Reproducibility of Molecular Phenotypes after Long-Term Differentiation to Human iPSC-Derived Neurons: A Multi-Site Omics Study

Publication date: Available online 20 September 2018Source: Stem Cell ReportsAuthor(s): Viola Volpato, James Smith, Cynthia Sandor, Janina S. Ried, Anna Baud, Adam Handel, Sarah E. Newey, Frank Wessely, Moustafa Attar, Emma Whiteley, Satyan Chintawar, An Verheyen, Thomas Barta, Majlinda Lako, Lyle Armstrong, Caroline Muschet, Anna Artati, Carlo Cusulin, Klaus Christensen, Christoph PatschSummaryReproducibility in molecular and cellular studies is fundamental to scientific discovery. To establish the reproducibility of a well-defined long-term neuronal differentiation protocol, we repeated the cellular and molecular comparison of the same two iPSC lines across five distinct laboratories. Despite uncovering acceptable variability within individual laboratories, we detect poor cross-site reproducibility of the differential gene expression signature between these two lines. Factor analysis identifies the laboratory as the largest source of variation along with several variation-inflating confounders such as passaging effects and progenitor storage. Single-cell transcriptomics shows substantial cellular heterogeneity underlying inter-laboratory variability and being responsible for biases in differential gene expression inference. Factor analysis-based normalization of the combined dataset can remove the nuisance technical effects, enabling the execution of robust hypothesis-generating studies. Our study shows that multi-center collaborations can expose systematic biases and iden...
Source: Stem Cell Reports - Category: Stem Cells Source Type: research