Cell type-specific in vitro gene expression profiling of stem cell-derived neural models

James A. Gregory, 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, Hemali Phatnani

Research output: Contribution to journalArticlepeer-review

3 Scopus citations


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.

Original languageEnglish
Article number1406
Pages (from-to)1-18
Number of pages18
Issue number6
StatePublished - Jun 2020


  • BacTRAP
  • Genomics
  • Glia
  • HiPSC
  • Neuron
  • RNA-seq
  • RiboTag


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