SRR4041365 Sample ID 675

Data sources
Paper identifier Engreitz2016local
SRP accession SRP082334
GEO accession GSE85798
Samples SRR4041365
Technical details
QC score 2
Replicate 1
Protocol PRO-seq
Library prep ligation
Spike-in None
Single/Paired end paired
Raw strandedness read1 reverse
Reverse complemented? False
Mapped strandedness read1 reverse
Timecourse False
Control/Experimental control
Wildtype & Untreated? False
Outlier No
Unusable No
Downloads
TDF visualization file TDF file 119 Mb
Stranded gene read counts TXT file 918 Kb
Unstranded bidirectional read counts TXT file 17 Mb
Tfit bidirectional regions BED file 3 Mb
dREG bidirectional regions BED file 888 Kb
All data files ZIP archive
Cellular details
Organism M. musculus
Sample type primary cell
Cell type ESC
Clone/Individual clone 2
Strain 129/SV-Jae x castaneus
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 Library prep is unclear, but citations indicate ligation
Analysis notes Originally processed as tech reps, but paper implies biological - kept tech rep data but removed SRZ labels from metadata; In db as Engreitz2016long until 2/8/21 - all older pipeline reports and out/err scripts reflect that; Ran qc redo nextflow
Sample metrics
Sample QC score 2
Sample NRO score 2
Raw read length 40
Read depth after trimming 15,826,487
Duplication proportion 0.12278
Proportion reads mapped 0.8454
Exon/intron ratio 3.96541
Unique read proportion 0.77312
Bidirectionals
Total # Tfit bidirectionals 36775
# Promoter Tfit bidirectionals 11573
# Intronic Tfit bidirectionals 10989
# Intergenic Tfit bidirectionals 10953
Total # dREG bidirectionals 20514
# Promoter dREG bidirectionals 6306
# Intronic dREG bidirectionals 5831
# Intergenic dREG bidirectionals 5930
Part of Tfit master merge? True
Part of dREG master merge? True