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SRR122341 Sample ID 2594
| Paper identifier | Wang2011reprogramming |
| SRP accession | SRP005967 |
| GEO accession | GSE27823 |
| Samples | SRR122341 |
| QC score | 3 |
| Replicate | 3 |
| 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 | 46 Mb |
| Stranded gene read counts | TXT file | 1 Mb |
| Unstranded bidirectional read counts | TXT file | 21 Mb |
| Tfit bidirectional regions | BED file | 974 Kb |
| dREG bidirectional regions | BED file | 273 Kb |
| All data files | ZIP archive | |
| Organism | H. sapiens |
| Sample type | cell line |
| Cell type | LNCaP |
| Clone/Individual | |
| Strain | |
| Genotype | |
| Construct | siRNA Foxa1 |
| Condition type | Treatment | Start time | End time | Duration |
| treatment | dihydrotestosterone | -1 hr | 0 hr | 1 hr |
| Pipeline info and software versions | |
| Sample notes | DHT concentration probably 100 nM, but not explicitly said |
| Analysis notes | Ran qc redo nextflow |
| Sample QC score | 3 |
| Sample NRO score | 1 |
| Raw read length | 36 |
| Read depth after trimming | 20,727,546 |
| Duplication proportion | 0.65032 |
| Proportion reads mapped | 0.6942 |
| Exon/intron ratio | 2.68731 |
| Unique read proportion | 0.36089 |
| Total # Tfit bidirectionals | 11242 |
| # Promoter Tfit bidirectionals | 5353 |
| # Intronic Tfit bidirectionals | 4513 |
| # Intergenic Tfit bidirectionals | 1172 |
| Total # dREG bidirectionals | 6344 |
| # Promoter dREG bidirectionals | 3724 |
| # Intronic dREG bidirectionals | 1764 |
| # Intergenic dREG bidirectionals | 969 |
| Part of Tfit master merge? | True |
| Part of dREG master merge? | True |