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SRR1661579 Sample ID 808
| Paper identifier | Fong2014pre |
| SRP accession | SRP050215 |
| GEO accession | GSE63375 |
| Samples | SRR1661579 |
| QC score | 5 |
| Replicate | 1 |
| Protocol | GRO-seq |
| Library prep | ligation |
| Spike-in | None |
| Single/Paired end | single |
| Raw strandedness | forward |
| Reverse complemented? | False |
| Mapped strandedness | forward |
| Timecourse | True |
| Control/Experimental | experimental |
| Wildtype & Untreated? | False |
| Outlier | No |
| Unusable | No |
| TDF visualization file | TDF file | 15 Mb |
| Stranded gene read counts | TXT file | 1 Mb |
| Unstranded bidirectional read counts | TXT file | 21 Mb |
| Tfit bidirectional regions | BED file | 56 Kb |
| dREG bidirectional regions | BED file | 27 Kb |
| All data files | ZIP archive | |
| Organism | H. sapiens |
| Sample type | cell line |
| Cell type | HEK293 Flp-In |
| Clone/Individual | |
| Strain | |
| Genotype | alpha-amanitin resistant, dox-inducible Rpb1 N792D/E1126G (Flp knock-in) |
| Construct |
| Condition type | Treatment | Start time | End time | Duration |
| treatment | DRB (100 microM) | -200 min | -20 min | 3 hr |
| treatment | alpha-amanitin (2.5 microg/mL) | -2720 min | -200 min | 42 hr |
| treatment | doxycycline (2 microg/mL) | -3560 min | -2720 min | 14 hr |
| Pipeline info and software versions | |
| Sample notes | |
| Analysis notes | Very dirty data, contamination, many reads thrown out - about half sparse or very sparse; Ran qc redo nextflow |
| Sample QC score | 5 |
| Sample NRO score | 1 |
| Raw read length | 40 |
| Read depth after trimming | 6,778,957 |
| Duplication proportion | 0.72988 |
| Proportion reads mapped | 0.4837 |
| Exon/intron ratio | 2.59259 |
| Unique read proportion | 0.2333 |
| Total # Tfit bidirectionals | 613 |
| # Promoter Tfit bidirectionals | 295 |
| # Intronic Tfit bidirectionals | 264 |
| # Intergenic Tfit bidirectionals | 91 |
| Total # dREG bidirectionals | 629 |
| # Promoter dREG bidirectionals | 223 |
| # Intronic dREG bidirectionals | 184 |
| # Intergenic dREG bidirectionals | 265 |
| Part of Tfit master merge? | True |
| Part of dREG master merge? | True |