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SRZ4012394 Sample ID 588
| Paper identifier | Danko2018dynamic |
| SRP accession | SRP081110 |
| GEO accession | GSE85337 |
| Samples | SRR4012394 |
| SRR4012395 | |
| SRR4012398 | |
| SRR4012399 |
| QC score | 3 |
| Replicate | 2 |
| Protocol | PRO-seq |
| Library prep | ligation |
| Spike-in | None |
| Single/Paired end | single |
| Raw strandedness | reverse |
| Reverse complemented? | True |
| Mapped strandedness | forward |
| Timecourse | False |
| 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 | primary cell |
| Cell type | CD4+ T cell |
| Clone/Individual | individual 2 |
| Strain | |
| Genotype | |
| Construct |
| Condition type | Treatment | Start time | End time | Duration |
| treatment | ionomycin (1 mM) | -30 min | 0 min | 30 min |
| treatment | phorbol 12-myristate 13-acetate (25 ng/mL) | -30 min | 0 min | 30 min |
| Pipeline info and software versions | |
| Sample notes | Two separate blood draws/cell preps from individual 2, so kid of bio reps, kind of tech reps; References Kwak2013precise for library prep, no specifics in paper or GEO |
| Analysis notes |
| Sample QC score | 3 |
| Sample NRO score | 2 |
| Raw read length | 50 |
| Read depth after trimming | 78,323,360 |
| Duplication proportion | 0.79467 |
| Proportion reads mapped | 0.8116 |
| Exon/intron ratio | 4.27758 |
| Unique read proportion | 0.4718 |
| Total # Tfit bidirectionals | 20455 |
| # Promoter Tfit bidirectionals | 7933 |
| # Intronic Tfit bidirectionals | 9259 |
| # Intergenic Tfit bidirectionals | 3013 |
| Total # dREG bidirectionals | 16646 |
| # Promoter dREG bidirectionals | 6716 |
| # Intronic dREG bidirectionals | 7180 |
| # Intergenic dREG bidirectionals | 2661 |
| Part of Tfit master merge? | True |
| Part of dREG master merge? | True |