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SRR8206345 Sample ID 957
| Paper identifier | Herold2019recruitment |
| SRP accession | SRP135799 |
| GEO accession | GSE111905 |
| Samples | SRR8206345 |
| QC score | 4 |
| 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 | experimental |
| Wildtype & Untreated? | False |
| Outlier | No |
| Unusable | Yes |
| TDF visualization file | TDF file | 101 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 | 761 Kb |
| All data files | ZIP archive | |
| Organism | H. sapiens |
| Sample type | cell line |
| Cell type | SHEP |
| Clone/Individual | |
| Strain | |
| Genotype | shRNA Brca1 (stable) |
| Construct |
| Condition type | Treatment | Start time | End time | Duration |
| treatment | various | None | None | None |
| Pipeline info and software versions | |
| Sample notes | Strangely, only a single sample here. From the paper 'For GRO-seq, reads of all biological conditions (4-OHT, BRCA1 shRNA) were pooled'. Not useful data. |
| Analysis notes | preseq required separate run, but no -D required; Ran qc redo nextflow |
| Sample QC score | 4 |
| Sample NRO score | 3 |
| Raw read length | 50 |
| Read depth after trimming | 152,062,827 |
| Duplication proportion | 0.87767 |
| Proportion reads mapped | 0.8542 |
| Exon/intron ratio | 5.80022 |
| Unique read proportion | 0.16323 |
| Total # Tfit bidirectionals | 21406 |
| # Promoter Tfit bidirectionals | 6597 |
| # Intronic Tfit bidirectionals | 10155 |
| # Intergenic Tfit bidirectionals | 3055 |
| Total # dREG bidirectionals | 17635 |
| # Promoter dREG bidirectionals | 6523 |
| # Intronic dREG bidirectionals | 7583 |
| # Intergenic dREG bidirectionals | 2946 |
| Part of Tfit master merge? | True |
| Part of dREG master merge? | True |