biostudies-arrayexpressMetabolomicsUnknownTranscriptomicsGenomicsProteomicsClaudia Pommerenkegenotyping by arrayHomo sapiensHomo sapienshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-15176This dataset accompanies our step-by-step guide for analyzing chromosomal integrity in human pluripotent stem cells (hPSCs) using SNP arrays. It includes raw .idat files, a preconfigured GenomeStudio project, the sample sheet, manifest file, and cluster file. The data allows researchers - especially those new to GenomeStudio - to practice data import, normalization, and CNV detection using the cnvPartition plugin. This resource is intended for training and educational use in stem cell quality control workflows.biostudies-arrayexpressNucleic Acid Extraction - Genomic DNA was extracted using the QIAamp DNA Blood Mini Kit (Qiagen).Labeling - Biotin (C and G) or 2,4-Dinitrophenol (DNP) for A and T labelled, the detection is based on fluorophore-labelled antibody (for A/T) and fluorophore-labelled streptavidin (C/G), respectively.Scaning - Samples were processed on Global Screening Array v3.0 (GSAMD24v3-0, Illumina, Inc. San Diego) by LIFE&BRAIN GmbH (Bonn, Germany).Sample Collection - Samples were collectect from cell culture.Hybridization - Samples were processed on Global Screening Array v3.0 (GSAMD24v3-0, Illumina, Inc. San Diego) by LIFE&BRAIN GmbH (Bonn, Germany).MIAME ScoreRaw DataOrganizationAssays and DataMAGE-TAB FilesArray DesignsClaudia PommerenkeData Transformation - SNP calling was performed using GenomeStudio V2.0.5 with a GenCall threshold of 0.2. CNV Analysis was performed using cnvPartition 3.2.0.falseChromosomal quality control via SNP array in different hPSC linesThis dataset accompanies our step-by-step guide for analyzing chromosomal integrity in human pluripotent stem cells (hPSCs) using SNP arrays. It includes raw .idat files, a preconfigured GenomeStudio project, the sample sheet, manifest file, and cluster file. The data allows researchers - especially those new to GenomeStudio - to practice data import, normalization, and CNV detection using the cnvPartition plugin. This resource is intended for training and educational use in stem cell quality control workflows.2025-06-03T00:00:00Z2025-06-11T12:12:16.659Z2025-05-29T09:28:29.197ZE-MTAB-15176EFO_0002944EFO_0003814EFO_0003813EFO_0002767EFO_0005518EFO_0003816EFO_0003815