biostudies-arrayexpressUnknownTranscriptomicsGenomicsProteomicsPaolo AretiniNextSeq 2000DNA-seqHomo sapiensHomo sapienshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-16563Low-pass sequencing for copy number alteration analysis on whole-genome amplification of epithelial/mesenchymal osteosarcoma CTCs and Hoechst-positive cells. All cells were isolated via a marker-independent enrichment and recovered thought the DEPArray platform from patient-derived PBMCs.biostudies-arrayexpressNucleic Acid Extraction - DNA from CTCs enrichment pool was extracted using Maxwell 16 Cell LEV DNA Purification Kit (Promega, Madison, WI, USA), following the manufacturer’s instructions.Library Construction - Whole-genome amplification and Low Pass analysis on all recovered CTCs was performed using the SMARTer Picoplex Gold Single Cell DNA-Seq kit (Takara Bio, Muntain View, USA) following the manufacturer’s instructions to detect chromosomal aneuploidies and CNAs with a low sequencing depth.Sequencing - To sequence our libraries, we used NextSeq 2000 (Illumina, San Diego, CA, USA) with 151 bp of read length loading on NextSeq 1000/2000 P2 Reagents (300 Cycles) v3 for 96 cells per run.Sample Collection - Five milliliters of blood was collected in EDTA tubes for CTCs detection at the time of the surgery. Peripheral blood mononuclear cells (PBMCs) were obtained from whole blood through density gradient centrifugation (Ficoll Paque GE17-1440-02, Sigma-Aldrich) as the standard procedure. The pellet obtained was frozen vital and stored at -140 °C.OrganizationMINSEQE ScoreAssays and DataMAGE-TAB FilesPaolo AretinifalseCopy number alterations in osteosarcoma CTCLow-pass sequencing for copy number alteration analysis on whole-genome amplification of epithelial/mesenchymal osteosarcoma CTCs and Hoechst-positive cells. All cells were isolated via a marker-independent enrichment and recovered thought the DEPArray platform from patient-derived PBMCs.2026-06-25T00:00:00Z2026-06-25T01:01:02.996Z2026-01-23T15:24:01.462ZE-MTAB-16563ERP188093EFO_0002944EFO_0004170EFO_0002693EFO_0005518EFO_0004184