Table 2.

Overview of methods for eccDNA investigation

Methods	Description	Advantage or Limitation	References
Electron microscopy	Localization, identification, quantification	No sequence information	[9]
Karyotype	Localization, identification, quantification	No sequence information	[7]
2D gel electrophoresis	Identification	No sequence information	[98, 100]
Southern blotting	Quantification	Little sequence information	[98]
Inverse PCR	Quantification, identification	Little but useful sequence information	[15, 42]
FISH	Localization, identification, quantification	Little sequence information	[7–9]
Density gradient centrifugation	Isolation and purification	Laborious	[47]
Methods based on next-generation sequencing	Localization, quantification, high resolution, (1) tagmentation method is more sensitive than (2) nuclease digestion (Msp); (3) exonuclease III digestion; (4) exonuclease V digestion; (5) rolling-amplification	High throughput, high resolution, sensitive, expensive	[4–9, 26, 34]