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SRR3728893 Sample ID 1808
| Paper identifier | Malinen2017crosstalk |
| SRP accession | SRP077580 |
| GEO accession | GSE83860 |
| Samples | SRR3728893 |
| QC score | 2 |
| Replicate | 2 |
| 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 | 74 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 | 594 Kb |
| All data files | ZIP archive | |
| Organism | H. sapiens |
| Sample type | cell line |
| Cell type | LNCaP |
| Clone/Individual | |
| Strain | |
| Genotype | |
| Construct |
| Condition type | Treatment | Start time | End time | Duration |
| treatment | TNF-alpha (1000 U/mL) | -2 hr | 0 hr | 2 hr |
| Pipeline info and software versions | |
| Sample notes | |
| Analysis notes | Ran qc redo nextflow |
| Sample QC score | 2 |
| Sample NRO score | 1 |
| Raw read length | 51 |
| Read depth after trimming | 19,331,982 |
| Duplication proportion | 0.43374 |
| Proportion reads mapped | 0.9043 |
| Exon/intron ratio | 2.46609 |
| Unique read proportion | 0.58855 |
| Total # Tfit bidirectionals | 19666 |
| # Promoter Tfit bidirectionals | 8196 |
| # Intronic Tfit bidirectionals | 8057 |
| # Intergenic Tfit bidirectionals | 3262 |
| Total # dREG bidirectionals | 13775 |
| # Promoter dREG bidirectionals | 6671 |
| # Intronic dREG bidirectionals | 5197 |
| # Intergenic dREG bidirectionals | 2337 |
| Part of Tfit master merge? | True |
| Part of dREG master merge? | True |