DBNascent | Samples

SRR4041366 Sample ID 676

**Data sources**
Paper identifier	Engreitz2016local
SRP accession	SRP082334
GEO accession	GSE85798
Samples	SRR4041366

**Technical details**
QC score	3
Replicate	2
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	control
Wildtype & Untreated?	False
Outlier	No
Unusable	No

**Downloads**
TDF visualization file	TDF file	98 Mb
Stranded gene read counts	TXT file	916 Kb
Unstranded bidirectional read counts	TXT file	17 Mb
Tfit bidirectional regions	BED file	3 Mb
dREG bidirectional regions	BED file	913 Kb
All data files	ZIP archive

**Cellular details**
Organism	M. musculus
Sample type	primary cell
Cell type	ESC
Clone/Individual	clone 2
Strain	129/SV-Jae x castaneus
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	Library prep is unclear, but citations indicate ligation
Analysis notes	Originally processed as tech reps, but paper implies biological - kept tech rep data but removed SRZ labels from metadata; 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	13,498,684
Duplication proportion	0.11214
Proportion reads mapped	0.8294
Exon/intron ratio	4.5738
Unique read proportion	0.736

**Bidirectionals**
Total # Tfit bidirectionals	38273
# Promoter Tfit bidirectionals	11747
# Intronic Tfit bidirectionals	11718
# Intergenic Tfit bidirectionals	11559
Total # dREG bidirectionals	21102
# Promoter dREG bidirectionals	6783
# Intronic dREG bidirectionals	5897
# Intergenic dREG bidirectionals	5857
Part of Tfit master merge?	True
Part of dREG master merge?	True