SRR6660300 Sample ID 1545

Data sources
Paper identifier Link2018analysis
SRP accession SRP131922
GEO accession GSE109965
Samples SRR6660300
Technical details
QC score 5
Replicate 1
Protocol GRO-cap
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 No
Downloads
TDF visualization file TDF file 8 Mb
Stranded gene read counts TXT file 895 Kb
Unstranded bidirectional read counts TXT file 17 Mb
Tfit bidirectional regions BED file 139 Kb
dREG bidirectional regions BED file 111 Kb
All data files ZIP archive
Cellular details
Organism M. musculus
Sample type primary cell
Cell type bone marrow derived macrophage
Clone/Individual
Strain NOD/ShiLtJ
Genotype
Construct
Conditions and treatments
Condition type Treatment Start time End time Duration
treatment Kdo2-Lipid A (10 ng/mL) -1 hr 0 hr 1 hr
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 5
Sample NRO score 1
Raw read length 50
Read depth after trimming 7,238,337
Duplication proportion 0.88643
Proportion reads mapped 0.4538
Exon/intron ratio 2.32203
Unique read proportion 0.06497
Bidirectionals
Total # Tfit bidirectionals 1644
# Promoter Tfit bidirectionals 753
# Intronic Tfit bidirectionals 489
# Intergenic Tfit bidirectionals 211
Total # dREG bidirectionals 2592
# Promoter dREG bidirectionals 1694
# Intronic dREG bidirectionals 493
# Intergenic dREG bidirectionals 248
Part of Tfit master merge? False
Part of dREG master merge? False