Dataset: Comprehensive extrachromosomal circular DNA (eccDNA) profiles from human cancers and plants generated by Multi-modal Circle-seq (MMC-seq).

This dataset contains the complete catalog of extrachromosomal circular DNA (eccDNA) identified in the study "MMC-seq reveals a hidden dimension of genome plasticity in eccDNA". The data was generated from diverse biological systems, including human cancer cell lines, primary brain tumors, and plant genomes, using our novel high-sensitivity method, Multi-modal Circle-seq (MMC-seq). This approach combines optimized rolling-circle amplification with PacBio HiFi long-read sequencing to achieve unprecedented detection depth with minimal starting material. This rich collection supports a new framework where distinct eccDNA classes reflect different temporal dimensions of genome instability: multi-locus eccDNAs (MeccDNAs) trace past events, unique-locus eccDNAs (UeccDNAs) capture ongoing cellular stress, and chimeric eccDNAs (CeccDNAs) can generate novel fusion transcripts that foreshadow future evolution. Furthermore, the data shows that eccDNA length profiles carry regulatory information tied to cellular states like apoptosis or active transcription. All eccDNA sequences are classified (e.g., UeccDNA, MeccDNA, CeccDNA) using our custom pipeline, CircleSeeker, to facilitate downstream analysis and reuse.