biostudies-arrayexpressLízia BrancoHomo sapienshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-17432This 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.biostudies-arrayexpressSequencing - 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.OrganizationMINSEQE ScoreAssays and DataMAGE-TAB FilesMetabolomicsUnknownTranscriptomicsGenomicsProteomicsIllumina NovaSeq 6000RNA-seq of coding RNA from single cellsHomo sapiensCharacterization of structural variants in KOLF2.1J iPSCs and their potential impact on forebrain organoid differentiationZeynep YentürLízia BrancoLízia 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 MayerfalseSingle-cell RNA sequencing data of human dorsal forebrain organoids derived from three iPSC linesThis 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.2026-08-03T00:00:00Z2026-08-03T10:57:27.991Z2026-07-31T11:42:13.428ZE-MTAB-17432ERP203142EFO_0002944EFO_0004170EFO_0005684EFO_0005518EFO_0004184