DBNascent | Samples

SRR8713374 Sample ID 2566

**Data sources**
Paper identifier	Vihervaara2021stress
SRP accession	SRP188184
GEO accession	GSE128160
Samples	SRR8713374

**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	23 Mb
Stranded gene read counts	TXT file	902 Kb
Unstranded bidirectional read counts	TXT file	17 Mb
Tfit bidirectional regions	BED file	968 Kb
dREG bidirectional regions	BED file	280 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)	-180750 s	-177150 s	1 hr
treatment	heat shock (42 Celsius)	-750 s	0 s	750 s

**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	9,493,340
Duplication proportion	0.35516
Proportion reads mapped	0.4228
Exon/intron ratio	4.54375
Unique read proportion	0.59374

**Bidirectionals**
Total # Tfit bidirectionals	11454
# Promoter Tfit bidirectionals	5412
# Intronic Tfit bidirectionals	3422
# Intergenic Tfit bidirectionals	800
Total # dREG bidirectionals	6499
# Promoter dREG bidirectionals	3781
# Intronic dREG bidirectionals	1250
# Intergenic dREG bidirectionals	342
Part of Tfit master merge?	True
Part of dREG master merge?	True