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SRR8713366 Sample ID 2562
| Paper identifier | Vihervaara2021stress |
| SRP accession | SRP188184 |
| GEO accession | GSE128160 |
| Samples | SRR8713366 |
| QC score | 5 |
| Replicate | 1 |
| Protocol | PRO-seq |
| Library prep | ligation |
| Spike-in | D. melanogaster |
| Single/Paired end | single |
| Raw strandedness | reverse |
| Reverse complemented? | True |
| Mapped strandedness | forward |
| Timecourse | True |
| Control/Experimental | experimental |
| Wildtype & Untreated? | False |
| Outlier | No |
| Unusable | No |
| TDF visualization file | TDF file | 20 Mb |
| Stranded gene read counts | TXT file | 901 Kb |
| Unstranded bidirectional read counts | TXT file | 17 Mb |
| Tfit bidirectional regions | BED file | 1 Mb |
| dREG bidirectional regions | BED file | 462 Kb |
| All data files | ZIP archive | |
| Organism | M. musculus |
| Sample type | cell line |
| Cell type | MEF |
| Clone/Individual | |
| Strain | |
| Genotype | |
| Construct |
| Condition type | Treatment | Start time | End time | Duration |
| treatment | heat shock (42 Celsius) | -60 min | 0 min | 1 hr |
| Pipeline info and software versions | |
| Sample notes | Cites Kwak2013 for protocol and library prep and also implies ligation with adapters, but not explicitly stated |
| Analysis notes | Previously in DB until 6/29/2021 as Mahat2020unpublished - all previous outerr and log files reflect previous id; dirty data - did fastq-dump manually, trimmed first 10 bp and bp 50+, ran pipeline on trimmed fastqs; ran tech reps on pre-trimmed fastqs |
| Sample QC score | 5 |
| Sample NRO score | 3 |
| Raw read length | 41 |
| Read depth after trimming | 5,133,951 |
| Duplication proportion | 0.31584 |
| Proportion reads mapped | 0.5959 |
| Exon/intron ratio | 5.52893 |
| Unique read proportion | 0.55317 |
| Total # Tfit bidirectionals | 14723 |
| # Promoter Tfit bidirectionals | 7344 |
| # Intronic Tfit bidirectionals | 4570 |
| # Intergenic Tfit bidirectionals | 1239 |
| Total # dREG bidirectionals | 10707 |
| # Promoter dREG bidirectionals | 6022 |
| # Intronic dREG bidirectionals | 2558 |
| # Intergenic dREG bidirectionals | 741 |
| Part of Tfit master merge? | True |
| Part of dREG master merge? | True |