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SRR3051603 Sample ID 406
| Paper identifier | Busslinger2017cohesin |
| SRP accession | SRP067744 |
| GEO accession | GSE76303 |
| Samples | SRR3051603 |
| QC score | 5 |
| Replicate | 3 |
| 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 | 19 Mb |
| Stranded gene read counts | TXT file | 894 Kb |
| Unstranded bidirectional read counts | TXT file | 17 Mb |
| Tfit bidirectional regions | BED file | 129 Kb |
| dREG bidirectional regions | BED file | 18 Kb |
| All data files | ZIP archive | |
| Organism | M. musculus |
| Sample type | cell line |
| Cell type | MEF |
| Clone/Individual | |
| Strain | C57BL/6 |
| Genotype | Ctcf fl/fl; WapI fl/fl |
| Construct |
| Condition type | Treatment | Start time | End time | Duration |
| no treatment | None | None | None |
| Pipeline info and software versions | |
| Sample notes | |
| Analysis notes | Low read depth and strange looking (almost but not quite single stranded); Ran qc redo nextflow |
| Sample QC score | 5 |
| Sample NRO score | 1 |
| Raw read length | 18 |
| Read depth after trimming | 3,554,903 |
| Duplication proportion | 0.07686 |
| Proportion reads mapped | 0.5481 |
| Exon/intron ratio | 2.08182 |
| Unique read proportion | 0.84 |
| Total # Tfit bidirectionals | 1561 |
| # Promoter Tfit bidirectionals | 702 |
| # Intronic Tfit bidirectionals | 389 |
| # Intergenic Tfit bidirectionals | 143 |
| Total # dREG bidirectionals | 419 |
| # Promoter dREG bidirectionals | 109 |
| # Intronic dREG bidirectionals | 88 |
| # Intergenic dREG bidirectionals | 110 |
| Part of Tfit master merge? | True |
| Part of dREG master merge? | True |