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SRR3051606 Sample ID 409
| Paper identifier | Busslinger2017cohesin |
| SRP accession | SRP067744 |
| GEO accession | GSE76303 |
| Samples | SRR3051606 |
| 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 | True |
| Control/Experimental | experimental |
| Wildtype & Untreated? | False |
| Outlier | No |
| Unusable | No |
| TDF visualization file | TDF file | 11 Mb |
| Stranded gene read counts | TXT file | 888 Kb |
| Unstranded bidirectional read counts | TXT file | 17 Mb |
| Tfit bidirectional regions | BED file | 237 Kb |
| dREG bidirectional regions | BED file | 28 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 |
| treatment | adeno-Cre virus (1 microL/million cells) | -244 hr | -240 hr | 4 hr |
| 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 | 4 |
| Raw read length | 18 |
| Read depth after trimming | 1,447,803 |
| Duplication proportion | 0.22124 |
| Proportion reads mapped | 0.5782 |
| Exon/intron ratio | 7.0 |
| Unique read proportion | 0.42317 |
| Total # Tfit bidirectionals | 2888 |
| # Promoter Tfit bidirectionals | 1419 |
| # Intronic Tfit bidirectionals | 688 |
| # Intergenic Tfit bidirectionals | 225 |
| Total # dREG bidirectionals | 654 |
| # Promoter dREG bidirectionals | 244 |
| # Intronic dREG bidirectionals | 127 |
| # Intergenic dREG bidirectionals | 137 |
| Part of Tfit master merge? | True |
| Part of dREG master merge? | True |