SRR6660368 Sample ID 1560

Data sources
Paper identifier Link2018analysis
SRP accession SRP131922
GEO accession GSE109965
Samples SRR6660368
Technical details
QC score 1
Replicate 2
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 control
Wildtype & Untreated? True
Outlier No
Unusable No
Downloads
TDF visualization file TDF file 100 Mb
Stranded gene read counts TXT file 917 Kb
Unstranded bidirectional read counts TXT file 17 Mb
Tfit bidirectional regions BED file
dREG bidirectional regions BED file 1 Mb
All data files ZIP archive
Cellular details
Organism M. musculus
Sample type primary cell
Cell type bone marrow derived macrophage
Clone/Individual
Strain PWK/PhJ
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
Analysis notes needs samtools/1.10 and 60Gb memory for samtools step; Major adapter contamination for some libraries and some very low/no read depth samples; Ran qc redo nextflow
Sample metrics
Sample QC score 1
Sample NRO score 1
Raw read length 50
Read depth after trimming 34,774,757
Duplication proportion 0.35239
Proportion reads mapped 0.7391
Exon/intron ratio 1.52463
Unique read proportion 0.73385
Bidirectionals
Total # Tfit bidirectionals None
# Promoter Tfit bidirectionals None
# Intronic Tfit bidirectionals None
# Intergenic Tfit bidirectionals None
Total # dREG bidirectionals 23689
# Promoter dREG bidirectionals 6959
# Intronic dREG bidirectionals 9261
# Intergenic dREG bidirectionals 6101
Part of Tfit master merge? False
Part of dREG master merge? False