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SRR1542328 Sample ID 1619
| Paper identifier | Liu2014enhancer |
| SRP accession | SRP045391 |
| GEO accession | GSE60271 |
| Samples | SRR1542328 |
| QC score | 2 |
| Replicate | 1 |
| Protocol | GRO-seq |
| Library prep | circularization |
| Spike-in | None |
| Single/Paired end | single |
| Raw strandedness | forward |
| Reverse complemented? | False |
| Mapped strandedness | forward |
| Timecourse | False |
| Control/Experimental | experimental |
| Wildtype & Untreated? | False |
| Outlier | No |
| Unusable | No |
| TDF visualization file | TDF file | |
| Stranded gene read counts | TXT file | |
| Unstranded bidirectional read counts | TXT file | |
| Tfit bidirectional regions | BED file | |
| dREG bidirectional regions | BED file | |
| All data files | ZIP archive | |
| Organism | H. sapiens |
| Sample type | cell line |
| Cell type | MCF7 |
| Clone/Individual | |
| Strain | |
| Genotype | |
| Construct | shRNA RAR-alpha/RAR-gamma |
| Condition type | Treatment | Start time | End time | Duration |
| treatment | retinoic acid (1 microM) | -1 hr | 0 hr | 1 hr |
| Pipeline info and software versions | |
| Sample notes | |
| Analysis notes | Ran qc redo nextflow |
| Sample QC score | 2 |
| Sample NRO score | 2 |
| Raw read length | 50 |
| Read depth after trimming | 22,855,043 |
| Duplication proportion | 0.5763 |
| Proportion reads mapped | 0.8958 |
| Exon/intron ratio | 3.64536 |
| Unique read proportion | 0.44127 |
| Total # Tfit bidirectionals | 18271 |
| # Promoter Tfit bidirectionals | 8704 |
| # Intronic Tfit bidirectionals | 7343 |
| # Intergenic Tfit bidirectionals | 2279 |
| Total # dREG bidirectionals | 13949 |
| # Promoter dREG bidirectionals | 7641 |
| # Intronic dREG bidirectionals | 4877 |
| # Intergenic dREG bidirectionals | 1827 |
| Part of Tfit master merge? | True |
| Part of dREG master merge? | True |