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Updated: Feb 21, 2026

Isolation and Quantification of Axonal mRNAs Using Porous Membrane Inserts and RTddPCR

Isolation and Quantification of Axonal mRNAs Using Porous Membrane Inserts and RTddPCR

Published on: February 6, 2026

Optimized Whole Transcriptome Profiling of Motor Axons.

Lena Saal-Bauernschubert¹, Michael Briese¹, Michael Sendtner²

¹Institute for Clinical Neurobiology, University Hospital Wuerzburg, 97078, Wuerzburg, Germany.

Methods in Molecular Biology (Clifton, N.J.)

|October 8, 2017

Summary

Researchers developed a new method to analyze RNA in distinct neuronal compartments. This technique allows for the study of the whole transcriptome in axons versus somatodendritic regions of neurons.

Keywords:

Axons Compartmentalized cultures Primary motoneurons RNA RNA-Seq Transcriptome

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Last Updated: Feb 21, 2026

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Published on: February 6, 2026

Production of RNA for Transcriptomic Analysis from Mouse Spinal Cord Motor Neuron Cell Bodies by Laser Capture Microdissection

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Published on: January 13, 2014

Expanding the Toolkit for In Vivo Imaging of Axonal Transport

Expanding the Toolkit for In Vivo Imaging of Axonal Transport

Published on: December 23, 2021

Area of Science:

Neuroscience
Molecular Biology
Genomics

Background:

Highly polarized cells like neurons exhibit non-random RNA distribution.
Analyzing RNA in distinct subcellular compartments of neurons is methodologically challenging.

Purpose of the Study:

To establish a method for analyzing the transcriptome in separated axonal and somatodendritic compartments of primary motoneurons.
To enable high-throughput sequencing of RNA from these distinct neuronal regions.

Main Methods:

Primary motoneurons were cultured in compartmentalized chambers to physically separate axons from the somatodendritic region.
Whole transcriptome amplification was performed on RNA isolated from each compartment.
High-throughput sequencing was employed to analyze the RNA composition of both compartments.

Main Results:

Successfully cultured primary motoneurons in a manner that allows for compartment-specific RNA isolation.
Developed and validated a protocol for whole transcriptome amplification and sequencing from these separated neuronal compartments.
Generated data on the distinct RNA composition of axonal versus somatodendritic compartments.

Conclusions:

The described method enables the analysis of compartment-specific transcriptomes in neurons.
This technique provides a valuable tool for understanding RNA localization and function in neuronal polarity.
Advances the study of neuronal gene expression and regulation in distinct cellular compartments.