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SRZ2084584 Sample ID 436
| Paper identifier | Chen2015paf1 |
| SRP accession | SRP060227 |
| GEO accession | GSE70408 |
| Samples | SRR2084584 |
| SRR2084585 | |
| SRR2084586 | |
| SRR2084587 |
| 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? | False |
| Outlier | No |
| Unusable | No |
| TDF visualization file | TDF file | 69 Mb |
| Stranded gene read counts | TXT file | 1 Mb |
| Unstranded bidirectional read counts | TXT file | 21 Mb |
| Tfit bidirectional regions | BED file | 2 Mb |
| dREG bidirectional regions | BED file | 798 Kb |
| All data files | ZIP archive | |
| Organism | H. sapiens |
| Sample type | cell line |
| Cell type | HCT116 |
| Clone/Individual | |
| Strain | |
| Genotype | |
| Construct | shRNA control |
| Condition type | Treatment | Start time | End time | Duration |
| no treatment | None | None | None |
| Pipeline info and software versions | |
| Sample notes | Not clear whether library prep was ligation or circularization |
| Analysis notes |
| Sample QC score | 3 |
| Sample NRO score | 2 |
| Raw read length | 35 |
| Read depth after trimming | 62,965,454 |
| Duplication proportion | 0.67243 |
| Proportion reads mapped | 0.4716 |
| Exon/intron ratio | 4.69901 |
| Unique read proportion | 0.38018 |
| Total # Tfit bidirectionals | 28322 |
| # Promoter Tfit bidirectionals | 11649 |
| # Intronic Tfit bidirectionals | 11311 |
| # Intergenic Tfit bidirectionals | 5077 |
| Total # dREG bidirectionals | 18477 |
| # Promoter dREG bidirectionals | 8743 |
| # Intronic dREG bidirectionals | 6295 |
| # Intergenic dREG bidirectionals | 3469 |
| Part of Tfit master merge? | True |
| Part of dREG master merge? | True |