{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Chikako Shibata"],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-16119"],"description":["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."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Growth Protocol - COLO320DM, COLO320HSR, and RPE1 cells were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM) low glucose supplemented with 10% FBS. H2170, SNU-16, and SK-BR-3-Luc cells were cultured in Roswell Park Memorial Institute (RPMI) 1640 Medium supplemented with 10% FBS. PC-3 cells were cultured in Kaighn’s modification (F12K) of Ham’s F12 medium supplemented with 10% FBS. All cells were incubated at 37℃, 20% O2 and 5% CO2.","Sequencing - Next generation sequencing was performed in 2 x 75 bp paired-end using NextSeq550 platform (Illumina), generating 50-60 million reads per library.","Library Construction - Cells were processed using the Mission Bio Tapestri platform according to the manufacturer’s instructions. Within droplets, targeted PCR amplification was performed to generate single-cell DNA libraries. The library was prepared according to the manufacturer’s instructions. Briefly, following targeted PCR, the emulsion was disrupted, the reaction was enzymically cleaned up, and the product were purified with AMPure XP beads. To add indexes, 10 cycles second PCR was performed, followed by purification with AMPure XP beads. Library quality was assessed by Quantus and Tapestation 4200 with D5000 Screen Tape."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Raw read counts were normalized based on reference regions with low variability (top 20 regions with the smallest coefficient of variation in RPE1 cells). For each cell, the mean count across the reference regions was used for depth normalization. Correction factors were then calculated for each target region by trimming extreme values and aligning the modal copy number of the RPE1 cells to two."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Tapestri Platform","NextSeq 550"],"study_type":["DNA-seq"],"species":["Homo sapiens"],"pubmed_authors":["Reo Maruyama","Chikako Shibata"],"additional_accession":[]},"is_claimable":false,"name":"Single-cell DNA sequencing analysis of ecDNA copy-number dynamics during drug adaptation","description":"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.","dates":{"release":"2026-05-25T00:00:00Z","modification":"2026-05-26T20:15:54.398Z","creation":"2025-11-14T12:14:18.902Z"},"accession":"E-MTAB-16119","cross_references":{"ENA":["ERP193462"],"EFO":["EFO_0004170","EFO_0003789","EFO_0002693","EFO_0003816","EFO_0004184"]}}