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SRR3555069 Sample ID 1208
| Paper identifier | Kim2018pluripotency |
| SRP accession | SRP075469 |
| GEO accession | GSE81677 |
| Samples | SRR3555069 |
| QC score | 5 |
| Replicate | 1 |
| Protocol | PRO-cap |
| 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 |
| TDF visualization file | TDF file | 9 Mb |
| Stranded gene read counts | TXT file | 903 Kb |
| Unstranded bidirectional read counts | TXT file | 17 Mb |
| Tfit bidirectional regions | BED file | 243 Kb |
| dREG bidirectional regions | BED file | 98 Kb |
| All data files | ZIP archive | |
| Organism | M. musculus |
| Sample type | primary cell |
| Cell type | peritoneal macrophage |
| Clone/Individual | |
| Strain | |
| Genotype | |
| Construct |
| Condition type | Treatment | Start time | End time | Duration |
| no treatment | None | None | None |
| Pipeline info and software versions | |
| Sample notes | Paper and data indicate ligation library prep, GEO metadata says circularization, no poly-A tail; Not completely clear if there was treatment, but I don't think so |
| Analysis notes |
| Sample QC score | 5 |
| Sample NRO score | 3 |
| Raw read length | 51 |
| Read depth after trimming | 16,356,331 |
| Duplication proportion | 0.90975 |
| Proportion reads mapped | 0.2382 |
| Exon/intron ratio | 6.36434 |
| Unique read proportion | 0.06168 |
| Total # Tfit bidirectionals | 2875 |
| # Promoter Tfit bidirectionals | 1438 |
| # Intronic Tfit bidirectionals | 759 |
| # Intergenic Tfit bidirectionals | 219 |
| Total # dREG bidirectionals | 2280 |
| # Promoter dREG bidirectionals | 1730 |
| # Intronic dREG bidirectionals | 303 |
| # Intergenic dREG bidirectionals | 78 |
| Part of Tfit master merge? | True |
| Part of dREG master merge? | True |