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SRR3728886 Sample ID 1801
| Paper identifier | Malinen2017crosstalk |
| SRP accession | SRP077580 |
| GEO accession | GSE83860 |
| Samples | SRR3728886 |
| 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 | 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 |
| treatment | dihydrotestosterone (100 nM) | -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 | 17,955,778 |
| Duplication proportion | 0.39307 |
| Proportion reads mapped | 0.9128 |
| Exon/intron ratio | 2.15843 |
| Unique read proportion | 0.62912 |
| Total # Tfit bidirectionals | 18823 |
| # Promoter Tfit bidirectionals | 7942 |
| # Intronic Tfit bidirectionals | 7648 |
| # Intergenic Tfit bidirectionals | 2948 |
| Total # dREG bidirectionals | 12059 |
| # Promoter dREG bidirectionals | 5832 |
| # Intronic dREG bidirectionals | 4370 |
| # Intergenic dREG bidirectionals | 2012 |
| Part of Tfit master merge? | True |
| Part of dREG master merge? | True |