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SRR1342253 Sample ID 889
| Paper identifier | Gardini2014integrator |
| SRP accession | SRP015419 |
| GEO accession | GSE40632 |
| Samples | SRR1342253 |
| QC score | 3 |
| Replicate | 2 |
| Protocol | GRO-seq |
| Library prep | circularization |
| Spike-in | None |
| Single/Paired end | single |
| Raw strandedness | forward |
| Reverse complemented? | False |
| 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 | HeLa |
| Clone/Individual | |
| Strain | |
| Genotype | |
| Construct | dox-inducible shRNA Ints11 |
| Condition type | Treatment | Start time | End time | Duration |
| treatment | EGF (100 ng/mL) | -30 min | 0 min | 30 min |
| treatment | doxycycline (1 microg/mL) | -96 hr | 0 hr | 4 day |
| treatment | serum starvation (0.5% FBS) | -24 hr | 0 hr | 1 day |
| Pipeline info and software versions | |
| Sample notes | Treatment times don't match between GEO and paper - used paper |
| Analysis notes | Ran qc redo nextflow |
| Sample QC score | 3 |
| Sample NRO score | 2 |
| Raw read length | 50 |
| Read depth after trimming | 71,256,583 |
| Duplication proportion | 0.78388 |
| Proportion reads mapped | 0.8716 |
| Exon/intron ratio | 4.08512 |
| Unique read proportion | 0.38079 |
| Total # Tfit bidirectionals | 44019 |
| # Promoter Tfit bidirectionals | 14569 |
| # Intronic Tfit bidirectionals | 18326 |
| # Intergenic Tfit bidirectionals | 9971 |
| Total # dREG bidirectionals | 27014 |
| # Promoter dREG bidirectionals | 9124 |
| # Intronic dREG bidirectionals | 11298 |
| # Intergenic dREG bidirectionals | 6547 |
| Part of Tfit master merge? | True |
| Part of dREG master merge? | True |