DBNascent | Samples

SRR4041369 Sample ID 679

**Data sources**
Paper identifier	Engreitz2016local
SRP accession	SRP082334
GEO accession	GSE85798
Samples	SRR4041369

**Technical details**
QC score	3
Replicate	1
Protocol	PRO-seq
Library prep	ligation
Spike-in	None
Single/Paired end	paired
Raw strandedness	read1 reverse
Reverse complemented?	False
Mapped strandedness	read1 reverse
Timecourse	False
Control/Experimental	experimental
Wildtype & Untreated?	False
Outlier	No
Unusable	No

**Downloads**
TDF visualization file	TDF file	60 Mb
Stranded gene read counts	TXT file	912 Kb
Unstranded bidirectional read counts	TXT file	17 Mb
Tfit bidirectional regions	BED file	2 Mb
dREG bidirectional regions	BED file	574 Kb
All data files	ZIP archive

**Cellular details**
Organism	M. musculus
Sample type	primary cell
Cell type	ESC
Clone/Individual
Strain	129/SV-Jae x castaneus
Genotype	linc1319 promoter +/-
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	Heterozygous mutations to determine cis/trans effects; Library prep is unclear, but citations indicate ligation
Analysis notes	In db as Engreitz2016long until 2/8/21 - all older pipeline reports and out/err scripts reflect that; Ran qc redo nextflow

**Sample metrics**
Sample QC score	3
Sample NRO score	2
Raw read length	40
Read depth after trimming	15,860,611
Duplication proportion	0.43046
Proportion reads mapped	0.702
Exon/intron ratio	4.23455
Unique read proportion	0.40593

**Bidirectionals**
Total # Tfit bidirectionals	24140
# Promoter Tfit bidirectionals	8365
# Intronic Tfit bidirectionals	7278
# Intergenic Tfit bidirectionals	6091
Total # dREG bidirectionals	13294
# Promoter dREG bidirectionals	6012
# Intronic dREG bidirectionals	3205
# Intergenic dREG bidirectionals	2689
Part of Tfit master merge?	True
Part of dREG master merge?	True