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BaseScope™ Approach to Visualize Alternative Splice Variants in Tissue

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Alternative Splicing

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2537))

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Abstract

Defining the cell-specific alternative splicing landscape in complex tissues is an important goal to gain functional insights. Deep-sequencing techniques coupled to genetic strategies for cell identification has provided important cues on cell-specific exon usage in complex tissues like the nervous system. BaseScope™ has emerged as a powerful and highly sensitive alternative to in situ hybridization to determine exon composition in tissue with spatial and morphological context. In this protocol, we will review how BaseScope was utilized to detect the e37a-Cacna1b splice variant of the presynaptic calcium channel CaV2.2 or N-type. This splice variant arises from a pair of mutually exclusive exons (e37a and e37b). E37a-Cacna1b is heavily underrepresented relative to e37b-Cacna1b and both exons share 60% of their sequence. By using BaseScope™, we were able to discover that e37a-Cacna1b is expressed in excitatory pyramidal neurons of hippocampus and cortex, as well as motor neurons of the ventral horn of the spinal cord.

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Acknowledgments

This work was supported by NIMH grant R00-MH099405.

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Authors and Affiliations

  1. Department of Biological Sciences, College of Life Sciences and Agriculture, University of New Hampshire, Durham, NH, USA

    Alexandra Bunda & Arturo Andrade

  2. Robert J. and Nancy D. Carney Institute for Brain Science, Brown University, Providence, RI, USA

    Arturo Andrade

Authors
  1. Alexandra Bunda
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  2. Arturo Andrade
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Corresponding author

Correspondence to Arturo Andrade .

Editor information

Editors and Affiliations

  1. Biozentrum, University of Basel, Basel, Switzerland

    Peter Scheiffele

  2. Biozentrum, University of Basel, Basel, Switzerland

    Oriane Mauger

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Bunda, A., Andrade, A. (2022). BaseScope™ Approach to Visualize Alternative Splice Variants in Tissue. In: Scheiffele, P., Mauger, O. (eds) Alternative Splicing. Methods in Molecular Biology, vol 2537. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2521-7_11

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  • DOI: https://doi.org/10.1007/978-1-0716-2521-7_11

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-2520-0

  • Online ISBN: 978-1-0716-2521-7

  • eBook Packages: Springer Protocols

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