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SRR2226208 Sample ID 790
| Paper identifier | Flynn20167skbaf |
| SRP accession | SRP058597 |
| GEO accession | GSE69142 |
| Samples | SRR2226208 |
| QC score | 1 |
| Replicate | 4 |
| 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 | experimental |
| Wildtype & Untreated? | False |
| Outlier | No |
| Unusable | No |
| TDF visualization file | TDF file | 150 Mb |
| Stranded gene read counts | TXT file | 926 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 | cell line |
| Cell type | ESC |
| Clone/Individual | V6.5 |
| Strain | |
| Genotype | |
| Construct |
| Condition type | Treatment | Start time | End time | Duration |
| treatment | 7SK antisense oligonucleotide (1 nmole/2 million cells) | -12 hr | 0 hr | 12 hr |
| Pipeline info and software versions | |
| Sample notes | |
| Analysis notes | dirty data - did fastq-dump manually, force trimmed first 25 bp and bp 65+ prior to running pipeline, ran pipeline on trimmed fastqs (with normal bbduk trimming included), a few samples still sparse due to major adapter contamination |
| Sample QC score | 1 |
| Sample NRO score | 2 |
| Raw read length | 31 |
| Read depth after trimming | 67,790,614 |
| Duplication proportion | 0.45576 |
| Proportion reads mapped | 0.6368 |
| Exon/intron ratio | 2.49613 |
| Unique read proportion | 0.66386 |
| Total # Tfit bidirectionals | 39193 |
| # Promoter Tfit bidirectionals | 10447 |
| # Intronic Tfit bidirectionals | 12164 |
| # Intergenic Tfit bidirectionals | 13573 |
| Total # dREG bidirectionals | 33342 |
| # Promoter dREG bidirectionals | 8004 |
| # Intronic dREG bidirectionals | 11778 |
| # Intergenic dREG bidirectionals | 11811 |
| Part of Tfit master merge? | False |
| Part of dREG master merge? | False |