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Cells
Volume 9
Issue 6
10.3390/cells9061406
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Article

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

by
James A. Gregory
1,*,
Emily Hoelzli
1,
Rawan Abdelaal
1,
Catherine Braine
2,
Miguel Cuevas
2,
Madeline Halpern
3,
Natalie Barretto
3,
Nadine Schrode
3,
Güney Akbalik
1,
Kristy Kang
1,
Esther Cheng
3,
Kathryn Bowles
4,
Steven Lotz
5,
Susan Goderie
5,
Celeste M. Karch
6,
Sally Temple
5,
Alison Goate
4,
Kristen J. Brennand
3 and
Hemali Phatnani
1,2
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)
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Abstract

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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MDPI and ACS Style

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. https://doi.org/10.3390/cells9061406

AMA Style

Gregory JA, 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 CM, Temple S, Goate A, Brennand KJ, Phatnani H. Cell Type-Specific In Vitro Gene Expression Profiling of Stem Cell-Derived Neural Models. Cells. 2020; 9(6):1406. https://doi.org/10.3390/cells9061406

Chicago/Turabian Style

Gregory, James A., Emily Hoelzli, Rawan Abdelaal, Catherine Braine, Miguel Cuevas, Madeline Halpern, Natalie Barretto, Nadine Schrode, Güney Akbalik, Kristy Kang, Esther Cheng, Kathryn Bowles, Steven Lotz, Susan Goderie, Celeste M. Karch, Sally Temple, Alison Goate, Kristen J. Brennand, and Hemali Phatnani. 2020. "Cell Type-Specific In Vitro Gene Expression Profiling of Stem Cell-Derived Neural Models" Cells 9, no. 6: 1406. https://doi.org/10.3390/cells9061406

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