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SRR1501091 Sample ID 1440
| Paper identifier | Leveille2015genome |
| SRP accession | SRP034626 |
| GEO accession | GSE53499 |
| Samples | SRR1501091 |
| QC score | 3 |
| Replicate | 1 |
| Protocol | GRO-seq |
| 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 | 213 Mb |
| Stranded gene read counts | TXT file | 1 Mb |
| Unstranded bidirectional read counts | TXT file | 21 Mb |
| Tfit bidirectional regions | BED file | 3 Mb |
| dREG bidirectional regions | BED file | 1 Mb |
| All data files | ZIP archive | |
| Organism | H. sapiens |
| Sample type | cell line |
| Cell type | MCF7 |
| 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 cites Wang2011 (circularization) but GEO says Core 2008 and describes ligation. |
| Analysis notes | Ran qc redo nextflow |
| Sample QC score | 3 |
| Sample NRO score | 2 |
| Raw read length | 51 |
| Read depth after trimming | 144,145,553 |
| Duplication proportion | 0.78181 |
| Proportion reads mapped | 0.9713 |
| Exon/intron ratio | 3.23915 |
| Unique read proportion | 0.43669 |
| Total # Tfit bidirectionals | 34444 |
| # Promoter Tfit bidirectionals | 14491 |
| # Intronic Tfit bidirectionals | 13260 |
| # Intergenic Tfit bidirectionals | 6236 |
| Total # dREG bidirectionals | 26397 |
| # Promoter dREG bidirectionals | 8280 |
| # Intronic dREG bidirectionals | 10456 |
| # Intergenic dREG bidirectionals | 6795 |
| Part of Tfit master merge? | True |
| Part of dREG master merge? | True |