA kit; This dataset, labeled incorrectly as GRO-seq (and some RNA-seq and ChIP-seq) are associated with this paper, but not actually mentioned, so marked as not published
Analysis notes	Ran qc redo nextflow

**Sample metrics**
Sample QC score	5
Sample NRO score	5
Raw read length	35
Read depth after trimming	3,863,330
Duplication proportion	0.13795
Proportion reads mapped	0.745
Exon/intron ratio	9.3959
Unique read proportion	0.60667

**Bidirectionals**
Total # Tfit bidirectionals	8430
# Promoter Tfit bidirectionals	1457
# Intronic Tfit bidirectionals	3640
# Intergenic Tfit bidirectionals	404
Total # dREG bidirectionals	1756
# Promoter dREG bidirectionals	437
# Intronic dREG bidirectionals	491
# Intergenic dREG bidirectionals	253
Part of Tfit master merge?	True
Part of dREG master merge?	True