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SRR4041366 Sample ID 676
| Paper identifier | Engreitz2016local |
| SRP accession | SRP082334 |
| GEO accession | GSE85798 |
| Samples | SRR4041366 |
| QC score | 3 |
| Replicate | 2 |
| 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 | 98 Mb |
| Stranded gene read counts | TXT file | 916 Kb |
| Unstranded bidirectional read counts | TXT file | 17 Mb |
| Tfit bidirectional regions | BED file | 3 Mb |
| dREG bidirectional regions | BED file | 913 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 | 3 |
| Sample NRO score | 2 |
| Raw read length | 40 |
| Read depth after trimming | 13,498,684 |
| Duplication proportion | 0.11214 |
| Proportion reads mapped | 0.8294 |
| Exon/intron ratio | 4.5738 |
| Unique read proportion | 0.736 |
| Total # Tfit bidirectionals | 38273 |
| # Promoter Tfit bidirectionals | 11747 |
| # Intronic Tfit bidirectionals | 11718 |
| # Intergenic Tfit bidirectionals | 11559 |
| Total # dREG bidirectionals | 21102 |
| # Promoter dREG bidirectionals | 6783 |
| # Intronic dREG bidirectionals | 5897 |
| # Intergenic dREG bidirectionals | 5857 |
| Part of Tfit master merge? | True |
| Part of dREG master merge? | True |