DBNascent | Samples

SRR3004200 Sample ID 2408

**Data sources**
Paper identifier	Sumida2018ultra
SRP accession	SRP067415
GEO accession	GSE76043
Samples	SRR3004200

**Technical details**
QC score	4
Replicate	2
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	45 Mb
Stranded gene read counts	TXT file	1 Mb
Unstranded bidirectional read counts	TXT file	21 Mb
Tfit bidirectional regions	BED file	1 Mb
dREG bidirectional regions	BED file	117 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	4
Sample NRO score	2
Raw read length	35
Read depth after trimming	5,282,934
Duplication proportion	0.10167
Proportion reads mapped	0.8125
Exon/intron ratio	4.96505
Unique read proportion	0.73686

**Bidirectionals**
Total # Tfit bidirectionals	13350
# Promoter Tfit bidirectionals	2370
# Intronic Tfit bidirectionals	6839
# Intergenic Tfit bidirectionals	767
Total # dREG bidirectionals	2703
# Promoter dREG bidirectionals	882
# Intronic dREG bidirectionals	952
# Intergenic dREG bidirectionals	355
Part of Tfit master merge?	True
Part of dREG master merge?	True