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SRZ942429 Sample ID 2157
| Paper identifier | Saponaro2014recql5 |
| SRP accession | SRP028170 |
| GEO accession | GSE49133 |
| Samples | SRR942429 |
| SRR942430 | |
| SRR942431 | |
| SRR942432 |
| QC score | 4 |
| 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 | 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 | HEK293T |
| Clone/Individual | clone 18 |
| Strain | |
| Genotype | shRNA Recql5 endogenous (stable); dox-inducible Recql5 exogenous (stable) |
| Construct |
| Condition type | Treatment | Start time | End time | Duration |
| treatment | DRB (100 microM) | -220 min | -10 min | 210 min |
| treatment | doxycycline withdrawal | -5980 min | 0 min | 5980 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 | 4 |
| Sample NRO score | 2 |
| Raw read length | 36 |
| Read depth after trimming | 97,442,857 |
| Duplication proportion | 0.83145 |
| Proportion reads mapped | 0.8843 |
| Exon/intron ratio | 4.26031 |
| Unique read proportion | 0.21101 |
| Total # Tfit bidirectionals | 44664 |
| # Promoter Tfit bidirectionals | 12537 |
| # Intronic Tfit bidirectionals | 22274 |
| # Intergenic Tfit bidirectionals | 4147 |
| Total # dREG bidirectionals | 22465 |
| # Promoter dREG bidirectionals | 6069 |
| # Intronic dREG bidirectionals | 11455 |
| # Intergenic dREG bidirectionals | 2888 |
| Part of Tfit master merge? | True |
| Part of dREG master merge? | True |