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Related Experiment Video

Updated: Jun 19, 2026

Large-scale Three-dimensional Imaging of Cellular Organization in the Mouse Neocortex
09:55

Large-scale Three-dimensional Imaging of Cellular Organization in the Mouse Neocortex

Published on: September 5, 2018

Areal and laminar differentiation in the mouse neocortex using large scale gene expression data.

Mike Hawrylycz1, Amy Bernard, Chris Lau

  • 1Allen Institute for Brain Science, 551 N. 34th Street, Seattle, WA 98103, USA.

Methods (San Diego, Calif.)
|October 6, 2009
PubMed
Summary

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Researchers developed a new method to map gene expression patterns in the mouse cortex. This approach reveals a consistent, layer-based genetic organization across different cortical areas.

Area of Science:

  • Neuroscience
  • Genomics
  • Computational Biology

Background:

  • Cortical cytoarchitecture is well-defined, but distinguishing between cortical areas based on architectural differences remains challenging.
  • Current methods like MRI and tracing identify gross structures, while gene expression analysis often lacks direct functional correlation.
  • Gene expression in the cortex typically spans entire laminae, making areal patterning difficult to discern with individual markers.

Purpose of the Study:

  • To develop a novel methodology for clustering gene expression correlation profiles in the mouse cortex.
  • To identify large-scale genetic relationships between cortical layers and areas.
  • To reveal a consistent, layer-based genetic organization of areal patterning.

Main Methods:

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Differentiation of a Human Neural Stem Cell Line on Three Dimensional Cultures, Analysis of MicroRNA and Putative Target Genes
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Differentiation of a Human Neural Stem Cell Line on Three Dimensional Cultures, Analysis of MicroRNA and Putative Target Genes

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Related Experiment Videos

Last Updated: Jun 19, 2026

Large-scale Three-dimensional Imaging of Cellular Organization in the Mouse Neocortex
09:55

Large-scale Three-dimensional Imaging of Cellular Organization in the Mouse Neocortex

Published on: September 5, 2018

Mining Spatial Transcriptomics Datasets using DeepSpaceDB
10:16

Mining Spatial Transcriptomics Datasets using DeepSpaceDB

Published on: September 5, 2025

Differentiation of a Human Neural Stem Cell Line on Three Dimensional Cultures, Analysis of MicroRNA and Putative Target Genes
10:48

Differentiation of a Human Neural Stem Cell Line on Three Dimensional Cultures, Analysis of MicroRNA and Putative Target Genes

Published on: April 12, 2015

  • Utilized the Anatomic Gene Expression Atlas (AGEA) from the Allen Brain Atlas, which contains in situ hybridization data.
  • Applied a methodology for clustering gene expression correlation profiles in the C57Bl/6J mouse cortex.
  • Employed surface-based mapping and visualization techniques to represent genetic relationships.

    • Main Results:

    • Demonstrated a consistent, expression-based organization of areal patterning in the mouse cortex when data is clustered on a laminar basis.
    • Identified large-scale genetic relationships between cortical layers and areas through gene expression correlation profiles.
    • Visualizations clarified the complex genetic relationships within the cortical architecture.

    Conclusions:

    • The developed methodology effectively identifies large-scale genetic relationships within the mouse cortex.
    • A consistent, layer-based genetic organization underlies areal patterning in the cortex.
    • This approach provides a new framework for understanding cortical organization through gene expression patterns.