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SRZ4012400 Sample ID 590
| Paper identifier | Danko2018dynamic |
| SRP accession | SRP081110 |
| GEO accession | GSE85337 |
| Samples | SRR4012400 |
| SRR4012401 |
| QC score | 3 |
| Replicate | 3 |
| 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 | control |
| Wildtype & Untreated? | True |
| 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 3 |
| Strain | |
| Genotype | |
| Construct |
| Condition type | Treatment | Start time | End time | Duration |
| vehicle | ethanol | -30 min | 0 min | 30 min |
| vehicle | DMSO | -30 min | 0 min | 30 min |
| Pipeline info and software versions | |
| Sample notes | References Kwak2013precise for library prep, no specifics in paper or GEO |
| Analysis notes |
| Sample QC score | 3 |
| Sample NRO score | 3 |
| Raw read length | 51 |
| Read depth after trimming | 16,263,064 |
| Duplication proportion | 0.75617 |
| Proportion reads mapped | 0.8229 |
| Exon/intron ratio | 5.01931 |
| Unique read proportion | 0.29171 |
| Total # Tfit bidirectionals | 15660 |
| # Promoter Tfit bidirectionals | 7405 |
| # Intronic Tfit bidirectionals | 6169 |
| # Intergenic Tfit bidirectionals | 1773 |
| Total # dREG bidirectionals | 12432 |
| # Promoter dREG bidirectionals | 6873 |
| # Intronic dREG bidirectionals | 4222 |
| # Intergenic dREG bidirectionals | 1363 |
| Part of Tfit master merge? | True |
| Part of dREG master merge? | True |