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SRR1930089 Sample ID 2344
| Paper identifier | Stender2017structural |
| SRP accession | SRP056552 |
| GEO accession | GSE67295 |
| Samples | SRR1930089 |
| QC score | 4 |
| 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 | 20 Mb |
| Stranded gene read counts | TXT file | 1 Mb |
| Unstranded bidirectional read counts | TXT file | 21 Mb |
| Tfit bidirectional regions | BED file | 61 Kb |
| dREG bidirectional regions | BED file | 20 Kb |
| 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 | interleukin-1b | -30 min | 0 min | 30 min |
| Pipeline info and software versions | |
| Sample notes | not clear on whether vehicle is DMSO or ethanol for this experiment, doesn't explicitly say treatment concentrations for GRO-seq exps |
| Analysis notes | Ran qc redo nextflow |
| Sample QC score | 4 |
| Sample NRO score | 2 |
| Raw read length | 50 |
| Read depth after trimming | 10,359,368 |
| Duplication proportion | 0.77197 |
| Proportion reads mapped | 0.6702 |
| Exon/intron ratio | 3.83916 |
| Unique read proportion | 0.19571 |
| Total # Tfit bidirectionals | 680 |
| # Promoter Tfit bidirectionals | 160 |
| # Intronic Tfit bidirectionals | 314 |
| # Intergenic Tfit bidirectionals | 38 |
| Total # dREG bidirectionals | 454 |
| # Promoter dREG bidirectionals | 154 |
| # Intronic dREG bidirectionals | 194 |
| # Intergenic dREG bidirectionals | 113 |
| Part of Tfit master merge? | True |
| Part of dREG master merge? | True |