Explore DBNascent | browse or search sample metadata
Search
Advanced Search
All Samples
Samples By Dataset
Sample Details
SRR3407138 Sample ID 553
| Paper identifier | Daniel2018nuclear |
| SRP accession | SRP073648 |
| GEO accession | GSE110464 |
| Samples | SRR3407138 |
| QC score | 3 |
| 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 | 24 Mb |
| Stranded gene read counts | TXT file | 904 Kb |
| Unstranded bidirectional read counts | TXT file | 17 Mb |
| Tfit bidirectional regions | BED file | 471 Kb |
| dREG bidirectional regions | BED file | 138 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 |
| treatment | interleukin-4 (20 ng/microL) | -25 hr | -1 hr | 1 day |
| vehicle | DMSO/ethanol | -1 hr | 0 hr | 1 hr |
| Pipeline info and software versions | |
| Sample notes | |
| Analysis notes | Ran qc redo nextflow |
| Sample QC score | 3 |
| Sample NRO score | 2 |
| Raw read length | 30 |
| Read depth after trimming | 18,761,218 |
| Duplication proportion | 0.66818 |
| Proportion reads mapped | 0.4508 |
| Exon/intron ratio | 3.80441 |
| Unique read proportion | 0.33204 |
| Total # Tfit bidirectionals | 5554 |
| # Promoter Tfit bidirectionals | 1812 |
| # Intronic Tfit bidirectionals | 2185 |
| # Intergenic Tfit bidirectionals | 415 |
| Total # dREG bidirectionals | 3206 |
| # Promoter dREG bidirectionals | 1684 |
| # Intronic dREG bidirectionals | 769 |
| # Intergenic dREG bidirectionals | 262 |
| Part of Tfit master merge? | True |
| Part of dREG master merge? | True |