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Related Experiment Video

Updated: Jul 3, 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

Connecting single-cell transcriptomes to projectomes in the mouse visual cortex.

Staci A Sorensen1, Nathan W Gouwens2, Yun Wang2

  • 1Allen Institute for Brain Science, Seattle, WA, USA. stacis@alleninstitute.org.

Nature
|July 1, 2026
PubMed

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Summary
This summary is machine-generated.

Researchers created a new way to classify brain cells by linking gene activity to their structure and electrical signals. This helps map neuron connections and understand brain circuitry, advancing our knowledge of the mammalian brain.

Area of Science:

  • Neuroscience
  • Genomics
  • Computational Biology

Background:

  • Mammalian brains have diverse neuron types with distinct functions.
  • Single-cell RNA sequencing has enabled transcriptomic cell-type classification.
  • Patch-seq links transcriptomics to morphology and electrophysiology, but axonal projections remain poorly understood.

Purpose of the Study:

  • To integrate transcriptomic, morphological, and electrophysiological data to classify neuron types.
  • To predict long-range axonal projection targets based on cell type.
  • To establish a comprehensive taxonomy of cortical excitatory neuron types.

Main Methods:

  • Collected Patch-seq data from 1,528 mouse visual cortex excitatory neurons.
  • Acquired whole-neuron morphologies for 341 excitatory neurons.

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Multiplexed Single Cell mRNA Sequencing Analysis of Mouse Embryonic Cells
08:30

Multiplexed Single Cell mRNA Sequencing Analysis of Mouse Embryonic Cells

Published on: January 7, 2020

Related Experiment Videos

Last Updated: Jul 3, 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

Multiplexed Single Cell mRNA Sequencing Analysis of Mouse Embryonic Cells
08:30

Multiplexed Single Cell mRNA Sequencing Analysis of Mouse Embryonic Cells

Published on: January 7, 2020

  • Developed a multistep classifier to integrate multimodal cell data and predict projection targets.

    • Main Results:

    • Defined 17 morphoelectric-transcriptomic neuron types.
    • Transcriptomic variation correlates with morphological and electrophysiological phenotypes.
    • Gene expression and location predict projection targets, revealing novel signatures for layer 5 neurons.

    Conclusions:

    • Established a comprehensive, integrated taxonomy of cortical excitatory neurons.
    • Developed a high-dimensional cell-type classification system applicable brain-wide and across species.
    • Provided new insights into the axonal circuitry of specific neuron populations.