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SRR6492230 Sample ID 535
| Paper identifier | Cuartero2020control |
| SRP accession | SRP130916 |
| GEO accession | GSE108584 |
| Samples | SRR6492230 |
| QC score | 2 |
| 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 | True |
| Control/Experimental | experimental |
| Wildtype & Untreated? | False |
| Outlier | No |
| Unusable | No |
| TDF visualization file | TDF file | 98 Mb |
| Stranded gene read counts | TXT file | 918 Kb |
| Unstranded bidirectional read counts | TXT file | 17 Mb |
| Tfit bidirectional regions | BED file | 2 Mb |
| dREG bidirectional regions | BED file | 1 Mb |
| All data files | ZIP archive | |
| Organism | M. musculus |
| Sample type | primary cell |
| Cell type | bone marrow derived macrophage |
| Clone/Individual | |
| Strain | |
| Genotype | Rad21 fl/fl; tamoxifen-inducible Cre/+ |
| Construct |
| Condition type | Treatment | Start time | End time | Duration |
| treatment | hydroxytamoxifen (200 nM) | -78 hr | -6 hr | 3 day |
| treatment | lipopolysaccharide (10 ng/mL) | -6 hr | 0 hr | 6 hr |
| Pipeline info and software versions | |
| Sample notes | hydroxytamoxifen induces nuclear translocation of ERt2-Cre to knock out floxed fragment |
| Analysis notes | Ran qc redo nextflow |
| Sample QC score | 2 |
| Sample NRO score | 1 |
| Raw read length | 50 |
| Read depth after trimming | 43,984,083 |
| Duplication proportion | 0.55858 |
| Proportion reads mapped | 0.755 |
| Exon/intron ratio | 1.73785 |
| Unique read proportion | 0.6329 |
| Total # Tfit bidirectionals | 25452 |
| # Promoter Tfit bidirectionals | 7935 |
| # Intronic Tfit bidirectionals | 8894 |
| # Intergenic Tfit bidirectionals | 6893 |
| Total # dREG bidirectionals | 24032 |
| # Promoter dREG bidirectionals | 6897 |
| # Intronic dREG bidirectionals | 9185 |
| # Intergenic dREG bidirectionals | 6388 |
| Part of Tfit master merge? | True |
| Part of dREG master merge? | True |