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SRR8669171 Sample ID 2549
| Paper identifier | Vihervaara2021stress |
| SRP accession | SRP187541 |
| GEO accession | GSE127844 |
| Samples | SRR8669171 |
| QC score | 1 |
| 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 | 121 Mb |
| Stranded gene read counts | TXT file | 1 Mb |
| Unstranded bidirectional read counts | TXT file | 21 Mb |
| Tfit bidirectional regions | BED file | 3 Mb |
| dREG bidirectional regions | BED file | 1 Mb |
| 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) | -1 hr | 0 hr | 1 hr |
| treatment | heat shock (42 Celsius) | -101 hr | -100 hr | 1 hr |
| treatment | heat shock (42 Celsius) | -104 hr | -103 hr | 1 hr |
| treatment | heat shock (42 Celsius) | -50 hr | -49 hr | 1 hr |
| treatment | heat shock (42 Celsius) | -53 hr | -52 hr | 1 hr |
| treatment | heat shock (42 Celsius) | -56 hr | -55 hr | 1 hr |
| treatment | heat shock (42 Celsius) | -74 hr | -73 hr | 1 hr |
| treatment | heat shock (42 Celsius) | -77 hr | -76 hr | 1 hr |
| treatment | heat shock (42 Celsius) | -80 hr | -79 hr | 1 hr |
| treatment | heat shock (42 Celsius) | -98 hr | -97 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 | 1 |
| Sample NRO score | 2 |
| Raw read length | 76 |
| Read depth after trimming | 33,079,796 |
| Duplication proportion | 0.42235 |
| Proportion reads mapped | 0.9188 |
| Exon/intron ratio | 4.05729 |
| Unique read proportion | 0.66862 |
| Total # Tfit bidirectionals | 39333 |
| # Promoter Tfit bidirectionals | 15260 |
| # Intronic Tfit bidirectionals | 14526 |
| # Intergenic Tfit bidirectionals | 10200 |
| Total # dREG bidirectionals | 33741 |
| # Promoter dREG bidirectionals | 9511 |
| # Intronic dREG bidirectionals | 13921 |
| # Intergenic dREG bidirectionals | 9578 |
| Part of Tfit master merge? | True |
| Part of dREG master merge? | True |