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SRZ5944049 Sample ID 2109
| Paper identifier | Rahnamoun2017mutant |
| SRP accession | SRP115797 |
| GEO accession | GSE102796 |
| Samples | SRR5944049 |
| SRR5944051 |
| QC score | 1 |
| 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 | 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 | cell line |
| Cell type | SW480 |
| Clone/Individual | |
| Strain | |
| Genotype | |
| Construct |
| Condition type | Treatment | Start time | End time | Duration |
| treatment | TNF-alpha (12.5 ng/mL) | -16 hr | 0 hr | 16 hr |
| Pipeline info and software versions | |
| Sample notes | Replicate information is a guess - states 2 biological replicates, but no idea which SRRs are tech reps of each other |
| Analysis notes |
| Sample QC score | 1 |
| Sample NRO score | 1 |
| Raw read length | 50 |
| Read depth after trimming | 25,950,895 |
| Duplication proportion | 0.4009 |
| Proportion reads mapped | 0.8297 |
| Exon/intron ratio | 2.91069 |
| Unique read proportion | 0.62286 |
| Total # Tfit bidirectionals | 32770 |
| # Promoter Tfit bidirectionals | 11993 |
| # Intronic Tfit bidirectionals | 13157 |
| # Intergenic Tfit bidirectionals | 6346 |
| Total # dREG bidirectionals | 20021 |
| # Promoter dREG bidirectionals | 8074 |
| # Intronic dREG bidirectionals | 7305 |
| # Intergenic dREG bidirectionals | 4366 |
| Part of Tfit master merge? | True |
| Part of dREG master merge? | True |