Sample Overview
| Sample ID: | Sample-01-0001 |
| Type: | CAGE |
| Species: | Homo sapiens |
| Tissue Type: | Lung |
| Biosample Type: | Cell line |
| Cell Type: | A549 |
| Experiment Type: | CAGE |
| Accesion Number: | ENCFF000TRV |
| Experiment Number: | ENCFF000TRV |
| Source: | ENCODE |
Genome
proportion
Peak
distribution
Chromosome
distributioneRNA Detail
| eRNA ID | Position | Fow Start | Fow End | Size | Risk SNP | Common SNP | CRISPR | eQTL | TFBS | Enhancer | Super Enhancer | Target Gene |
|---|
Information Description of Sample and Annotation
| Super enhancer: | SEdb 2.0; SEA 3.0; dbSUPER |
| Enhancer: | HACER; FANTOM5; Enhancer Atlas 2.0; DENdb; ENdb; ENCODE |
| Common SNP: | dbSNP |
| eQTL: | PancanQTL; seeQTL; SCAN; GTEx; OncoBase |
| Risk SNP: | GWAS Catalog; GWASdb v2.0 |
| TFBS: | TFBS Conserved of UCSC |
| CRISPR/Cas9 target site: | CRISPR Targets of UCSC |
Software and Parameters
| Quality Control: | fastp --adapter_sequence --low_complexity_filter -l 14 -w 16 |
| Reads Alignment: | STAR --runThreadN 16 --genomeDir hg38/mm10 --outSAMtype BAM SortedByCoordinate |
| eRNA Identification: | pints_caller --bam --exp-type ** --thread 16 |
| Candidate eRNAs: | bedtools intersect -a bidirectional_peaks.bed -b promoters.bed -v > bidirectional_peaks.distalTREs.bed |