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SRR13242138 Sample ID 467
| Paper identifier | Chivu2020unpublished |
| SRP accession | SRP297660 |
| GEO accession | GSE163043 |
| Samples | SRR13242138 |
| QC score | 0 |
| Replicate | 1 |
| Protocol | ChRO-seq |
| Library prep | not noted in GEO or publication |
| 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 | 73 Mb |
| Stranded gene read counts | TXT file | 1 Mb |
| Unstranded bidirectional read counts | TXT file | 21 Mb |
| Tfit bidirectional regions | BED file | 1 Mb |
| dREG bidirectional regions | BED file | 273 Kb |
| All data files | ZIP archive | |
| Organism | H. sapiens |
| Sample type | cell line |
| Cell type | K562 |
| Clone/Individual | |
| Strain | |
| Genotype | |
| Construct |
| Condition type | Treatment | Start time | End time | Duration |
| treatment | triptolide (500 nM) | -1 hr | 0 hr | 1 hr |
| Pipeline info and software versions | |
| Sample notes | CHRO-seq, Library prep kit noted is a DNA prep kit - unknown; I think this is referred to in bioRxiv paper https://doi.org/10.1101/2020.04.08.032730 |
| Analysis notes | Lots of adapter contamination, did fastq-dump manually, force trimmed first 14 bp of R1 reads and last 14 bp of R2 reads prior to running pipeline, ran pipeline on trimmed fastqs (with normal bbduk trimming included) |
| Sample QC score | 0 |
| Sample NRO score | 2 |
| Raw read length | 28 |
| Read depth after trimming | 19,823,798 |
| Duplication proportion | None |
| Proportion reads mapped | 0.3359 |
| Exon/intron ratio | 3.09815 |
| Unique read proportion | None |
| Total # Tfit bidirectionals | 11870 |
| # Promoter Tfit bidirectionals | 6296 |
| # Intronic Tfit bidirectionals | 4132 |
| # Intergenic Tfit bidirectionals | 1119 |
| Total # dREG bidirectionals | 6349 |
| # Promoter dREG bidirectionals | 3813 |
| # Intronic dREG bidirectionals | 1692 |
| # Intergenic dREG bidirectionals | 748 |
| Part of Tfit master merge? | True |
| Part of dREG master merge? | True |