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scEccDNAdb: an integrated single-cell eccDNA resource for human and mouse.

Wenqing Wang1, Xinyu Zhao1, Tianyu Ma1

  • 1School of Life Sciences and Engineering, Southwest Jiaotong University, No.111, North 1st Section of Second Ring Road, Chengdu, Sichuan 610031, China.

Database : the Journal of Biological Databases and Curation
|December 18, 2024
PubMed
Summary
This summary is machine-generated.

A new database, scEccDNAdb, offers a comprehensive resource for analyzing single-cell extrachromosomal circular DNA (eccDNA). It provides millions of eccDNA entries and analysis tools to advance research in cellular heterogeneity and function.

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Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Extrachromosomal circular DNA (eccDNA) is prevalent in eukaryotes, but single-cell analysis is challenging due to limited high-throughput methods.
  • Understanding eccDNA at the single-cell level is vital for insights into cellular heterogeneity, evolution, and function.

Purpose of the Study:

  • To develop a comprehensive database for single-cell eccDNA analysis.
  • To provide accessible tools for researchers studying eccDNA.

Main Methods:

  • Built scEccDNAdb using single-cell whole-genome sequencing data.
  • Integrated 3,195,464 single-cell eccDNA entries from human and mouse samples.
  • Included extensive annotations and nine online analysis/visualization tools.

Main Results:

  • scEccDNAdb contains a large-scale collection of single-cell eccDNA data.
  • Annotations cover oncogenes, enhancers, regulatory elements, genetic variations, and chromatin features.
  • Online tools facilitate publication-quality figure generation from user data.

Conclusions:

  • scEccDNAdb is a valuable, comprehensive resource for single-cell eccDNA analysis.
  • The database supports research across diverse cell types, tissues, and species.
  • Facilitates deeper understanding of eccDNA's role in cellular processes.