DBNascent | Samples

SRR8669177 Sample ID 2555

**Data sources**
Paper identifier	Vihervaara2021stress
SRP accession	SRP187541
GEO accession	GSE127844
Samples	SRR8669177

**Technical details**
QC score	1
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	experimental
Wildtype & Untreated?	False
Outlier	No
Unusable	No

**Downloads**
TDF visualization file	TDF file	128 Mb
Stranded gene read counts	TXT file	1 Mb
Unstranded bidirectional read counts	TXT file	21 Mb
Tfit bidirectional regions	BED file	3 Mb
dREG bidirectional regions	BED file	2 Mb
All data files	ZIP archive

**Cellular details**
Organism	H. sapiens
Sample type	cell line
Cell type	K562
Clone/Individual
Strain
Genotype
Construct	shRNA Hsf1

**Conditions and treatments**
Condition type	Treatment	Start time	End time	Duration
treatment	heat shock (42 Celsius)	-1 hr	0 hr	1 hr
treatment	heat shock (42 Celsius)	-101 hr	-100 hr	1 hr
treatment	heat shock (42 Celsius)	-104 hr	-103 hr	1 hr
treatment	heat shock (42 Celsius)	-50 hr	-49 hr	1 hr
treatment	heat shock (42 Celsius)	-53 hr	-52 hr	1 hr
treatment	heat shock (42 Celsius)	-56 hr	-55 hr	1 hr
treatment	heat shock (42 Celsius)	-74 hr	-73 hr	1 hr
treatment	heat shock (42 Celsius)	-77 hr	-76 hr	1 hr
treatment	heat shock (42 Celsius)	-80 hr	-79 hr	1 hr
treatment	heat shock (42 Celsius)	-98 hr	-97 hr	1 hr

**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	1
Sample NRO score	2
Raw read length	76
Read depth after trimming	35,555,948
Duplication proportion	0.43659
Proportion reads mapped	0.9134
Exon/intron ratio	4.08812
Unique read proportion	0.66149

**Bidirectionals**
Total # Tfit bidirectionals	40911
# Promoter Tfit bidirectionals	15214
# Intronic Tfit bidirectionals	15191
# Intergenic Tfit bidirectionals	11192
Total # dREG bidirectionals	36630
# Promoter dREG bidirectionals	9292
# Intronic dREG bidirectionals	15438
# Intergenic dREG bidirectionals	10950
Part of Tfit master merge?	True
Part of dREG master merge?	True