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SRR9961461 Sample ID 2802
| Paper identifier | Zhang2019fundamental |
| SRP accession | SRP193758 |
| GEO accession | GSE130266 |
| Samples | SRR9961461 |
| QC score | 2 |
| Replicate | 3 |
| 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 | 141 Mb |
| Stranded gene read counts | TXT file | 918 Kb |
| Unstranded bidirectional read counts | TXT file | 17 Mb |
| Tfit bidirectional regions | BED file | 4 Mb |
| dREG bidirectional regions | BED file | 0 |
| 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 | 2 |
| Sample NRO score | 3 |
| Raw read length | 76 |
| Read depth after trimming | 17,747,958 |
| Duplication proportion | 0.20998 |
| Proportion reads mapped | 0.8546 |
| Exon/intron ratio | 1.74226 |
| Unique read proportion | 0.75642 |
| Total # Tfit bidirectionals | 46029 |
| # Promoter Tfit bidirectionals | 1510 |
| # Intronic Tfit bidirectionals | 29629 |
| # Intergenic Tfit bidirectionals | 11402 |
| Total # dREG bidirectionals | 0 |
| # Promoter dREG bidirectionals | 0 |
| # Intronic dREG bidirectionals | 0 |
| # Intergenic dREG bidirectionals | 0 |
| Part of Tfit master merge? | False |
| Part of dREG master merge? | False |