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SRR9961462 Sample ID 2803
| Paper identifier | Zhang2019fundamental |
| SRP accession | SRP193758 |
| GEO accession | GSE130266 |
| Samples | SRR9961462 |
| QC score | 3 |
| Replicate | 4 |
| Protocol | GRO-seq |
| Library prep | ligation |
| Spike-in | None |
| Single/Paired end | paired |
| Raw strandedness | read1 forward |
| Reverse complemented? | True |
| Mapped strandedness | read1 forward |
| Timecourse | False |
| Control/Experimental | experimental |
| Wildtype & Untreated? | False |
| Outlier | No |
| Unusable | No |
| TDF visualization file | TDF file | 45 Mb |
| Stranded gene read counts | TXT file | 911 Kb |
| Unstranded bidirectional read counts | TXT file | 17 Mb |
| Tfit bidirectional regions | BED file | 2 Mb |
| dREG bidirectional regions | BED file | 386 Kb |
| All data files | ZIP archive | |
| Organism | M. musculus |
| Sample type | cell line |
| Cell type | CH12F3 |
| Clone/Individual | |
| Strain | |
| Genotype | CH +/-; Aid -/-; I-alpha -/- |
| Construct |
| Condition type | Treatment | Start time | End time | Duration |
| treatment | TGF-beta (0.5 ng/mL) | -24 hr | 0 hr | 1 day |
| treatment | anti-CD40 (1 microg/mL) | -24 hr | 0 hr | 1 day |
| treatment | interleukin-4 (20 ng/mL) | -24 hr | 0 hr | 1 day |
| Pipeline info and software versions | |
| Sample notes | CH +/-: KO of heavy chain locus non-productive allele |
| Analysis notes | Ran qc redo nextflow |
| Sample QC score | 3 |
| Sample NRO score | 1 |
| Raw read length | 76 |
| Read depth after trimming | 15,371,526 |
| Duplication proportion | 0.61307 |
| Proportion reads mapped | 0.6867 |
| Exon/intron ratio | 1.9715 |
| Unique read proportion | 0.36487 |
| Total # Tfit bidirectionals | 19171 |
| # Promoter Tfit bidirectionals | 5336 |
| # Intronic Tfit bidirectionals | 7617 |
| # Intergenic Tfit bidirectionals | 3268 |
| Total # dREG bidirectionals | 8935 |
| # Promoter dREG bidirectionals | 2950 |
| # Intronic dREG bidirectionals | 3003 |
| # Intergenic dREG bidirectionals | 1873 |
| Part of Tfit master merge? | False |
| Part of dREG master merge? | False |