This page provides a comprehensive catalog of molecular markers used to identify and characterize different cell types in the brain. Cell type markers are essential for interpreting single-cell RNA sequencing data, guiding experimental design, and validating cell type identity in experimental models.
Markers span multiple modalities: gene expression (RNA), protein expression, and functional properties. No single marker defines a cell type—combinations of markers are used for robust identification.
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| Cell Type | Primary Markers | Secondary Markers | Function |
|-----------|----------------|-------------------|----------|
| Layer 2/3 pyramidal | CUX2, SATB2 | NR2A, VGLUT1 | Cortical excitation |
| Layer 5 pyramidal | CTIP2, TLE4 | VGLUT1, Thy1 | Corticospinal output |
| CA1 pyramidal | PROX1, SLC17A6 | Calb1, Wnt2 | Hippocampal circuit |
| CA3 pyramidal | WNT2, GRIK1 | Calb2, CNR1 | Trisynaptic circuit |
| Dentate granule | PROX1, SLC17A7 | Calb1, NeuroD1 | Encoding |
| Subiculum | CUX2, FOXP2 | VGLUT2, CaMK2A | Output |
| Cell Type |
Primary Markers |
Secondary Markers |
Function |
| Parvalbumin (PV) |
PVALB, GAD1 |
Kv3.1, CNR1 |
Fast spiking |
| Somatostatin (SST) |
SST, GAD1 |
NPY, CALB1 |
Dendritic inhibition |
| VIP |
VIP, GAD2 |
CR, CaMK2A |
Disinhibition |
| Cholecystokinin (CCK) |
CCK, GAD1 |
CB1, CaMK2A |
Plasticity |
| Chandelier |
PAX6, SLC6A1 |
Kv3.1 |
Axon initial segment |
| Cell Type |
Markers |
Neurotransmitter |
| Dopaminergic (SNc) |
TH, DAT, GIRK2 |
Dopamine |
| Dopaminergic (VTA) |
TH, DAT, CALB1 |
Dopamine |
| Noradrenergic (LC) |
DBH, NET, PHOX2A |
Norepinephrine |
| Serotonergic (Raphe) |
TPH2, SERT, PET1 |
Serotonin |
| Cell Type |
Markers |
Function |
| Basal forebrain |
CHAT, VAChT, p75NTR |
Memory modulation |
| Brainstem |
CHAT, VAChT |
Arousal |
| Striatal interneurons |
CHAT, SST, Calb1 |
Modulation |
| Marker |
Expression |
Notes |
| GFAP |
High |
Intermediate filament |
| ALDH1L1 |
High |
Metabolic enzyme |
| AQP4 |
High |
Water channel |
| EAAT1 (GLAST) |
High |
Glutamate uptake |
| EAAT2 (GLT1) |
High |
Glutamate uptake |
| S100B |
Medium |
Calcium binding |
| Marker |
Expression |
Notes |
| P2RY12 |
High |
Resting state |
| TMEM119 |
High |
CNS resident |
| CX3CR1 |
High |
Chemokine receptor |
| IBA1 (AIF1) |
Medium |
Pan-marker |
| CD68 |
Low |
Activated state |
| TREM2 |
Low |
Disease-associated |
| Stage |
Markers |
Notes |
| OPC |
PDGFRA, CSPG4 |
Proliferation |
| Pre-OL |
OLIG2, NKX2.2 |
Differentiation |
| Mature OL |
MBP, PLP, CNP |
Myelin production |
| Marker |
Expression Change |
Function |
| TREM2 |
Upregulated |
Phagocytosis |
| APOE |
Upregulated |
Lipid metabolism |
| CD9 |
Upregulated |
Phagocytosis |
| TYROBP |
Upregulated |
Signaling |
| CST3 |
Upregulated |
Protease inhibitor |
A1 (Neurotoxic)
| Marker |
Change |
| C3 |
Upregulated |
| Serping1 |
Upregulated |
| Ligp1 |
Upregulated |
A2 (Neuroprotective)
| Marker |
Change |
| S100A10 |
Upregulated |
| Ptx3 |
Upregulated |
| Marker |
Change |
Significance |
| GFAP |
Increased |
Reactivity |
| YKL-40 |
Increased |
Inflammatory state |
| S100B |
Increased |
Pro-inflammatory |
- RNA markers indicate transcription but not protein levels
- Protein markers confirm functional expression
- Post-translational modifications affect activity
- Many markers conserved between mouse and human
- Some markers species-specific
- Need to validate in relevant species