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bioRxiv · 10.1101/2024.07.18.604058

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

wang, w.·Zhao, X.·Ma, T.·Zung, T.·Yang, Y.·Guo, Y.·guo, z.
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Abstract

Extrachromosomal circular DNA (eccDNA), an extrachromosomal circular structured DNA, is extensively found in eukaryotes. Exploring eccDNA at the single-cell level contributes to understanding heterogeneity, evolution, development, and specific functions within cells. Nevertheless, the high-throughput identification methods for single-cell eccDNA are complex, and currently mature and widely applicable technologies are lacking. Those factors have led to a scarcity of resources for studying eccDNA at the single-cell level. Therefore, using available single-cell whole-genome sequencing (WGS) data, we have constructed a comprehensive eccDNA database named scEccDNAdb (https://lcbb.swjtu.edu.cn/scEccDNAdb/). Presently, scEccDNAdb comprises 3,195,464 single-cell eccDNA entries from both disease/health human and mouse samples, which provides comprehensive annotations including oncogenes, typical enhancers, super-enhancers, CTCF binding sites, SNPs, chromatin accessibility, eQTLs, transcription factor binding sites, motifs, and SVs. Additionally, it provides nine online analysis and visualization tools, facilitating the generation of publication-quality figures for eccDNA analysis through the upload of customized files. Overall, scEccDNAdb represents the first comprehensive database known to us for exploring and analyzing single-cell eccDNA data in diverse cell types, tissues, and species. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=108 SRC="FIGDIR/small/604058v1_ufig1.gif" ALT="Figure 1"> View larger version (32K): org.highwire.dtl.DTLVardef@bd23f8org.highwire.dtl.DTLVardef@1847c7eorg.highwire.dtl.DTLVardef@109717forg.highwire.dtl.DTLVardef@fa56b7_HPS_FORMAT_FIGEXP M_FIG C_FIG

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wang, w., Zhao, X., Ma, T., Zung, T., Yang, Y., Guo, Y., guo, z.. 2024-07-22. scEccDNAdb: an integrated single-cell eccDNA resource for human and mouse. https://doi.org/10.1101/2024.07.18.604058

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