Single-cell DNA sequencing analysis of ecDNA copy-number dynamics during drug adaptation
Single-cell DNA sequencing was performed using the Mission Bio Tapestri platform to analyze ecDNA-associated copy-number dynamics across cancer cell lines, single-cell-derived clones, and drug-treated conditions. Droplet-based targeted PCR amplification was carried out according to the manufacturer's instructions using custom primer panels designed to quantify ecDNA-associated loci, control genomic regions, and barcode sequences. The dataset includes parental cancer cell lines, including COLO320DM, COLO320HSR, H2170, SNU-16, PC-3, and RPE1 control cells, as well as multiple COLO320DM-derived single-cell clones. Selected clones were analyzed under basal conditions and after drug treatment, including DMSO and JQ1. Sequencing libraries were prepared following the manufacturer's protocol and sequenced using the Illumina NextSeq 550 platform with 2 × 75 bp paired-end reads.
Single-cell DNA sequencing was performed using the Mission Bio Tapestri platform to analyze ecDNA-associated copy-number dynamics across cancer cell lines, single-cell-derived clones, and drug-treated conditions. Droplet-based targeted PCR amplification was carried out according to the manufacturer's instructions using custom primer panels designed to quantify ecDNA-associated loci, control genomic regions, and barcode sequences. The dataset includes parental cancer cell lines, including COLO320DM, COLO320HSR, H2170, SNU-16, PC-3, and RPE1 control cells, as well as multiple COLO320DM-derived single-cell clones. Selected clones were analyzed under basal conditions and after drug treatment, including DMSO and JQ1. Sequencing libraries were prepared following the manufacturer's protocol and sequenced using the Illumina NextSeq 550 platform with 2 × 75 bp paired-end reads.
European Bioinformatics Institute