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SRR7518314 Sample ID 2868
| Paper identifier | Zhu2018rna |
| SRP accession | SRP153346 |
| GEO accession | GSE117014 |
| Samples | SRR7518314 |
| QC score | 4 |
| Replicate | 2 |
| Protocol | NET-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 | control |
| Wildtype & Untreated? | True |
| Outlier | No |
| Unusable | No |
| TDF visualization file | TDF file | 13 Mb |
| Organism | A. thaliana |
| Sample type | tissue |
| Cell type | seedling |
| Clone/Individual | |
| Strain | Col-0 |
| Genotype | |
| Construct |
| Condition type | Treatment | Start time | End time | Duration |
| vehicle | DMSO | -1 hr | 0 hr | 1 hr |
| Pipeline info and software versions | |
| Sample notes | Antibody: 8WG16; unphosphorylated Pol II CTD antibody |
| Analysis notes | did fastq-dump manually, force trimmed first 10 bp and bp 100+ prior to running pipeline, ran pipeline on trimmed fastqs (w/normal bbduk trimming); ran tech reps on pre-trimmed fastqs directly |
| Sample QC score | 4 |
| Sample NRO score | 1 |
| Raw read length | 91 |
| Read depth after trimming | 22,388,340 |
| Duplication proportion | 0.74413 |
| Proportion reads mapped | 0.2954 |
| Exon/intron ratio | 1.77404 |
| Unique read proportion | 0.20742 |
| Total # Tfit bidirectionals | None |
| # Promoter Tfit bidirectionals | None |
| # Intronic Tfit bidirectionals | None |
| # Intergenic Tfit bidirectionals | None |
| Total # dREG bidirectionals | None |
| # Promoter dREG bidirectionals | None |
| # Intronic dREG bidirectionals | None |
| # Intergenic dREG bidirectionals | None |
| Part of Tfit master merge? | False |
| Part of dREG master merge? | False |