DBNascent | Samples

SRR8713375 Sample ID 2567

**Data sources**
Paper identifier	Vihervaara2021stress
SRP accession	SRP188184
GEO accession	GSE128160
Samples	SRR8713375

**Technical details**
QC score	5
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	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	903 Kb
dREG bidirectional regions	BED file	252 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	5
Sample NRO score	2
Raw read length	41
Read depth after trimming	8,674,230
Duplication proportion	0.3193
Proportion reads mapped	0.434
Exon/intron ratio	4.18868
Unique read proportion	0.6225

**Bidirectionals**
Total # Tfit bidirectionals	10682
# Promoter Tfit bidirectionals	5027
# Intronic Tfit bidirectionals	3183
# Intergenic Tfit bidirectionals	773
Total # dREG bidirectionals	5849
# Promoter dREG bidirectionals	3552
# Intronic dREG bidirectionals	1073
# Intergenic dREG bidirectionals	283
Part of Tfit master merge?	True
Part of dREG master merge?	True