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SRR4041371 Sample ID 681
| Paper identifier | Engreitz2016local |
| SRP accession | SRP082334 |
| GEO accession | GSE85798 |
| Samples | SRR4041371 |
| QC score | 2 |
| Replicate | 1 |
| Protocol | PRO-seq |
| Library prep | ligation |
| Spike-in | None |
| Single/Paired end | paired |
| Raw strandedness | read1 reverse |
| Reverse complemented? | False |
| Mapped strandedness | read1 reverse |
| Timecourse | False |
| Control/Experimental | experimental |
| Wildtype & Untreated? | False |
| Outlier | No |
| Unusable | No |
| TDF visualization file | TDF file | 92 Mb |
| Stranded gene read counts | TXT file | 916 Kb |
| Unstranded bidirectional read counts | TXT file | 17 Mb |
| Tfit bidirectional regions | BED file | 3 Mb |
| dREG bidirectional regions | BED file | 1 Mb |
| All data files | ZIP archive | |
| Organism | M. musculus |
| Sample type | primary cell |
| Cell type | ESC |
| Clone/Individual | |
| Strain | 129/SV-Jae x castaneus |
| Genotype | linc1319 +2kb instronic pAS insertion (+/-) |
| Construct |
| Condition type | Treatment | Start time | End time | Duration |
| no treatment | None | None | None |
| Pipeline info and software versions | |
| Sample notes | Heterozygous mutations to determine cis/trans effects; Library prep is unclear, but citations indicate ligation |
| Analysis notes | In db as Engreitz2016long until 2/8/21 - all older pipeline reports and out/err scripts reflect that; Ran qc redo nextflow |
| Sample QC score | 2 |
| Sample NRO score | 3 |
| Raw read length | 30 |
| Read depth after trimming | 19,995,331 |
| Duplication proportion | 0.28527 |
| Proportion reads mapped | 0.7654 |
| Exon/intron ratio | 5.49156 |
| Unique read proportion | 0.52651 |
| Total # Tfit bidirectionals | 41025 |
| # Promoter Tfit bidirectionals | 14508 |
| # Intronic Tfit bidirectionals | 12017 |
| # Intergenic Tfit bidirectionals | 11082 |
| Total # dREG bidirectionals | 23737 |
| # Promoter dREG bidirectionals | 7902 |
| # Intronic dREG bidirectionals | 6800 |
| # Intergenic dREG bidirectionals | 6407 |
| Part of Tfit master merge? | True |
| Part of dREG master merge? | True |