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Open AccessArticle

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

1
Center for Genomics of Neurodegenerative Disease, New York Genome Center, New York, NY 10013, USA
2
Department of Neurology, Columbia University Medical Center, New York, NY 10068, USA
3
Pamela Sklar Division of Psychiatric Genomics, Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
4
Ronald M. Loeb Center for Alzheimer’s Disease, Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
5
Neural Stem Cell Institute, One Discovery Drive, Rensselaer, NY 12144, USA
6
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; https://doi.org/10.3390/cells9061406
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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