RNA FISH for neuroscience

Visualisation and quantification of neuroscience-related single RNA transcripts, using Stellaris™ RNA fluorescence in situ hybridization (RNA FISH) or smFISH, offers the unique ability to observe altered disease or region-specific expression in fixed cells or tissues, including an entire intact brain or organism.

Custom Stellaris Probe sets can be designed against almost any RNA target using our free online designer. We also offer positive control ShipReady probe sets and professionally designed DesignReady Probe sets, which undergo rigorous bioinformatic screening. The Stellaris buffer set streamlines your experiments and improves the quality of your images by decreasing troublesome background fluorescence.

stellaris rna fish neuron tubb3 mrna
stellaris rna fish astrocyte gfap mrna
stellaris rna fish oligodendrocytes olig2 mrna

stelaris rna fish video

Learn about the Stellaris RNA FISH technology in this entertaining yet informative video that contains 3 segments: introduction, animated RNA FISH mechanism, and interview portion discussing the applications of Stellaris FISH.

Advanced neuroscience applications:

The breadth of information which can be gathered using Stellaris RNA FISH encompasses individual RNA transcript counting, transcription bursting within a single cell, and visualising wide bands of expression within an entire intact brain or organism. As the image above demonstrates, Stellaris RNA FISH probe sets can be used to differentiate between cell types in the brain and is completely compatible with either cells or tissue.

Whole brain imaging can relay an incredible amount of information about RNA expression. Stellaris has been published utilizing the whole tissue clearing technology CLARITY which allowed for visualisation of RNA distribution in an entire 3D intact mouse brain. Stellaris RNA FISH is also compatible with super resolution microscopy and whole mount preparations.

Stellaris RNA FISH resources for neuroscience

Professionally-designed neuro-specific probe sets include:

Stellaris RNA FISH in whole mount

Tyrosine Hydroxylase (green)
Honey Bee Brain whole mount
Courtesy of: Matthew McNeill and Gene Robinson

Neuro-specific support materials:

Fluorescent microscopy can be challenging in the brain due to high autofluorescence, so we’ve developed a specific protocol for use of Stellaris RNA FISH probe sets in mouse brain and a tech article to walk you through some applications.

Protocol: Protocol for Fresh Frozen Mouse Brain Tissue

Article: Unraveling the Neural Web: Stellaris® RNA FISH for Neuroscience Research

Bitesize Bio Article: Challenges of Autofluorescence in Neuroscience

Publication highlights

Highlighted neuroscience publications citing Stellaris RNA FISH Probe sets.
Over 33% of publications citing Stellaris RNA FISH publish in Cell, Nature, or Science

Simultaneous RNA FISH and immunofluorescence

Image of simultaneous RNA FISH and immunofluorescence assay. eGFP RNA molecules (red), protein marker GFP (green), DAPI (blue) in mouse E13 primary DRG neuron culture cells (submitted by Adi Minis).

Stellarvision™ Imaging Platform

Whole tissue section to single RNA transcripts in one image

Target RNA expression in regions of the brain and also perform single transcript counting in a single image. Below is an entire section of mouse brain probed with Stellaris RNA FISH probes against Plp1 mRNA (green) and imaged using the Stellarvision imaging platform. The resulting image allows you to zoom in on single transcripts from the full brain section view.

stellaris rna fish mouse brain plp1 zoomed out


stellaris rna fish mouse brain plp1 zoom in


stellaris rna fish mouse brain plp1 zoomed in

Zoomed in single molecule resolution
Mouse Brain
Plp1 mRNA labeled with Stellaris RNA FISH probes (green),
DAPI (red) and imaged with Stellarvision
(For more information on the Stellarvision imaging platform email Optical Biosystems.)