DBNascent | Samples

SRR8669162 Sample ID 2540

**Data sources**
Paper identifier	Vihervaara2021stress
SRP accession	SRP187541
GEO accession	GSE127844
Samples	SRR8669162

**Technical details**
QC score	2
Replicate	1
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	76 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	872 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	2
Sample NRO score	2
Raw read length	76
Read depth after trimming	17,342,044
Duplication proportion	0.30887
Proportion reads mapped	0.8426
Exon/intron ratio	3.95993
Unique read proportion	0.73315

**Bidirectionals**
Total # Tfit bidirectionals	28311
# Promoter Tfit bidirectionals	13614
# Intronic Tfit bidirectionals	10033
# Intergenic Tfit bidirectionals	5110
Total # dREG bidirectionals	20134
# Promoter dREG bidirectionals	8908
# Intronic dREG bidirectionals	6998
# Intergenic dREG bidirectionals	4090
Part of Tfit master merge?	True
Part of dREG master merge?	True