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SRR8669168 Sample ID 2546
| Paper identifier | Vihervaara2021stress |
| SRP accession | SRP187541 |
| GEO accession | GSE127844 |
| Samples | SRR8669168 |
| QC score | 4 |
| Replicate | 2 |
| 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 | 43 Mb |
| Stranded gene read counts | TXT file | 1 Mb |
| Unstranded bidirectional read counts | TXT file | 21 Mb |
| Tfit bidirectional regions | BED file | 2 Mb |
| dREG bidirectional regions | BED file | 662 Kb |
| All data files | ZIP archive | |
| Organism | H. sapiens |
| Sample type | cell line |
| Cell type | K562 |
| Clone/Individual | |
| Strain | |
| Genotype | |
| Construct | shRNA control |
| Condition type | Treatment | Start time | End time | Duration |
| treatment | heat shock (42 Celsius) | -100 hr | -99 hr | 1 hr |
| treatment | heat shock (42 Celsius) | -103 hr | -102 hr | 1 hr |
| treatment | heat shock (42 Celsius) | -49 hr | -48 hr | 1 hr |
| treatment | heat shock (42 Celsius) | -52 hr | -51 hr | 1 hr |
| treatment | heat shock (42 Celsius) | -55 hr | -54 hr | 1 hr |
| treatment | heat shock (42 Celsius) | -73 hr | -72 hr | 1 hr |
| treatment | heat shock (42 Celsius) | -76 hr | -75 hr | 1 hr |
| treatment | heat shock (42 Celsius) | -79 hr | -78 hr | 1 hr |
| treatment | heat shock (42 Celsius) | -97 hr | -96 hr | 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 Vihervaara2020unpublished - scripts have been changed, but all previous outerr and log files reflect previous id |
| Sample QC score | 4 |
| Sample NRO score | 2 |
| Raw read length | 76 |
| Read depth after trimming | 8,332,849 |
| Duplication proportion | 0.35111 |
| Proportion reads mapped | 0.8672 |
| Exon/intron ratio | 4.80342 |
| Unique read proportion | 0.62402 |
| Total # Tfit bidirectionals | 18710 |
| # Promoter Tfit bidirectionals | 9625 |
| # Intronic Tfit bidirectionals | 6836 |
| # Intergenic Tfit bidirectionals | 2616 |
| Total # dREG bidirectionals | 15385 |
| # Promoter dREG bidirectionals | 8992 |
| # Intronic dREG bidirectionals | 4672 |
| # Intergenic dREG bidirectionals | 2136 |
| Part of Tfit master merge? | True |
| Part of dREG master merge? | True |