Profiling_heterogeneity_in_Human_derived_IPSC_neurons

The impact of genetic variants on molecular pathways that give rise to neurodegenerative diseases such as Alzheimer’s and Parkinson’s is best elucidated in the appropriate cell types and molecular contexts. Existing studies have focused on bulk profiling of mixed cell types, but have ignored assaying genetic effects across development and cell differentiation. At the core of this proposal is the idea to use single-cell assays to study genetic effects during differentiation of dopaminergic and cortical neurons to identify the sequence of molecular events from variants to healthy and diseased cell states in a cell-specific manner. 1) This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute please see http://www.sanger.ac.uk/datasharing/

Type: Transcriptome Analysis
Archiver: European Genome-Phenome Archive (EGA)

1 Dataset 5 Publications

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Dataset ID	Description	Technology	Samples
EGAD00001006157	The impact of genetic variants on molecular pathways that give rise to neurodegenerative diseases such as Alzheimer's and Parkinson's is best elucidated in the appropriate cell types and molecular contexts. Existing studies have focused on bulk profiling of mixed cell types, but have ignored assaying genetic effects across development and cell differentiation. At the core of this proposal is the idea to use single-cell assays to study genetic effects during differentiation of dopaminergic and cortical neurons to identify the sequence of molecular events from variants to healthy and diseased cell states in a cell-specific manner. 1) This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute please see http://www.sanger.ac.uk/datasharing/ . This dataset contains all the data available for this study on 2020-05-18.	Illumina HiSeq 4000	42

Publications	Citations
Population-scale single-cell RNA-seq profiling across dopaminergic neuron differentiation. Jerber J, Seaton DD, Cuomo ASE, Kumasaka N, Haldane J, Steer J, Patel M, Pearce D, Andersson M, Bonder MJ, Mountjoy E, Ghoussaini M, Lancaster MA, HipSci Consortium, Marioni JC, Merkle FT, Gaffney DJ, Stegle O. Nat Genet 53: 2021 304-312	109
splatPop: simulating population scale single-cell RNA sequencing data. Azodi CB, Zappia L, Oshlack A, McCarthy DJ. Genome Biol 22: 2021 341	8
Somatic mutations alter the differentiation outcomes of iPSC-derived neurons. Puigdevall P, Jerber J, Danecek P, Castellano S, Kilpinen H. Cell Genom 3: 2023 100280	3
Expression Pattern of Trace Amine-Associated Receptors during Differentiation of Human Pluripotent Stem Cells to Dopaminergic Neurons. Katolikova NV, Vaganova AN, Shafranskaya DD, Efimova EV, Malashicheva AB, Gainetdinov RR. Int J Mol Sci 24: 2023 15313	3
Multiplexed bulk and single-cell RNA-seq hybrid enables cost-efficient disease modeling with chimeric organoids. Cheng C, Wang G, Zhu Y, Wu H, Zhang L, Liu Z, Huang Y, Zhang J. Nat Commun 15: 2024 3946	0