DBNascent | Samples

SRR8206345 Sample ID 957

**Data sources**
Paper identifier	Herold2019recruitment
SRP accession	SRP135799
GEO accession	GSE111905
Samples	SRR8206345

**Technical details**
QC score	4
Replicate	1
Protocol	GRO-seq
Library prep	ligation
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	Yes

**Downloads**
TDF visualization file	TDF file	101 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	761 Kb
All data files	ZIP archive

**Cellular details**
Organism	H. sapiens
Sample type	cell line
Cell type	SHEP
Clone/Individual
Strain
Genotype	shRNA Brca1 (stable)
Construct

**Conditions and treatments**
Condition type	Treatment	Start time	End time	Duration
treatment	various	None	None	None

**Extended notes**
Pipeline info and software versions
Sample notes	Strangely, only a single sample here. From the paper 'For GRO-seq, reads of all biological conditions (4-OHT, BRCA1 shRNA) were pooled'. Not useful data.
Analysis notes	preseq required separate run, but no -D required; Ran qc redo nextflow

**Sample metrics**
Sample QC score	4
Sample NRO score	3
Raw read length	50
Read depth after trimming	152,062,827
Duplication proportion	0.87767
Proportion reads mapped	0.8542
Exon/intron ratio	5.80022
Unique read proportion	0.16323

**Bidirectionals**
Total # Tfit bidirectionals	21406
# Promoter Tfit bidirectionals	6597
# Intronic Tfit bidirectionals	10155
# Intergenic Tfit bidirectionals	3055
Total # dREG bidirectionals	17635
# Promoter dREG bidirectionals	6523
# Intronic dREG bidirectionals	7583
# Intergenic dREG bidirectionals	2946
Part of Tfit master merge?	True
Part of dREG master merge?	True