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SRR1519039 Sample ID 830
| Paper identifier | Franco2015tnfalpha |
| SRP accession | SRP044608 |
| GEO accession | GSE59531 |
| Samples | SRR1519039 |
| QC score | 1 |
| Replicate | 2 |
| Protocol | GRO-seq |
| Library prep | circularization |
| 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 | MCF7 |
| Clone/Individual | |
| Strain | |
| Genotype | |
| Construct |
| Condition type | Treatment | Start time | End time | Duration |
| treatment | TNF-alpha (25 ng/mL) | -40 min | 0 min | 40 min |
| Pipeline info and software versions | |
| Sample notes | |
| Analysis notes | Requires "qin=33" flag for bbduk - issue with recognizing phred encoding; Ran qc redo nextflow |
| Sample QC score | 1 |
| Sample NRO score | 3 |
| Raw read length | 50 |
| Read depth after trimming | 23,706,691 |
| Duplication proportion | 0.38141 |
| Proportion reads mapped | 0.9005 |
| Exon/intron ratio | 3.3085 |
| Unique read proportion | 0.69924 |
| Total # Tfit bidirectionals | 20884 |
| # Promoter Tfit bidirectionals | 1708 |
| # Intronic Tfit bidirectionals | 14339 |
| # Intergenic Tfit bidirectionals | 2214 |
| Total # dREG bidirectionals | 21810 |
| # Promoter dREG bidirectionals | 1260 |
| # Intronic dREG bidirectionals | 15313 |
| # Intergenic dREG bidirectionals | 2710 |
| Part of Tfit master merge? | True |
| Part of dREG master merge? | True |