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SRR6660158 Sample ID 1527
| Paper identifier | Link2018analysis |
| SRP accession | SRP131922 |
| GEO accession | GSE109965 |
| Samples | SRR6660158 |
| QC score | 4 |
| Replicate | 1 |
| Protocol | GRO-cap |
| Library prep | ligation |
| 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 | 18 Mb |
| Stranded gene read counts | TXT file | 903 Kb |
| Unstranded bidirectional read counts | TXT file | 17 Mb |
| Tfit bidirectional regions | BED file | 1 Mb |
| dREG bidirectional regions | BED file | 625 Kb |
| All data files | ZIP archive | |
| Organism | M. musculus |
| Sample type | primary cell |
| Cell type | bone marrow derived macrophage |
| Clone/Individual | |
| Strain | BALB/cJ |
| Genotype | |
| Construct |
| Condition type | Treatment | Start time | End time | Duration |
| treatment | Kdo2-Lipid A (10 ng/mL) | -1 hr | 0 hr | 1 hr |
| Pipeline info and software versions | |
| Sample notes | |
| Analysis notes | needs samtools/1.10 and 60Gb memory for samtools step; Major adapter contamination for some libraries and some very low/no read depth samples; Ran qc redo nextflow |
| Sample QC score | 4 |
| Sample NRO score | 2 |
| Raw read length | 50 |
| Read depth after trimming | 10,221,634 |
| Duplication proportion | 0.76796 |
| Proportion reads mapped | 0.6288 |
| Exon/intron ratio | 3.63348 |
| Unique read proportion | 0.1908 |
| Total # Tfit bidirectionals | 14787 |
| # Promoter Tfit bidirectionals | 4909 |
| # Intronic Tfit bidirectionals | 5976 |
| # Intergenic Tfit bidirectionals | 2930 |
| Total # dREG bidirectionals | 14537 |
| # Promoter dREG bidirectionals | 6251 |
| # Intronic dREG bidirectionals | 4716 |
| # Intergenic dREG bidirectionals | 2641 |
| Part of Tfit master merge? | False |
| Part of dREG master merge? | False |