Neuronal Subtype Markers

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. Learn about newly identified molecular markers to facilitate the study of serotonergic neurons, retinal ganglion cells, and sensory (mechanosensitive and nociceptive) neurons.

New Neuronal Subtype Specific Markers

R2-1, R2-2 Subtypes
Serotonergic Neurons (R2 5HT sub-lineage) Neuronal Subtype Specific Properties

Vglut3 low/Thp2/GLI2 high
Unresponsive to senktide

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

Vglut3 high/Thp2/GLI2 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.

Subtype 3, 27, 34
Retinal Ganglion Cells (RGCs) Neuronal Subtype Specific Properties
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
Follistatin+ high
  • Enriched for the expression of transcription factors Rhox5 and Irx4

NF-1, NF-2, NF-3 Class
Sensory Neurons Neuronal Subtype Specific Properties


  • 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.

ZIC1 belongs to the family of C2H2-type zinc finger proteins, its expression is detected in the cerebellum of mouse brain through immunohistochemistry.


GLI-2 belongs to the C2H2-type zinc finger subclass of GLI proteins, its expression is detected in HeLa cell nuclei.

ZIC1 was detected in immersion fixed frozen sections of mouse brain (cerebellum) using 15 µg/mL Goat Anti-Human/Mouse ZIC1 Antigen Affinity-purified Polyclonal Antibody (AF4978) overnight at 4°C. Tissue was stained (brown) with the Anti-Goat HRP-DAB Cell & Tissue Staining Kit (CTS008) and counterstained with hematoxylin (blue).


GLI-2 expression was detected in HeLa cells with GLI-2 Rabbit Polyclonal Antibody [NBP2-23602] DyLight 488 (green). Nuclei and alpha-tubulin were counterstained with DAPI (blue) and DyLight 550 (red). An antibody dilution of 1:50 was used.

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 about Dual ISH-IHC