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SRR531825 Sample ID 2596
| Paper identifier | Wang2014rna |
| SRP accession | SRP014688 |
| GEO accession | GSE39878 |
| Samples | SRR531825 |
| QC score | 2 |
| 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 | False |
| Control/Experimental | control |
| Wildtype & Untreated? | True |
| Outlier | No |
| Unusable | No |
| TDF visualization file | TDF file | 408 Mb |
| Stranded gene read counts | TXT file | 1 Mb |
| Unstranded bidirectional read counts | TXT file | 21 Mb |
| Tfit bidirectional regions | BED file | 4 Mb |
| dREG bidirectional regions | BED file | 2 Mb |
| All data files | ZIP archive | |
| Organism | H. sapiens |
| Sample type | cell line |
| Cell type | B cell |
| Clone/Individual | individual GM12750 |
| Strain | |
| Genotype | |
| Construct |
| Condition type | Treatment | Start time | End time | Duration |
| no treatment | None | None | None |
| Pipeline info and software versions | |
| Sample notes | paper repeatedly states that two pro-seq libraries were prepped, one in each lab, but the only full experiment list I could fine from GEO based on the inferred SRP says there are two GRO-seq libaries and one PRO-seq one. |
| Analysis notes | Ran qc redo nextflow |
| Sample QC score | 2 |
| Sample NRO score | 1 |
| Raw read length | 100 |
| Read depth after trimming | 169,436,074 |
| Duplication proportion | 0.60197 |
| Proportion reads mapped | 0.8924 |
| Exon/intron ratio | 2.63798 |
| Unique read proportion | 0.74327 |
| Total # Tfit bidirectionals | 47173 |
| # Promoter Tfit bidirectionals | 16558 |
| # Intronic Tfit bidirectionals | 18549 |
| # Intergenic Tfit bidirectionals | 11757 |
| Total # dREG bidirectionals | 52570 |
| # Promoter dREG bidirectionals | 9287 |
| # Intronic dREG bidirectionals | 26041 |
| # Intergenic dREG bidirectionals | 15571 |
| Part of Tfit master merge? | True |
| Part of dREG master merge? | True |