Explore DBNascent | browse or search sample metadata
Search
Advanced Search
All Samples
Samples By Dataset
Sample Details
SRZ6376824 Sample ID 1699
| Paper identifier | Liu2018rna-directed |
| SRP accession | SRP126767 |
| GEO accession | GSE108078 |
| Samples | SRR6376824 |
| SRR6874232 |
| QC score | 0 |
| Replicate | 2 |
| 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 | 27 Mb |
| Organism | A. thaliana |
| Sample type | tissue |
| Cell type | inflorescence and meristem |
| Clone/Individual | |
| Strain | Wassilewskija |
| Genotype | Ago4 mut; Ago4 D762A exogenous (stable) |
| Construct |
| Condition type | Treatment | Start time | End time | Duration |
| no treatment | None | None | None |
| Pipeline info and software versions | |
| Sample notes | |
| Analysis notes | dirty data - did fastq-dump manually, force trimmed first 4 bp and bp 60+ prior to running pipeline, ran pipeline on trimmed fastqs (with normal bbduk trimming included); ran tech reps on pre-trimmed fastqs directly |
| Sample QC score | 0 |
| Sample NRO score | 2 |
| Raw read length | 10 |
| Read depth after trimming | 54,714,680 |
| Duplication proportion | 0.89814 |
| Proportion reads mapped | 0.6448 |
| Exon/intron ratio | 4.23807 |
| Unique read proportion | None |
| 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 |