scEccDNAdb

scEccDNAdb curates single-cell extrachromosomal circular DNA (eccDNA) entries from human and mouse samples and provides comprehensive genomic annotations and online analysis capabilities for investigating eccDNA heterogeneity, evolution, development, and cell-specific functions.

Key Features:

• Comprehensive eccDNA annotations: Each entry is annotated with oncogenes, typical enhancers, super-enhancers, CTCF binding sites, SNPs, chromatin accessibility, eQTLs, transcription factor binding sites, motifs, and structural variants (SVs).
• Online analysis and visualization tools: Nine integrated tools enable generation of publication-quality figures for eccDNA analysis through upload of customized files.
• Cross-species and cross-condition coverage: The database contains 3,195,464 single-cell eccDNA entries from both disease and healthy human and mouse samples across diverse cell types and tissues.

Scientific Applications:

• Single-cell eccDNA heterogeneity research: Enables investigation of eccDNA variation and distribution patterns across individual cells to understand cellular diversity.
• Cancer and disease eccDNA studies: Supports analysis of eccDNA involvement in disease states through comprehensive oncogene and regulatory element annotations.
• Functional genomics of eccDNA: Facilitates exploration of eccDNA contributions to gene regulation through integration of enhancer, CTCF binding site, chromatin accessibility, and transcription factor binding site data.
• Custom eccDNA data analysis: Allows researchers to analyze and visualize their own single-cell eccDNA datasets using the platform's computational tools.

Methodology:

scEccDNAdb was constructed using available single-cell whole-genome sequencing (WGS) data. The specific computational pipeline for eccDNA identification from these data is not explicitly detailed in the sources.