DBNascent | Samples

SRR8669163 Sample ID 2541

**Data sources**
Paper identifier	Vihervaara2021stress
SRP accession	SRP187541
GEO accession	GSE127844
Samples	SRR8669163

**Technical details**
QC score	4
Replicate	2
Protocol	PRO-seq
Library prep	ligation
Spike-in	D. melanogaster
Single/Paired end	single
Raw strandedness	reverse
Reverse complemented?	True
Mapped strandedness	forward
Timecourse	True
Control/Experimental	control
Wildtype & Untreated?	False
Outlier	No
Unusable	No

**Downloads**
TDF visualization file	TDF file	39 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	592 Kb
All data files	ZIP archive

**Cellular details**
Organism	H. sapiens
Sample type	cell line
Cell type	K562
Clone/Individual
Strain
Genotype
Construct	shRNA control

**Conditions and treatments**
Condition type	Treatment	Start time	End time	Duration
no treatment		None	None	None

**Extended notes**
Pipeline info and software versions
Sample notes	Cites Kwak2013 for protocol and library prep and also implies ligation with adapters, but not explicitly stated
Analysis notes	Previously in DB until 6/29/2021 as Vihervaara2020unpublished - scripts have been changed, but all previous outerr and log files reflect previous id

**Sample metrics**
Sample QC score	4
Sample NRO score	2
Raw read length	76
Read depth after trimming	6,695,221
Duplication proportion	0.27797
Proportion reads mapped	0.8576
Exon/intron ratio	4.28502
Unique read proportion	0.67496

**Bidirectionals**
Total # Tfit bidirectionals	18830
# Promoter Tfit bidirectionals	9868
# Intronic Tfit bidirectionals	6738
# Intergenic Tfit bidirectionals	2478
Total # dREG bidirectionals	13768
# Promoter dREG bidirectionals	8385
# Intronic dREG bidirectionals	3969
# Intergenic dREG bidirectionals	1857
Part of Tfit master merge?	True
Part of dREG master merge?	True