Wang Wenqing, Zhao Xinyu, Ma Tianyu, Zhong Tengwei, Zheng Junnuo, Guo Zhiyun
School of Life Sciences and Engineering, Southwest Jiaotong University, No.111, North 1st Section of Second Ring Road, Chengdu, Sichuan 610031, China.
Database (Oxford). 2024 Dec 18;2024. doi: 10.1093/database/baae126.
Extrachromosomal circular DNA (eccDNA), an extrachromosomal circular structured DNA, is extensively found in eukaryotes. Investigating eccDNA at the single-cell level is crucial for understanding cellular heterogeneity, evolution, development, and specific cellular functions. However, high-throughput identification methods for single-cell eccDNA are complex, and the lack of mature, widely applicable technologies has resulted in limited resources. To address this gap, we built scEccDNAdb, a database based on single-cell whole-genome sequencing data. It contains 3 195 464 single-cell eccDNA entries from human and mouse samples, with annotations including oncogenes, typical enhancers, super-enhancers, CCCTC-binding factor-binding sites, single nucleotide polymorphisms, chromatin accessibility, expression quantitative trait loci, transcription factor binding sites, motifs, and structural variants. Additionally, it provides nine online analysis and visualization tools, which enable the creation of publication-quality figures through user-uploaded files. Overall, scEccDNAdb is a comprehensive database for analyzing single-cell eccDNA data across diverse cell types, tissues, and species. Database URL: https://lcbb.swjtu.edu.cn/scEccDNAdb/.
染色体外环状DNA（eccDNA）是一种染色体外的环状结构DNA，在真核生物中广泛存在。在单细胞水平上研究eccDNA对于理解细胞异质性、进化、发育和特定细胞功能至关重要。然而，单细胞eccDNA的高通量鉴定方法复杂，且缺乏成熟、广泛适用的技术导致相关资源有限。为填补这一空白，我们构建了scEccDNAdb，一个基于单细胞全基因组测序数据的数据库。它包含来自人类和小鼠样本的3195464个单细胞eccDNA条目，注释包括癌基因、典型增强子、超级增强子、CCCTC结合因子结合位点、单核苷酸多态性、染色质可及性、表达数量性状位点、转录因子结合位点、基序和结构变异。此外，它提供了九个在线分析和可视化工具，可通过用户上传的文件创建具有发表质量的图表。总体而言，scEccDNAdb是一个用于分析跨多种细胞类型、组织和物种的单细胞eccDNA数据的综合数据库。数据库网址：https://lcbb.swjtu.edu.cn/scEccDNAdb/ 。
