DBNascent | Samples

SRR13242137 Sample ID 466

**Data sources**
Paper identifier	Chivu2020unpublished
SRP accession	SRP297660
GEO accession	GSE163043
Samples	SRR13242137

**Technical details**
QC score	0
Replicate	1
Protocol	ChRO-seq
Library prep	not noted in GEO or publication
Spike-in	None
Single/Paired end	paired
Raw strandedness	read1 forward
Reverse complemented?	True
Mapped strandedness	read1 forward
Timecourse	False
Control/Experimental	control
Wildtype & Untreated?	True
Outlier	No
Unusable	No

**Downloads**
TDF visualization file	TDF file	63 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	476 Kb
All data files	ZIP archive

**Cellular details**
Organism	H. sapiens
Sample type	cell line
Cell type	K562
Clone/Individual
Strain
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	CHRO-seq, Library prep kit noted is a DNA prep kit - unknown; I think this is referred to in bioRxiv paper https://doi.org/10.1101/2020.04.08.032730
Analysis notes	Lots of adapter contamination, did fastq-dump manually, force trimmed first 14 bp of R1 reads and last 14 bp of R2 reads prior to running pipeline, ran pipeline on trimmed fastqs (with normal bbduk trimming included)

**Sample metrics**
Sample QC score	0
Sample NRO score	2
Raw read length	28
Read depth after trimming	17,622,931
Duplication proportion	None
Proportion reads mapped	0.3089
Exon/intron ratio	3.77859
Unique read proportion	None

**Bidirectionals**
Total # Tfit bidirectionals	17918
# Promoter Tfit bidirectionals	8808
# Intronic Tfit bidirectionals	6712
# Intergenic Tfit bidirectionals	2634
Total # dREG bidirectionals	11072
# Promoter dREG bidirectionals	6377
# Intronic dREG bidirectionals	3211
# Intergenic dREG bidirectionals	1511
Part of Tfit master merge?	True
Part of dREG master merge?	True