Explore DBNascent | browse or search sample metadata
Search
Advanced Search
All Samples
Samples By Dataset
Sample Details
SRR2226207 Sample ID 789
| Paper identifier | Flynn20167skbaf |
| SRP accession | SRP058597 |
| GEO accession | GSE69142 |
| Samples | SRR2226207 |
| QC score | 2 |
| Replicate | 3 |
| 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 | 149 Mb |
| Stranded gene read counts | TXT file | 927 Kb |
| Unstranded bidirectional read counts | TXT file | 17 Mb |
| Tfit bidirectional regions | BED file | 3 Mb |
| dREG bidirectional regions | BED file | 1 Mb |
| All data files | ZIP archive | |
| Organism | M. musculus |
| Sample type | cell line |
| Cell type | ESC |
| Clone/Individual | V6.5 |
| Strain | |
| Genotype | |
| Construct |
| Condition type | Treatment | Start time | End time | Duration |
| treatment | 7SK antisense oligonucleotide (1 nmole/2 million cells) | -12 hr | 0 hr | 12 hr |
| Pipeline info and software versions | |
| Sample notes | |
| Analysis notes | dirty data - did fastq-dump manually, force trimmed first 25 bp and bp 65+ prior to running pipeline, ran pipeline on trimmed fastqs (with normal bbduk trimming included), a few samples still sparse due to major adapter contamination |
| Sample QC score | 2 |
| Sample NRO score | 2 |
| Raw read length | 31 |
| Read depth after trimming | 77,186,504 |
| Duplication proportion | 0.5234 |
| Proportion reads mapped | 0.6182 |
| Exon/intron ratio | 2.49366 |
| Unique read proportion | 0.63549 |
| Total # Tfit bidirectionals | 38230 |
| # Promoter Tfit bidirectionals | 10492 |
| # Intronic Tfit bidirectionals | 11854 |
| # Intergenic Tfit bidirectionals | 13019 |
| Total # dREG bidirectionals | 33503 |
| # Promoter dREG bidirectionals | 8100 |
| # Intronic dREG bidirectionals | 11876 |
| # Intergenic dREG bidirectionals | 11837 |
| Part of Tfit master merge? | False |
| Part of dREG master merge? | False |