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SRR3004200 Sample ID 2408
| Paper identifier | Sumida2018ultra |
| SRP accession | SRP067415 |
| GEO accession | GSE76043 |
| Samples | SRR3004200 |
| QC score | 4 |
| Replicate | 2 |
| 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 | |
| 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 | HCT116 |
| 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 | 4 |
| Sample NRO score | 2 |
| Raw read length | 35 |
| Read depth after trimming | 5,282,934 |
| Duplication proportion | 0.10167 |
| Proportion reads mapped | 0.8125 |
| Exon/intron ratio | 4.96505 |
| Unique read proportion | 0.73686 |
| Total # Tfit bidirectionals | 13350 |
| # Promoter Tfit bidirectionals | 2370 |
| # Intronic Tfit bidirectionals | 6839 |
| # Intergenic Tfit bidirectionals | 767 |
| Total # dREG bidirectionals | 2703 |
| # Promoter dREG bidirectionals | 882 |
| # Intronic dREG bidirectionals | 952 |
| # Intergenic dREG bidirectionals | 355 |
| Part of Tfit master merge? | True |
| Part of dREG master merge? | True |