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SRZ6427125 Sample ID 463
| Paper identifier | Chen2018rna |
| SRP accession | SRP099055 |
| GEO accession | GSE94662 |
| Samples | SRR6427125 |
| SRR6427126 |
| QC score | 4 |
| Replicate | 2 |
| 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 | 27 Mb |
| Stranded gene read counts | TXT file | 905 Kb |
| Unstranded bidirectional read counts | TXT file | 17 Mb |
| Tfit bidirectional regions | BED file | 506 Kb |
| dREG bidirectional regions | BED file | 162 Kb |
| All data files | ZIP archive | |
| Organism | M. musculus |
| Sample type | primary cell |
| Cell type | splenic B cell |
| Clone/Individual | |
| Strain | |
| Genotype | |
| Construct | shRNA Rod1 |
| Condition type | Treatment | Start time | End time | Duration |
| treatment | lipopolysaccharide (5 microg/mL) | -3 day | 0 day | 3 day |
| Pipeline info and software versions | |
| Sample notes | Biological replicates clearly labeled, assumed two runs per bio rep were technical replicates |
| Analysis notes | Ran qc redo nextflow |
| Sample QC score | 4 |
| Sample NRO score | 1 |
| Raw read length | 52 |
| Read depth after trimming | 72,438,479 |
| Duplication proportion | 0.92904 |
| Proportion reads mapped | 0.5837 |
| Exon/intron ratio | 1.90124 |
| Unique read proportion | 0.08672 |
| Total # Tfit bidirectionals | 6039 |
| # Promoter Tfit bidirectionals | 2275 |
| # Intronic Tfit bidirectionals | 1709 |
| # Intergenic Tfit bidirectionals | 113 |
| Total # dREG bidirectionals | 3767 |
| # Promoter dREG bidirectionals | 1865 |
| # Intronic dREG bidirectionals | 789 |
| # Intergenic dREG bidirectionals | 627 |
| Part of Tfit master merge? | True |
| Part of dREG master merge? | True |