| Library |
| Library name |
Construction protocol |
Strategy |
Source |
Selection |
Layout |
|
Three WPs and three LPs were selected for analysis of eccDNA and ecDNA in the ear samples. The DNA of ear sample was extracted use a commercial kit (Tiangen, China) and the quality was detected using Qubit (ThermoFisher, USA) and NanoDrop (ThermoFisher, USA). The library construction and sequencing were carried out according to the methods described by Moller et al. (16). The samples were processed by exonuclease V (NEB, USA) to degrade the linear genomic DNA For the restriction enzyme-based approach, circular DNA were digested using MspI (NEB, USA). Then, the library was sequenced on Novaseq 6000 (Illumina, USA) and 150 paired-end reads were generated (GeneDenovo, China). The high-quality clean reads were obtained from raw reads by Ffastp software. Q20 and Q30 were used to determine the quality of circular DNA. Large circular DNA in tumors is generally > 100 kb, while the other types of circular DNA are usually below 100 kb. Therefore, we used 101 kb as a threshould to distinguish eccDNA from ecDNA. The corresponding correlation analysis was performed independently. |
OTHER |
GENOMIC |
DNAse |
PAIRED
|
|
