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SRR828729 Sample ID 873
| Paper identifier | Galbraith2013hif1a |
| SRP accession | SRP013319 |
| GEO accession | GSE38140 |
| Samples | SRR828729 |
| QC score | 3 |
| Replicate | 3 |
| 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 | control |
| Wildtype & Untreated? | True |
| 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 | |
| Construct |
| Condition type | Treatment | Start time | End time | Duration |
| vehicle | DMSO | -1 hr | 0 hr | 1 hr |
| Pipeline info and software versions | |
| Sample notes | |
| Analysis notes | Ran qc redo nextflow; originally labeled and processed as tech reps, but clearly says in the paper that they're biological replicates |
| Sample QC score | 3 |
| Sample NRO score | 2 |
| Raw read length | 50 |
| Read depth after trimming | 136,926,976 |
| Duplication proportion | 0.73197 |
| Proportion reads mapped | 0.9291 |
| Exon/intron ratio | 3.53941 |
| Unique read proportion | 0.55826 |
| Total # Tfit bidirectionals | 52457 |
| # Promoter Tfit bidirectionals | 19420 |
| # Intronic Tfit bidirectionals | 19090 |
| # Intergenic Tfit bidirectionals | 12787 |
| Total # dREG bidirectionals | 41649 |
| # Promoter dREG bidirectionals | 8939 |
| # Intronic dREG bidirectionals | 18253 |
| # Intergenic dREG bidirectionals | 12995 |
| Part of Tfit master merge? | True |
| Part of dREG master merge? | True |