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SRR3160418 Sample ID 475
| Paper identifier | Compagno2017phosphatidylinositol |
| SRP accession | SRP069868 |
| GEO accession | GSE77788 |
| Samples | SRR3160418 |
| 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 | control |
| Wildtype & Untreated? | True |
| Outlier | No |
| Unusable | No |
| TDF visualization file | TDF file | 143 Mb |
| Stranded gene read counts | TXT file | 922 Kb |
| Unstranded bidirectional read counts | TXT file | 17 Mb |
| Tfit bidirectional regions | BED file | 3 Mb |
| dREG bidirectional regions | BED file | 967 Kb |
| 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 | interleukin-4 (20 ng/mL) | -2 day | 0 day | 2 day |
| vehicle | DMSO | -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 | 55,893,066 |
| Duplication proportion | 0.51666 |
| Proportion reads mapped | 0.8224 |
| Exon/intron ratio | 2.45807 |
| Unique read proportion | 0.68914 |
| Total # Tfit bidirectionals | 30104 |
| # Promoter Tfit bidirectionals | 8422 |
| # Intronic Tfit bidirectionals | 12626 |
| # Intergenic Tfit bidirectionals | 4648 |
| Total # dREG bidirectionals | 22048 |
| # Promoter dREG bidirectionals | 4473 |
| # Intronic dREG bidirectionals | 9414 |
| # Intergenic dREG bidirectionals | 5187 |
| Part of Tfit master merge? | True |
| Part of dREG master merge? | True |