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SRR13242380 Sample ID 469
| Paper identifier | Chivu2020unpublished |
| SRP accession | SRP297666 |
| GEO accession | GSE163048 |
| Samples | SRR13242380 |
| QC score | 5 |
| Replicate | 1 |
| Protocol | ChRO-seq |
| Library prep | not noted in GEO or publication |
| Spike-in | None |
| Single/Paired end | single |
| Raw strandedness | forward |
| Reverse complemented? | False |
| Mapped strandedness | forward |
| Timecourse | False |
| Control/Experimental | control |
| Wildtype & Untreated? | True |
| Outlier | No |
| Unusable | No |
| TDF visualization file | TDF file | 26 Mb |
| Organism | E. caballus |
| Sample type | tissue |
| Cell type | liver |
| Clone/Individual | Wild Guneva Star mare |
| Strain | |
| Genotype | |
| Construct |
| Condition type | Treatment | Start time | End time | Duration |
| no treatment | None | None | None |
| Pipeline info and software versions | |
| Sample notes | CHRO-seq; https://doi.org/10.1101/2020.04.08.032730 |
| Analysis notes | Lots of adapter contamination, did fastq-dump manually, force trimmed first 12 bases and base 65+ prior to running pipeline, ran pipeline on trimmed fastqs (with normal bbduk trimming included); Sparse |
| Sample QC score | 5 |
| Sample NRO score | 4 |
| Raw read length | 54 |
| Read depth after trimming | 25,375,127 |
| Duplication proportion | 0.97683 |
| Proportion reads mapped | 0.823 |
| Exon/intron ratio | 8.8402 |
| Unique read proportion | 0.04943 |
| Total # Tfit bidirectionals | None |
| # Promoter Tfit bidirectionals | None |
| # Intronic Tfit bidirectionals | None |
| # Intergenic Tfit bidirectionals | None |
| Total # dREG bidirectionals | None |
| # Promoter dREG bidirectionals | None |
| # Intronic dREG bidirectionals | None |
| # Intergenic dREG bidirectionals | None |
| Part of Tfit master merge? | True |
| Part of dREG master merge? | True |