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SRR2518199 Sample ID 2399
| Paper identifier | Strikoudis2016regulation |
| SRP accession | SRP064201 |
| GEO accession | GSE73441 |
| Samples | SRR2518199 |
| QC score | 4 |
| Replicate | 1 |
| Protocol | GRO-seq |
| Library prep | ligation |
| Spike-in | None |
| Single/Paired end | single |
| Raw strandedness | reverse |
| Reverse complemented? | True |
| Mapped strandedness | forward |
| Timecourse | False |
| Control/Experimental | experimental |
| Wildtype & Untreated? | False |
| Outlier | No |
| Unusable | No |
| TDF visualization file | TDF file | 26 Mb |
| Stranded gene read counts | TXT file | 906 Kb |
| Unstranded bidirectional read counts | TXT file | 17 Mb |
| Tfit bidirectional regions | BED file | 307 Kb |
| dREG bidirectional regions | BED file | 88 Kb |
| All data files | ZIP archive | |
| Organism | M. musculus |
| Sample type | cell line |
| Cell type | ESC |
| Clone/Individual | KH2 |
| Strain | C57BL/6 x 129/Sv |
| Genotype | dox-inducible shRNA Phf5a (stable) |
| Construct |
| Condition type | Treatment | Start time | End time | Duration |
| treatment | LIF (1000 U/mL) | None | None | None |
| treatment | doxycycline (2 microg/mL) | -3 day | 0 day | 3 day |
| Pipeline info and software versions | |
| Sample notes | LIF treatment maintains pluripotency |
| Analysis notes |
| Sample QC score | 4 |
| Sample NRO score | 2 |
| Raw read length | 51 |
| Read depth after trimming | 22,749,256 |
| Duplication proportion | 0.82872 |
| Proportion reads mapped | 0.7362 |
| Exon/intron ratio | 3.26326 |
| Unique read proportion | 0.18225 |
| Total # Tfit bidirectionals | 3604 |
| # Promoter Tfit bidirectionals | 797 |
| # Intronic Tfit bidirectionals | 1386 |
| # Intergenic Tfit bidirectionals | 272 |
| Total # dREG bidirectionals | 2056 |
| # Promoter dREG bidirectionals | 412 |
| # Intronic dREG bidirectionals | 668 |
| # Intergenic dREG bidirectionals | 697 |
| Part of Tfit master merge? | False |
| Part of dREG master merge? | False |