{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Lízia Branco"],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-17432"],"description":["This dataset contains single-cell RNA sequencing data generated from nine dorsal forebrain organoids collected at day 90 of differentiation. The organoids were derived from three human induced pluripotent stem cell lines: KOLF2.1J, BIONi010-C, and HMGU1. The primary objective of the study was to explore potential neurodevelopmental and differentiation-related differences among these lines, with a specific focus on the KOLF2.1J line, in which previously undetected structural variants were identified through optical genome mapping and long-read sequencing."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sequencing - Libraries were sequenced on the Illumina NovaSeq 6000 system.","Nucleic Acid Extraction - Approximately 25,000 cells per channel were loaded onto a Chromium Single Cell 3′ Chip (10x Genomics, Cat. no. PN-120236) and processed through the Chromium controller to generate single-cell gel beads in emulsion.","Library Construction - Library preparation was carried out according to the manufacturer’s protocol. Feature barcode libraries were created using a 10X accessory kit.","Sample Collection - Dorsal forebrain organoids were enzymatically dissociated using the Worthington Papain Dissociation System kit (Worthington Biochemical, Cat. no. LK003150). Multiplexing was performed by 3' CellPlex Kit Set A (10x Genomics, Cat. no. PN-1000261) following the manufacturer’s instructions. Multiplexed cells were counted and pooled in equal proportions to be processed by CeGat Tübingen for single cell sequencing."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","MAGE-TAB Files"],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000"],"study_type":["RNA-seq of coding RNA from single cells"],"species":["Homo sapiens"],"pubmed_title":["Characterization of structural variants in KOLF2.1J iPSCs and their potential impact on forebrain organoid differentiation"],"pubmed_authors":["Zeynep Yentür","Lízia Branco","Lízia Branco, Zeynep Yentür, Madison James Yang, Parithi Balachandran, Kamilla Sedov, G Kumar, Faria Zafar, Theresa Kagermeier, Kseniia Sarieva, Katharina Becker, Bill Skarnes, Christine Beck, Birgitt Schüle, Simone Mayer"],"additional_accession":[]},"is_claimable":false,"name":"Single-cell RNA sequencing data of human dorsal forebrain organoids derived from three iPSC lines","description":"This dataset contains single-cell RNA sequencing data generated from nine dorsal forebrain organoids collected at day 90 of differentiation. The organoids were derived from three human induced pluripotent stem cell lines: KOLF2.1J, BIONi010-C, and HMGU1. The primary objective of the study was to explore potential neurodevelopmental and differentiation-related differences among these lines, with a specific focus on the KOLF2.1J line, in which previously undetected structural variants were identified through optical genome mapping and long-read sequencing.","dates":{"release":"2026-08-03T00:00:00Z","modification":"2026-08-03T10:57:27.991Z","creation":"2026-07-31T11:42:13.428Z"},"accession":"E-MTAB-17432","cross_references":{"ENA":["ERP203142"],"EFO":["EFO_0002944","EFO_0004170","EFO_0005684","EFO_0005518","EFO_0004184"]}}