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education

lesson 2: cell types

Learn about brain cell types with the Mouse Patch Seq open dataset

resource type / 
Lesson Plan
topic / 
transcriptomics
published / November 5, 2026
audience / 
Undergraduate
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contributors

Claire Weichselbaum
Education & Engagement Specialist III
Rachel Dalley
Sr. Manager, Morphology
Staci Sorensen
Associate Director, Neuroanatomy
Dr. Marie Gadziola
Assistant Professor, University of Toronto Scarborough

about/

In this lesson, students will learn how scientists at the Allen Institute are using the multimodal Patch Seq technique to define brain cell types. They will explore how neuron morphology varies among different transcriptomically defined cell types in the mouse visual cortex using the Allen Institute’s Mouse Patch Seq open dataset.

learning outcomes/

  • Explain what brain cell types are and why they are important
  • Describe different ways that cell types can be defined
  • Evaluate the usefulness of multimodal data to define cell types
  • Compare and contrast the morphology of inhibitory neurons across layers of visualcortex and transcriptomic types

materials

slides
instructor guide
student activity
student activity key

Terms of use: This work is licensed under the Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0). To view a copy of this license, visit https://creativecommons.org/licenses/by-nc-sa/4.0/.

Note: this resource was originally published in 2021. It's original contributors include Lauren Alfiler, Kaitlyn Casimo, Clare Gamlin, and Staci Sorensen.

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