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SRR1661565 Sample ID 794
| Paper identifier | Fong2014pre |
| SRP accession | SRP050215 |
| GEO accession | GSE63375 |
| Samples | SRR1661565 |
| QC score | 4 |
| 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 | control |
| 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 | HEK293 Flp-In |
| Clone/Individual | |
| Strain | |
| Genotype | alpha-amanitin resistant, dox-inducible Rpb1 N792D (Flp knock-in) |
| Construct |
| Condition type | Treatment | Start time | End time | Duration |
| treatment | DRB (100 microM) | -3 hr | 0 hr | 3 hr |
| treatment | alpha-amanitin (2.5 microg/mL) | -45 hr | -3 hr | 42 hr |
| treatment | doxycycline (2 microg/mL) | -59 hr | -45 hr | 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 | 4 |
| Sample NRO score | 2 |
| Raw read length | 38 |
| Read depth after trimming | 13,307,153 |
| Duplication proportion | 0.80681 |
| Proportion reads mapped | 0.6611 |
| Exon/intron ratio | 3.76033 |
| Unique read proportion | 0.18641 |
| Total # Tfit bidirectionals | 12569 |
| # Promoter Tfit bidirectionals | 7612 |
| # Intronic Tfit bidirectionals | 4849 |
| # Intergenic Tfit bidirectionals | 732 |
| Total # dREG bidirectionals | 10551 |
| # Promoter dREG bidirectionals | 6883 |
| # Intronic dREG bidirectionals | 3088 |
| # Intergenic dREG bidirectionals | 713 |
| Part of Tfit master merge? | True |
| Part of dREG master merge? | True |