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SRR988344 Sample ID 1465
| Paper identifier | Li2013ncor |
| SRP accession | SRP029986 |
| GEO accession | GSE50944 |
| Samples | SRR988344 |
| QC score | 5 |
| Replicate | 2 |
| Protocol | GRO-seq |
| Library prep | circularization |
| Spike-in | None |
| Single/Paired end | single |
| Raw strandedness | forward |
| Reverse complemented? | False |
| Mapped strandedness | forward |
| Timecourse | True |
| Control/Experimental | experimental |
| Wildtype & Untreated? | False |
| Outlier | No |
| Unusable | No |
| TDF visualization file | TDF file | 18 Mb |
| Stranded gene read counts | TXT file | 898 Kb |
| Unstranded bidirectional read counts | TXT file | 17 Mb |
| Tfit bidirectional regions | BED file | 354 Kb |
| dREG bidirectional regions | BED file | 78 Kb |
| All data files | ZIP archive | |
| Organism | M. musculus |
| Sample type | primary cell |
| Cell type | peritoneal macrophage |
| Clone/Individual | |
| Strain | C57BL/6J |
| Genotype | NCoR fl/fl |
| Construct |
| Condition type | Treatment | Start time | End time | Duration |
| treatment | Kdo2-Lipid A (100 ng/mL) | -12 hr | 0 hr | 12 hr |
| Pipeline info and software versions | |
| Sample notes | replicate info not clear, but implies biological in paper |
| Analysis notes | Ran qc redo nextflow; Originally labeled and processed as technical replicates, but paper implies biological - kept tech rep processed data just in case but removed SRZ labels from metadata |
| Sample QC score | 5 |
| Sample NRO score | 1 |
| Raw read length | 34 |
| Read depth after trimming | 4,665,668 |
| Duplication proportion | 0.40937 |
| Proportion reads mapped | 0.6166 |
| Exon/intron ratio | 2.88652 |
| Unique read proportion | 0.4823 |
| Total # Tfit bidirectionals | 4200 |
| # Promoter Tfit bidirectionals | 1671 |
| # Intronic Tfit bidirectionals | 1418 |
| # Intergenic Tfit bidirectionals | 571 |
| Total # dREG bidirectionals | 1823 |
| # Promoter dREG bidirectionals | 905 |
| # Intronic dREG bidirectionals | 459 |
| # Intergenic dREG bidirectionals | 299 |
| Part of Tfit master merge? | True |
| Part of dREG master merge? | True |