DBNascent | Samples

SRR1519039 Sample ID 830

**Data sources**
Paper identifier	Franco2015tnfalpha
SRP accession	SRP044608
GEO accession	GSE59531
Samples	SRR1519039

**Technical details**
QC score	1
Replicate	2
Protocol	GRO-seq
Library prep	circularization
Spike-in	None
Single/Paired end	single
Raw strandedness	forward
Reverse complemented?	False
Mapped strandedness	forward
Timecourse	False
Control/Experimental	experimental
Wildtype & Untreated?	False
Outlier	No
Unusable	No

**Downloads**
TDF visualization file	TDF file	93 Mb
Stranded gene read counts	TXT file	1 Mb
Unstranded bidirectional read counts	TXT file	21 Mb
Tfit bidirectional regions	BED file	2 Mb
dREG bidirectional regions	BED file	935 Kb
All data files	ZIP archive

**Cellular details**
Organism	H. sapiens
Sample type	cell line
Cell type	MCF7
Clone/Individual
Strain
Genotype
Construct

**Conditions and treatments**
Condition type	Treatment	Start time	End time	Duration
treatment	TNF-alpha (25 ng/mL)	-40 min	0 min	40 min

**Extended notes**
Pipeline info and software versions
Sample notes
Analysis notes	Requires "qin=33" flag for bbduk - issue with recognizing phred encoding; Ran qc redo nextflow

**Sample metrics**
Sample QC score	1
Sample NRO score	3
Raw read length	50
Read depth after trimming	23,706,691
Duplication proportion	0.38141
Proportion reads mapped	0.9005
Exon/intron ratio	3.3085
Unique read proportion	0.69924

**Bidirectionals**
Total # Tfit bidirectionals	20884
# Promoter Tfit bidirectionals	1708
# Intronic Tfit bidirectionals	14339
# Intergenic Tfit bidirectionals	2214
Total # dREG bidirectionals	21810
# Promoter dREG bidirectionals	1260
# Intronic dREG bidirectionals	15313
# Intergenic dREG bidirectionals	2710
Part of Tfit master merge?	True
Part of dREG master merge?	True