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Open AccessArticle

Cell Type-Specific In Vitro Gene Expression Profiling of Stem Cell-Derived Neural Models

Center for Genomics of Neurodegenerative Disease, New York Genome Center, New York, NY 10013, USA
Department of Neurology, Columbia University Medical Center, New York, NY 10068, USA
Pamela Sklar Division of Psychiatric Genomics, Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
Ronald M. Loeb Center for Alzheimer’s Disease, Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
Neural Stem Cell Institute, One Discovery Drive, Rensselaer, NY 12144, USA
Department of Psychiatry, Washington University in St. Louis, St. Louis, MO 63110, USA
Author to whom correspondence should be addressed.
Cells 2020, 9(6), 1406;
Received: 11 May 2020 / Revised: 29 May 2020 / Accepted: 2 June 2020 / Published: 5 June 2020
(This article belongs to the Special Issue Neuron-Glia Interactions)
Genetic and genomic studies of brain disease increasingly demonstrate disease-associated interactions between the cell types of the brain. Increasingly complex and more physiologically relevant human-induced pluripotent stem cell (hiPSC)-based models better explore the molecular mechanisms underlying disease but also challenge our ability to resolve cell type-specific perturbations. Here, we report an extension of the RiboTag system, first developed to achieve cell type-restricted expression of epitope-tagged ribosomal protein (RPL22) in mouse tissue, to a variety of in vitro applications, including immortalized cell lines, primary mouse astrocytes, and hiPSC-derived neurons. RiboTag expression enables depletion of up to 87 percent of off-target RNA in mixed species co-cultures. Nonetheless, depletion efficiency varies across independent experimental replicates, particularly for hiPSC-derived motor neurons. The challenges and potential of implementing RiboTags in complex in vitro cultures are discussed. View Full-Text
Keywords: hiPSC; neuron; glia; RiboTag; bacTRAP; genomics; RNA-seq hiPSC; neuron; glia; RiboTag; bacTRAP; genomics; RNA-seq
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Gregory, J.A.; Hoelzli, E.; Abdelaal, R.; Braine, C.; Cuevas, M.; Halpern, M.; Barretto, N.; Schrode, N.; Akbalik, G.; Kang, K.; Cheng, E.; Bowles, K.; Lotz, S.; Goderie, S.; Karch, C.M.; Temple, S.; Goate, A.; Brennand, K.J.; Phatnani, H. Cell Type-Specific In Vitro Gene Expression Profiling of Stem Cell-Derived Neural Models. Cells 2020, 9, 1406.

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