Explore DBNascent | browse or search sample metadata
Search
Advanced Search
All Samples
Samples By Dataset
Sample Details
SRR3004197 Sample ID 2405
| Paper identifier | Sumida2018ultra |
| SRP accession | SRP067415 |
| GEO accession | GSE76043 |
| Samples | SRR3004197 |
| QC score | 5 |
| Replicate | 1 |
| Protocol | EU-seq |
| Library prep | ligation |
| Spike-in | None |
| Single/Paired end | paired |
| Raw strandedness | read1 reverse |
| Reverse complemented? | False |
| Mapped strandedness | read1 reverse |
| Timecourse | False |
| Control/Experimental | control |
| Wildtype & Untreated? | False |
| Outlier | No |
| Unusable | No |
| TDF visualization file | TDF file | 35 Mb |
| Stranded gene read counts | TXT file | 1 Mb |
| Unstranded bidirectional read counts | TXT file | 21 Mb |
| Tfit bidirectional regions | BED file | 1014 Kb |
| dREG bidirectional regions | BED file | 127 Kb |
| All data files | ZIP archive | |
| Organism | H. sapiens |
| Sample type | cell line |
| Cell type | HCEC |
| Clone/Individual | |
| Strain | |
| Genotype | |
| Construct |
| Condition type | Treatment | Start time | End time | Duration |
| treatment | ethynyl uridine (200 microM) | -1 hr | 0 hr | 1 hr |
| Pipeline info and software versions | |
| Sample notes | protocol/treatment are the click-IT EU nascent RNA kit; This dataset, labeled incorrectly as GRO-seq (and some RNA-seq and ChIP-seq) are associated with this paper, but not actually mentioned, so marked as not published |
| Analysis notes | Ran qc redo nextflow |
| Sample QC score | 5 |
| Sample NRO score | 5 |
| Raw read length | 35 |
| Read depth after trimming | 4,530,886 |
| Duplication proportion | 0.11068 |
| Proportion reads mapped | 0.7858 |
| Exon/intron ratio | 11.3167 |
| Unique read proportion | 0.64442 |
| Total # Tfit bidirectionals | 11627 |
| # Promoter Tfit bidirectionals | 1835 |
| # Intronic Tfit bidirectionals | 4642 |
| # Intergenic Tfit bidirectionals | 583 |
| Total # dREG bidirectionals | 2941 |
| # Promoter dREG bidirectionals | 754 |
| # Intronic dREG bidirectionals | 858 |
| # Intergenic dREG bidirectionals | 381 |
| Part of Tfit master merge? | True |
| Part of dREG master merge? | True |