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SRR3160420 Sample ID 477
| Paper identifier | Compagno2017phosphatidylinositol |
| SRP accession | SRP069868 |
| GEO accession | GSE77788 |
| Samples | SRR3160420 |
| QC score | 2 |
| Replicate | 1 |
| Protocol | GRO-seq |
| Library prep | not noted in GEO or publication |
| 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 | 171 Mb |
| Stranded gene read counts | TXT file | 924 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 | primary cell |
| Cell type | splenic B cell |
| Clone/Individual | |
| Strain | |
| Genotype | |
| Construct |
| Condition type | Treatment | Start time | End time | Duration |
| treatment | idelalisib (1 microM) | -2 day | 0 day | 2 day |
| treatment | interleukin-4 (20 ng/mL) | -2 day | 0 day | 2 day |
| treatment | anti-CD40 (1 microg/mL) | -2 day | 0 day | 2 day |
| Pipeline info and software versions | |
| Sample notes | Library preparation not stated in paper or on GEO "GRO-Seq libraries were prepared as previously described by Core et al., Science 2008"; treatment times unclear |
| Analysis notes |
| Sample QC score | 2 |
| Sample NRO score | 1 |
| Raw read length | 51 |
| Read depth after trimming | 71,101,815 |
| Duplication proportion | 0.56466 |
| Proportion reads mapped | 0.8385 |
| Exon/intron ratio | 2.50979 |
| Unique read proportion | 0.69616 |
| Total # Tfit bidirectionals | 29755 |
| # Promoter Tfit bidirectionals | 8314 |
| # Intronic Tfit bidirectionals | 12145 |
| # Intergenic Tfit bidirectionals | 4875 |
| Total # dREG bidirectionals | 24595 |
| # Promoter dREG bidirectionals | 4432 |
| # Intronic dREG bidirectionals | 10774 |
| # Intergenic dREG bidirectionals | 6099 |
| Part of Tfit master merge? | True |
| Part of dREG master merge? | True |