DBNascent | Samples

SRR9961462 Sample ID 2803

**Data sources**
Paper identifier	Zhang2019fundamental
SRP accession	SRP193758
GEO accession	GSE130266
Samples	SRR9961462

**Technical details**
QC score	3
Replicate	4
Protocol	GRO-seq
Library prep	ligation
Spike-in	None
Single/Paired end	paired
Raw strandedness	read1 forward
Reverse complemented?	True
Mapped strandedness	read1 forward
Timecourse	False
Control/Experimental	experimental
Wildtype & Untreated?	False
Outlier	No
Unusable	No

**Downloads**
TDF visualization file	TDF file	45 Mb
Stranded gene read counts	TXT file	911 Kb
Unstranded bidirectional read counts	TXT file	17 Mb
Tfit bidirectional regions	BED file	2 Mb
dREG bidirectional regions	BED file	386 Kb
All data files	ZIP archive

**Cellular details**
Organism	M. musculus
Sample type	cell line
Cell type	CH12F3
Clone/Individual
Strain
Genotype	CH +/-; Aid -/-; I-alpha -/-
Construct

**Conditions and treatments**
Condition type	Treatment	Start time	End time	Duration
treatment	TGF-beta (0.5 ng/mL)	-24 hr	0 hr	1 day
treatment	anti-CD40 (1 microg/mL)	-24 hr	0 hr	1 day
treatment	interleukin-4 (20 ng/mL)	-24 hr	0 hr	1 day

**Extended notes**
Pipeline info and software versions
Sample notes	CH +/-: KO of heavy chain locus non-productive allele
Analysis notes	Ran qc redo nextflow

**Sample metrics**
Sample QC score	3
Sample NRO score	1
Raw read length	76
Read depth after trimming	15,371,526
Duplication proportion	0.61307
Proportion reads mapped	0.6867
Exon/intron ratio	1.9715
Unique read proportion	0.36487

**Bidirectionals**
Total # Tfit bidirectionals	19171
# Promoter Tfit bidirectionals	5336
# Intronic Tfit bidirectionals	7617
# Intergenic Tfit bidirectionals	3268
Total # dREG bidirectionals	8935
# Promoter dREG bidirectionals	2950
# Intronic dREG bidirectionals	3003
# Intergenic dREG bidirectionals	1873
Part of Tfit master merge?	False
Part of dREG master merge?	False