DBNascent | Samples

SRR8950279 Sample ID 2797

**Data sources**
Paper identifier	Zhang2019fundamental
SRP accession	SRP193758
GEO accession	GSE130266
Samples	SRR8950279

**Technical details**
QC score	3
Replicate	3
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	80 Mb
Stranded gene read counts	TXT file	918 Kb
Unstranded bidirectional read counts	TXT file	17 Mb
Tfit bidirectional regions	BED file	2 Mb
dREG bidirectional regions	BED file	648 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 -/-; 3xCTCF-binding element knock-in
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; CBE = CTCF binding element
Analysis notes	Ran qc redo nextflow

**Sample metrics**
Sample QC score	3
Sample NRO score	1
Raw read length	76
Read depth after trimming	38,213,662
Duplication proportion	0.67
Proportion reads mapped	0.6406
Exon/intron ratio	2.02066
Unique read proportion	0.44325

**Bidirectionals**
Total # Tfit bidirectionals	25560
# Promoter Tfit bidirectionals	6318
# Intronic Tfit bidirectionals	10761
# Intergenic Tfit bidirectionals	5154
Total # dREG bidirectionals	14966
# Promoter dREG bidirectionals	4044
# Intronic dREG bidirectionals	5310
# Intergenic dREG bidirectionals	3837
Part of Tfit master merge?	False
Part of dREG master merge?	False