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SRR4041365 Sample ID 675
Paper identifier | Engreitz2016local |
SRP accession | SRP082334 |
GEO accession | GSE85798 |
Samples | SRR4041365 |
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 |
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 |
Organism | M. musculus |
Sample type | primary cell |
Cell type | ESC |
Clone/Individual | clone 2 |
Strain | 129/SV-Jae x castaneus |
Genotype | |
Construct |
Condition type | Treatment | Start time | End time | Duration |
no treatment | None | None | None |
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 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 |
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 |