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SRR8867622 Sample ID 2315
| Paper identifier | Steinparzer2019transcriptional |
| SRP accession | SRP191474 |
| GEO accession | GSE129501 |
| Samples | SRR8867622 |
| QC score | 3 |
| Replicate | 1 |
| Protocol | PRO-seq |
| Library prep | not noted in GEO or publication |
| Spike-in | None |
| Single/Paired end | single |
| Raw strandedness | reverse |
| Reverse complemented? | True |
| Mapped strandedness | forward |
| Timecourse | False |
| Control/Experimental | experimental |
| Wildtype & Untreated? | False |
| Outlier | No |
| Unusable | No |
| TDF visualization file | TDF file | |
| Stranded gene read counts | TXT file | |
| Unstranded bidirectional read counts | TXT file | |
| Tfit bidirectional regions | BED file | |
| dREG bidirectional regions | BED file | |
| All data files | ZIP archive | |
| Organism | H. sapiens |
| Sample type | cell line |
| Cell type | HCT116 |
| Clone/Individual | |
| Strain | |
| Genotype | Cdk8 F97G |
| Construct |
| Condition type | Treatment | Start time | End time | Duration |
| treatment | 3MB-PP1 (10 microM) | -45 min | 0 min | 45 min |
| vehicle | PBS | -45 min | 0 min | 45 min |
| Pipeline info and software versions | |
| Sample notes | This paper says it has GRO-seq and tons of other data too but it's not showing up in the GEO database except small snippets separately? I don't know what they did |
| Analysis notes |
| Sample QC score | 3 |
| Sample NRO score | 2 |
| Raw read length | 76 |
| Read depth after trimming | 99,490,631 |
| Duplication proportion | 0.71226 |
| Proportion reads mapped | 0.9412 |
| Exon/intron ratio | 3.87619 |
| Unique read proportion | 0.47686 |
| Total # Tfit bidirectionals | 45163 |
| # Promoter Tfit bidirectionals | 18200 |
| # Intronic Tfit bidirectionals | 15495 |
| # Intergenic Tfit bidirectionals | 11191 |
| Total # dREG bidirectionals | 34691 |
| # Promoter dREG bidirectionals | 9004 |
| # Intronic dREG bidirectionals | 13514 |
| # Intergenic dREG bidirectionals | 10716 |
| Part of Tfit master merge? | True |
| Part of dREG master merge? | True |