Neuroscience Cell Identity Markers

The nervous system consists of a complex variety of neurons and non-neuronal cells. The neuronal compartment alone contains billions of neurons, with a not yet fully characterized number of neuronal subtypes.

Major types of brain cells


Neurons are electrically excitable cells that transmit signals (electrical and chemical) supporting a wide range of functions including cognition, sensory perception and movement. Morphologically, neurons contain four well defined structural compartments including dendrites, soma, axon and synaptic terminal. Morphology and connectivity have traditionally been instrumental in neuronal identification. Nevertheless, depending on investigator’s objectives, neuronal identification often requires the detection of several molecular markers to:

  1. Distinguish neurons from other brain cells (e.g., neurons vs glial)
  2. Determine neuronal identity (e.g., subtypes)
  3. Define a neuron’s function (e.g., excitatory vs inhibitory)
  4. Establish synaptic partners (e.g., pre- and post-synaptic)

Commonly Used Neuronal Markers

Immature Neuron Markers Mature Neuron Markers Functional Neuron Markers Synaptic Neuron Markers

Doublecortin, NCAM, NeuroD1

Enolase 2/NSE, NeuN, MAP2*, beta-III Tubulin, Neurofilament Light, Neurofilament Medium, Neurofilament Heavy, GAP-43


PSD-95, Synaptophysin, Bassoon

Notes: *In comparison with beta-III Tubulin, MAP2 labels more mature neurons.

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Neuronal Subtypes

Identifying a neuron’s subtype may be key to understanding its function within a specific network. Recently, single-cell RNA sequencing approaches have facilitated the identification of new subtype specific molecular markers.

New Neuronal Subtype Specific Markers

Serotonergic Neurons (R2 5HT sub-lineage) Subtype Specific Properties

Vglut3 low/Thp2 high
Unresponsive to senktide

  • R2 5HT neurons arise from rhombomere 2 in the embryonic hindbrain and localize to the median raphe

Vglut3 high/Thp2 low
Unresponsive to oxytocin
  • The R2 5HT sub-lineage is now known to consist of two main subtypes (Okaty et al. 2015) and participates in sensorimotor gating.

neuronal cell types
Retinal Ganglion Cells (RGCs)  
Zic1+ high
  • RGC-subtype 34 is enriched in the right eye (Rheaume et al. 2018).
  • Ipsilateral projecting RGCs

Runx1+ high
  • Enriched for the expression of transcription factors Runx1 and Mef2c
Fst+ high
  • Enriched for the expression of transcription factors Rhox5 and Irx4

Sensory Neurons Subtype Specific Properties


  • Low threshold mechanoreceptors (Usoskin et al. 2014)
  • Neuropathic pain

  • Low threshold mechanoreceptors
  • Low threshold mechanoreceptors
  • Perception of inflammatory itch

*This list contains a subset of markers recently discovered by transcriptomic approaches which identify specific neuronal subtypes. This is not a comprehensive list.

RNAscope assays for neuronal subtype identification

Transcriptomic approaches have significantly advanced identification of neuronal subtypes. RNAscope® assays provide sensitive probes for the detection of multiple RNA targets at a single cell level in intact tissue.

Learn more about probes for neuronal cell types

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Glial cells are non-neuronal cells found in the central and peripheral nervous system including microglia and macroglia cells. Among these, macroglia cells include astrocytes, oligodendrocytes, ependymal cells, radial glia, Schwann cells and satellite cells. Glial cells function to support a variety of neuronal activities including migration, axonal outgrowth and synaptic activity. Additionally, glial cells provide neurons with trophic and metabolic support and help maintain synaptic homeostasis.

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Protoplasmic and fibrous astrocytes

Astrocytes are the most ubiquitous and diverse of the glial cells, being both functionally and molecularly diverse. Functionally, astrocytes play a role in neurotransmitter clearance, ion homeostasis and in the regulation of synapse number, thereby modulating neuronal activity through different mechanisms. Their molecular diversity is exemplified by the variable expression of key proteins including glial fibrillar acidic protein (GFAP), glutamate transporter (Glt1/EAAT2) and the gap junction protein connexin 30 (Cx30). Particularly, GFAP expression, often used as a reliable astrocyte marker, is not always expressed by astrocytes and is more common to reactive and white matter astrocytes. Markers for mature astrocytes include aldehyde dehydrogenase family 1 member L1 (Aldh1L1), aldolase C (AldoC), glutamate transporter-1 (Glt1), S100 calcium-binding protein B (S100b) and Aquaporin 4.

Two types of astrocytes are currently recognized, although morphological studies suggest a greater diversity.

Protoplasmic Fibrous
S100b + GFAP +
Gray matter White matter

GFAP expression in rat cerebellum IHC

Immunocytochemistry/Immunofluorescence: GFAP Antibody [NB300-141] - Analysis of a rat cerebellum section stained with rabbit polyclonal antibody to GFAP, NB300-141, dilution 1:5,000 in green and mouse monoclonal antibody to MeCP2, dilution 1:500, in red. The blue is DAPI staining of nuclear DNA. Following transcardial perfusion of rat with 4% paraformaldehyde, brain was post fixed for 1 hour, cut to 45uM, and free-floating sections were stained with above antibodies. The GFAP antibody stains the network of astrocytic cells and the processes of Bergmann glia in the molecular layer. The MeCP2 antibody specifically labels nuclei of certain neurons.

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Oligodendrocytes provide metabolic support and myelinate neuronal axons in the CNS. Insulating-myelin sheaths are indispensable for fast action potential conduction along the neuronal axon. Oligodendrocytes may be molecularly identified by the expression of various markers including myelin basic protein (MBP), myelin oligodendrocyte glycoprotein (MOG), carbonic anhydrase II, CNPase (2’,3’-cyclic nucleotide 3’-phosphohydrolase), Nogo-A and proteolipid protein (PLP). More recently a new marker for mature oligodendrocytes, Tmem10/Opalin, was identified which is co-expressed with other markers including MOG and MBP in myelinated fibers.

CNPase expression in adult mouse brain IHC

Immunohistochemistry: CNPase Antibody [NB100-1935] - A tissue section through an adult mouse brain showing CNPase (brown staining) in white matter tracts and the granule cell layer of the cerebellum.

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Microglia are the immune cells of the nervous system. They are macrophages that serve as the first line of immune defense in the CNS targeting damaged neurons, plaques and infectious agents for phagocytosis. Even in the absence of a trigger or insult to the brain, microglia constantly monitor their surrounding tissues and participate in the maintenance of homeostasis. During development, microglia derived factors influence neuronal survival, either supporting survival or inducing cell death via apoptosis.

Identification of microglia has traditionally relied on markers such as CD45 expression and more recently Cx3cr1. A nuance in the field has been the identification of Tmem119 as a microglia specific marker.

TMEM119 expression in human cerebral cortex IHC

Orthogonal Strategies Validation. Immunohistochemistry-Paraffin: TMEM119 Antibody [NBP2-30792] - Staining in human cerebral cortex and liver tissues. Corresponding TMEM119 RNA-seq data are presented for the same tissues. Staining of human cerebral cortex shows moderate to strong membranous positivity in microglia. Staining of human liver shows no positivity in hepatocytes as expected.

P2Y12/P2RY12 expression  in microglia of human cerebral cortex IHC

Immunohistochemistry-Paraffin: P2Y12/P2RY12 Antibody [NBP2-33870] - Staining of human cerebral cortex shows strong cytoplasmic positivity in microglia.

Following an insult to the brain, for example by infectious pathogens crossing the blood-brain barrier, microglia transform from a ramified to an amoeboid morphology, which correlate with their inactive and active states, respectively. Upon activation, microglia undergo changes in gene expression that underscore their new functionalities, for example the ability to produce inflammatory substances and phagocytose.

Microglia transform from ramified to amoeboid morphology upon activation

Genes modulated by LPS-induced microglia activation

Up-regulated expression Down-regulated expression
Lcn2 Tmem119
Ccl3 Fcrls
Cxcl10 Olfml3
Ccl5 Ltc4s
IL-1b Adora3
Tlr2 P2ry12

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