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SRR10486680 Sample ID 1939
| Paper identifier | Nguyen2020dichotomous |
| SRP accession | SRP230423 |
| GEO accession | GSE140573 |
| Samples | SRR10486680 |
| QC score | 2 |
| Replicate | 1 |
| Protocol | GRO-seq |
| Library prep | circularization |
| 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 | 62 Mb |
| Stranded gene read counts | TXT file | 914 Kb |
| Unstranded bidirectional read counts | TXT file | 17 Mb |
| dREG bidirectional regions | BED file | 570 Kb |
| All data files | ZIP archive | |
| Organism | M. musculus |
| Sample type | primary cell |
| Cell type | bone marrow derived macrophage |
| Clone/Individual | |
| Strain | |
| Genotype | Mhd3 -/- |
| Construct |
| Condition type | Treatment | Start time | End time | Duration |
| treatment | lipopolysaccharide (5 ng/mL) | -4 hr | 0 hr | 4 hr |
| Pipeline info and software versions | |
| Sample notes | |
| Analysis notes | Poor quality libraries, many are mostly poly-A or unknown contamination |
| Sample QC score | 2 |
| Sample NRO score | 1 |
| Raw read length | 100 |
| Read depth after trimming | 65,118,397 |
| Duplication proportion | 0.52124 |
| Proportion reads mapped | 0.2596 |
| Exon/intron ratio | 1.35868 |
| Unique read proportion | 0.56423 |
| Total # Tfit bidirectionals | None |
| # Promoter Tfit bidirectionals | None |
| # Intronic Tfit bidirectionals | None |
| # Intergenic Tfit bidirectionals | None |
| Total # dREG bidirectionals | 13229 |
| # Promoter dREG bidirectionals | 4443 |
| # Intronic dREG bidirectionals | 4693 |
| # Intergenic dREG bidirectionals | 3314 |
| Part of Tfit master merge? | False |
| Part of dREG master merge? | False |