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SRR4041369 Sample ID 679
| Paper identifier | Engreitz2016local |
| SRP accession | SRP082334 |
| GEO accession | GSE85798 |
| Samples | SRR4041369 |
| QC score | 3 |
| 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 | 60 Mb |
| Stranded gene read counts | TXT file | 912 Kb |
| Unstranded bidirectional read counts | TXT file | 17 Mb |
| Tfit bidirectional regions | BED file | 2 Mb |
| dREG bidirectional regions | BED file | 574 Kb |
| 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 promoter +/- |
| 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 | 3 |
| Sample NRO score | 2 |
| Raw read length | 40 |
| Read depth after trimming | 15,860,611 |
| Duplication proportion | 0.43046 |
| Proportion reads mapped | 0.702 |
| Exon/intron ratio | 4.23455 |
| Unique read proportion | 0.40593 |
| Total # Tfit bidirectionals | 24140 |
| # Promoter Tfit bidirectionals | 8365 |
| # Intronic Tfit bidirectionals | 7278 |
| # Intergenic Tfit bidirectionals | 6091 |
| Total # dREG bidirectionals | 13294 |
| # Promoter dREG bidirectionals | 6012 |
| # Intronic dREG bidirectionals | 3205 |
| # Intergenic dREG bidirectionals | 2689 |
| Part of Tfit master merge? | True |
| Part of dREG master merge? | True |