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SRZ1744512 Sample ID 2620
| Paper identifier | Wang2015molecular |
| SRP accession | SRP051769 |
| GEO accession | GSE64748 |
| Samples | SRR1744512 |
| SRR1744513 |
| QC score | 3 |
| 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 | True |
| Control/Experimental | experimental |
| Wildtype & Untreated? | False |
| Outlier | No |
| Unusable | No |
| TDF visualization file | TDF file | 44 Mb |
| Stranded gene read counts | TXT file | 909 Kb |
| Unstranded bidirectional read counts | TXT file | 17 Mb |
| Tfit bidirectional regions | BED file | 1 Mb |
| dREG bidirectional regions | BED file | 370 Kb |
| All data files | ZIP archive | |
| Organism | M. musculus |
| Sample type | cell line |
| Cell type | ESC |
| Clone/Individual | |
| Strain | |
| Genotype | Tdg -/- |
| Construct |
| Condition type | Treatment | Start time | End time | Duration |
| treatment | DRB (100 mM) | -190 min | -10 min | 3 hr |
| Pipeline info and software versions | |
| Sample notes | |
| Analysis notes | May needs samtools/1.10 and 60Gb memory for samtools step (that is in my notes but does not match running script, which uses samtools 1.8); One sample required rerun of picardtools; Ran qc redo nextflow |
| Sample QC score | 3 |
| Sample NRO score | 2 |
| Raw read length | 40 |
| Read depth after trimming | 38,368,620 |
| Duplication proportion | 0.72832 |
| Proportion reads mapped | 0.5075 |
| Exon/intron ratio | 2.13905 |
| Unique read proportion | 0.2844 |
| Total # Tfit bidirectionals | 17525 |
| # Promoter Tfit bidirectionals | 4333 |
| # Intronic Tfit bidirectionals | 6812 |
| # Intergenic Tfit bidirectionals | 4123 |
| Total # dREG bidirectionals | 8592 |
| # Promoter dREG bidirectionals | 2969 |
| # Intronic dREG bidirectionals | 2717 |
| # Intergenic dREG bidirectionals | 2278 |
| Part of Tfit master merge? | True |
| Part of dREG master merge? | True |