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SRR930687 Sample ID 1151
| Paper identifier | Kaikkonen2013remodeling |
| SRP accession | SRP026695 |
| GEO accession | GSE48759 |
| Samples | SRR930687 |
| 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 | 66 Mb |
| Stranded gene read counts | TXT file | 911 Kb |
| Unstranded bidirectional read counts | TXT file | 17 Mb |
| Tfit bidirectional regions | BED file | 2 Mb |
| dREG bidirectional regions | BED file | 750 Kb |
| All data files | ZIP archive | |
| Organism | M. musculus |
| Sample type | primary cell |
| Cell type | peritoneal macrophage |
| Clone/Individual | |
| Strain | C57BL/6 |
| Genotype | |
| Construct |
| Condition type | Treatment | Start time | End time | Duration |
| treatment | Kdo2-Lipid A (100 ng/mL) | -1 hr | 0 hr | 1 hr |
| vehicle | DMSO | -2 hr | 0 hr | 2 hr |
| treatment | serum starvation (0.5% FBS) | -15 hr | 0 hr | 15 hr |
| Pipeline info and software versions | |
| Sample notes | Replicate information unclear |
| Analysis notes | Ran qc redo nextflow |
| Sample QC score | 2 |
| Sample NRO score | 1 |
| Raw read length | 49 |
| Read depth after trimming | 18,845,726 |
| Duplication proportion | 0.34191 |
| Proportion reads mapped | 0.8174 |
| Exon/intron ratio | 2.25117 |
| Unique read proportion | 0.71865 |
| Total # Tfit bidirectionals | 22321 |
| # Promoter Tfit bidirectionals | 7140 |
| # Intronic Tfit bidirectionals | 8272 |
| # Intergenic Tfit bidirectionals | 5239 |
| Total # dREG bidirectionals | 17281 |
| # Promoter dREG bidirectionals | 5732 |
| # Intronic dREG bidirectionals | 6611 |
| # Intergenic dREG bidirectionals | 3731 |
| Part of Tfit master merge? | True |
| Part of dREG master merge? | True |