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SRR5714119 Sample ID 556
| Paper identifier | Daniel2018nuclear |
| SRP accession | SRP073648 |
| GEO accession | |
| Samples | SRR5714119 |
| QC score | 4 |
| Replicate | 1 |
| 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 | control |
| Wildtype & Untreated? | True |
| Outlier | No |
| Unusable | No |
| TDF visualization file | TDF file | 32 Mb |
| Stranded gene read counts | TXT file | 916 Kb |
| Unstranded bidirectional read counts | TXT file | 17 Mb |
| Tfit bidirectional regions | BED file | 923 Kb |
| dREG bidirectional regions | BED file | 433 Kb |
| All data files | ZIP archive | |
| Organism | M. musculus |
| Sample type | primary cell |
| Cell type | bone marrow derived macrophage |
| Clone/Individual | |
| Strain | C57BL/6 |
| Genotype | |
| Construct |
| Condition type | Treatment | Start time | End time | Duration |
| vehicle | DMSO | -1 hr | 0 hr | 1 hr |
| Pipeline info and software versions | |
| Sample notes | Not in GEO, experiment not specifically mentioned in paper - methods unclear |
| Analysis notes | Ran qc redo nextflow |
| Sample QC score | 4 |
| Sample NRO score | 1 |
| Raw read length | 35 |
| Read depth after trimming | 65,574,863 |
| Duplication proportion | 0.93592 |
| Proportion reads mapped | 0.6677 |
| Exon/intron ratio | 2.13612 |
| Unique read proportion | 0.14894 |
| Total # Tfit bidirectionals | 10799 |
| # Promoter Tfit bidirectionals | 4906 |
| # Intronic Tfit bidirectionals | 3267 |
| # Intergenic Tfit bidirectionals | 718 |
| Total # dREG bidirectionals | 10042 |
| # Promoter dREG bidirectionals | 5195 |
| # Intronic dREG bidirectionals | 2534 |
| # Intergenic dREG bidirectionals | 839 |
| Part of Tfit master merge? | True |
| Part of dREG master merge? | True |