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SRR579297 Sample ID 563
| Paper identifier | Danko2013signaling |
| SRP accession | SRP015987 |
| GEO accession | GSE41323 |
| Samples | SRR579297 |
| QC score | 2 |
| Replicate | 1 |
| Protocol | GRO-seq |
| Library prep | ligation |
| 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 | AC16 |
| Clone/Individual | |
| Strain | |
| Genotype | |
| Construct |
| Condition type | Treatment | Start time | End time | Duration |
| treatment | TNF-alpha (25 ng/mL) | -30 min | 0 min | 30 min |
| Pipeline info and software versions | |
| Sample notes | |
| Analysis notes | Ran qc redo nextflow |
| Sample QC score | 2 |
| Sample NRO score | 1 |
| Raw read length | 38 |
| Read depth after trimming | 15,902,227 |
| Duplication proportion | 0.33408 |
| Proportion reads mapped | 0.8235 |
| Exon/intron ratio | 2.45397 |
| Unique read proportion | 0.69053 |
| Total # Tfit bidirectionals | 32899 |
| # Promoter Tfit bidirectionals | 11220 |
| # Intronic Tfit bidirectionals | 14608 |
| # Intergenic Tfit bidirectionals | 7175 |
| Total # dREG bidirectionals | 20625 |
| # Promoter dREG bidirectionals | 7715 |
| # Intronic dREG bidirectionals | 8725 |
| # Intergenic dREG bidirectionals | 4228 |
| Part of Tfit master merge? | True |
| Part of dREG master merge? | True |