Protocol for rolling circle amplification-based nanopore sequencing of eccDNA from cell and plasma samples

Extrachromosomal circular DNAs (eccDNAs) can drive copy number variation and genomic rearrangements and act as mobile regulators of gene expression. Here, we detail a protocol for eccDNA identification from cell and plasma samples. We describe steps for sample preprocessing with circular DNA enrichment, rolling-circle amplification and debranching, library preparation and sequencing, along with quality control tailored to the key steps. For complete details on the use and execution of this protocol, please refer to Li et al.1.