Explore DBNascent | browse or search sample metadata
Search
Advanced Search
All Samples
Samples By Dataset
Sample Details
SRZ930701 Sample ID 1171
| Paper identifier | Kaikkonen2013remodeling |
| SRP accession | SRP026695 |
| GEO accession | GSE48759 |
| Samples | SRR930701 |
| SRR930702 | |
| SRR930703 | |
| SRR930704 | |
| SRR930705 | |
| SRR930706 |
| QC score | 4 |
| 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 | 23 Mb |
| Stranded gene read counts | TXT file | 904 Kb |
| Unstranded bidirectional read counts | TXT file | 17 Mb |
| Tfit bidirectional regions | BED file | 573 Kb |
| dREG bidirectional regions | BED file | 174 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 |
| treatment | actinomycin D (5 microg/mL) | -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 | 4 |
| Sample NRO score | 2 |
| Raw read length | 51 |
| Read depth after trimming | 21,591,056 |
| Duplication proportion | 0.83501 |
| Proportion reads mapped | 0.7317 |
| Exon/intron ratio | 3.58041 |
| Unique read proportion | 0.18549 |
| Total # Tfit bidirectionals | 6793 |
| # Promoter Tfit bidirectionals | 2782 |
| # Intronic Tfit bidirectionals | 2347 |
| # Intergenic Tfit bidirectionals | 155 |
| Total # dREG bidirectionals | 4035 |
| # Promoter dREG bidirectionals | 1910 |
| # Intronic dREG bidirectionals | 1084 |
| # Intergenic dREG bidirectionals | 401 |
| Part of Tfit master merge? | True |
| Part of dREG master merge? | True |