DBNascent | Samples

SRR8713361 Sample ID 2557

**Data sources**
Paper identifier	Vihervaara2021stress
SRP accession	SRP188184
GEO accession	GSE128160
Samples	SRR8713361

**Technical details**
QC score	4
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	control
Wildtype & Untreated?	True
Outlier	No
Unusable	No

**Downloads**
TDF visualization file	TDF file	27 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	473 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
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 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	10,105,065
Duplication proportion	0.35977
Proportion reads mapped	0.5007
Exon/intron ratio	4.66667
Unique read proportion	0.57858

**Bidirectionals**
Total # Tfit bidirectionals	16781
# Promoter Tfit bidirectionals	8257
# Intronic Tfit bidirectionals	5219
# Intergenic Tfit bidirectionals	1359
Total # dREG bidirectionals	10943
# Promoter dREG bidirectionals	5677
# Intronic dREG bidirectionals	2510
# Intergenic dREG bidirectionals	768
Part of Tfit master merge?	True
Part of dREG master merge?	True