{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"submitter":["Claudia Pommerenke"],"study_type":["genotyping by array"],"organism":["Homo sapiens"],"species":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15176"],"description":["This 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."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Nucleic 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)."],"figure_sub":["MIAME Score","Raw Data","Organization","Assays and Data","MAGE-TAB Files","Array Designs"],"pubmed_authors":["Claudia Pommerenke"],"data_protocol":["Data 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."],"additional_accession":[]},"is_claimable":false,"name":"Chromosomal quality control via SNP array in different hPSC lines","description":"This 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.","dates":{"release":"2025-06-03T00:00:00Z","modification":"2025-06-11T12:12:16.659Z","creation":"2025-05-29T09:28:29.197Z"},"accession":"E-MTAB-15176","cross_references":{"EFO":["EFO_0002944","EFO_0003814","EFO_0003813","EFO_0002767","EFO_0005518","EFO_0003816","EFO_0003815"]}}