Explore DBNascent | browse or search sample metadata
Search
Advanced Search
All Samples
Samples By Dataset
Sample Details
SRZ942439 Sample ID 2160
| Paper identifier | Saponaro2014recql5 |
| SRP accession | SRP028170 |
| GEO accession | GSE49133 |
| Samples | SRR942439 |
| SRR942440 | |
| SRR942441 | |
| SRR942442 |
| 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 | control |
| Wildtype & Untreated? | False |
| Outlier | No |
| Unusable | No |
| TDF visualization file | TDF file | 75 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 | 755 Kb |
| 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) | -210 min | 0 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 | 4 |
| Sample NRO score | 2 |
| Raw read length | 36 |
| Read depth after trimming | 93,694,888 |
| Duplication proportion | 0.87169 |
| Proportion reads mapped | 0.8089 |
| Exon/intron ratio | 4.06889 |
| Unique read proportion | 0.16695 |
| Total # Tfit bidirectionals | 34820 |
| # Promoter Tfit bidirectionals | 10718 |
| # Intronic Tfit bidirectionals | 16240 |
| # Intergenic Tfit bidirectionals | 3422 |
| Total # dREG bidirectionals | 17341 |
| # Promoter dREG bidirectionals | 5757 |
| # Intronic dREG bidirectionals | 7529 |
| # Intergenic dREG bidirectionals | 2207 |
| Part of Tfit master merge? | True |
| Part of dREG master merge? | True |