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SRZ942421 Sample ID 2154
| Paper identifier | Saponaro2014recql5 |
| SRP accession | SRP028170 |
| GEO accession | GSE49133 |
| Samples | SRR942421 |
| SRR942422 |
| QC score | 3 |
| Replicate | 1 |
| Protocol | GRO-seq |
| Library prep | not noted in GEO or publication |
| Spike-in | None |
| Single/Paired end | single |
| Raw strandedness | forward |
| Reverse complemented? | False |
| Mapped strandedness | forward |
| Timecourse | True |
| Control/Experimental | control |
| Wildtype & Untreated? | False |
| Outlier | No |
| Unusable | No |
| TDF visualization file | TDF file | 98 Mb |
| Stranded gene read counts | TXT file | 1 Mb |
| Unstranded bidirectional read counts | TXT file | 21 Mb |
| Tfit bidirectional regions | BED file | 3 Mb |
| dREG bidirectional regions | BED file | 687 Kb |
| All data files | ZIP archive | |
| Organism | H. sapiens |
| Sample type | cell line |
| Cell type | HEK293T |
| Clone/Individual | clone 15 |
| Strain | |
| Genotype | shRNA Recql5 endogenous (stable); dox-inducible Recql5 exogenous (stable) |
| Construct |
| Condition type | Treatment | Start time | End time | Duration |
| treatment | DRB (100 microM) | -235 min | -25 min | 210 min |
| Pipeline info and software versions | |
| Sample notes | Treatments incorrect in GEO as doxycycline instead of DRB, but paper methods are clear; Cells treated with 0.2 ng/mL doxycycline until 4 days before extraction, then some depleted; Clones not assumed to be replicates but could be treated as such |
| Analysis notes | Ran qc redo nextflow |
| Sample QC score | 3 |
| Sample NRO score | 2 |
| Raw read length | 36 |
| Read depth after trimming | 73,439,365 |
| Duplication proportion | 0.77243 |
| Proportion reads mapped | 0.8691 |
| Exon/intron ratio | 3.82471 |
| Unique read proportion | 0.28903 |
| Total # Tfit bidirectionals | 31919 |
| # Promoter Tfit bidirectionals | 9220 |
| # Intronic Tfit bidirectionals | 15640 |
| # Intergenic Tfit bidirectionals | 3746 |
| Total # dREG bidirectionals | 15885 |
| # Promoter dREG bidirectionals | 5482 |
| # Intronic dREG bidirectionals | 6402 |
| # Intergenic dREG bidirectionals | 2499 |
| Part of Tfit master merge? | True |
| Part of dREG master merge? | True |