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SRR2518204 Sample ID 2404
| Paper identifier | Strikoudis2016regulation |
| SRP accession | SRP064201 |
| GEO accession | GSE73441 |
| Samples | SRR2518204 |
| QC score | 3 |
| Replicate | 3 |
| 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 | 38 Mb |
| Stranded gene read counts | TXT file | 912 Kb |
| Unstranded bidirectional read counts | TXT file | 17 Mb |
| Tfit bidirectional regions | BED file | 450 Kb |
| dREG bidirectional regions | BED file | 151 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 Paf1 (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 | 3 |
| Sample NRO score | 1 |
| Raw read length | 51 |
| Read depth after trimming | 33,406,811 |
| Duplication proportion | 0.79421 |
| Proportion reads mapped | 0.6828 |
| Exon/intron ratio | 2.84994 |
| Unique read proportion | 0.26784 |
| Total # Tfit bidirectionals | 5241 |
| # Promoter Tfit bidirectionals | 1440 |
| # Intronic Tfit bidirectionals | 2016 |
| # Intergenic Tfit bidirectionals | 548 |
| Total # dREG bidirectionals | 3511 |
| # Promoter dREG bidirectionals | 979 |
| # Intronic dREG bidirectionals | 1046 |
| # Intergenic dREG bidirectionals | 952 |
| Part of Tfit master merge? | False |
| Part of dREG master merge? | False |