DBNascent | Samples

SRR8713376 Sample ID 2568

**Data sources**
Paper identifier	Vihervaara2021stress
SRP accession	SRP188184
GEO accession	GSE128160
Samples	SRR8713376

**Technical details**
QC score	4
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	32 Mb
Stranded gene read counts	TXT file	906 Kb
Unstranded bidirectional read counts	TXT file	17 Mb
Tfit bidirectional regions	BED file	1 Mb
dREG bidirectional regions	BED file	348 Kb
All data files	ZIP archive

**Cellular details**
Organism	M. musculus
Sample type	cell line
Cell type	MEF
Clone/Individual
Strain
Genotype
Construct

**Conditions and treatments**
Condition type	Treatment	Start time	End time	Duration
treatment	heat shock (42 Celsius)	-25 min	0 min	25 min
treatment	heat shock (42 Celsius)	-3025 min	-2965 min	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 Mahat2020unpublished - all previous outerr and log files reflect previous id; dirty data - did fastq-dump manually, trimmed first 10 bp and bp 50+, ran pipeline on trimmed fastqs; ran tech reps on pre-trimmed fastqs

**Sample metrics**
Sample QC score	4
Sample NRO score	2
Raw read length	41
Read depth after trimming	14,247,413
Duplication proportion	0.35083
Proportion reads mapped	0.4587
Exon/intron ratio	4.24727
Unique read proportion	0.62385

**Bidirectionals**
Total # Tfit bidirectionals	14036
# Promoter Tfit bidirectionals	6549
# Intronic Tfit bidirectionals	4242
# Intergenic Tfit bidirectionals	1078
Total # dREG bidirectionals	8060
# Promoter dREG bidirectionals	4302
# Intronic dREG bidirectionals	1656
# Intergenic dREG bidirectionals	578
Part of Tfit master merge?	True
Part of dREG master merge?	True