Cell Atlas Markers

Cell Atlas Markers

Overview

<table class="infobox infobox-cell">
<tr>
<th class="infobox-header" colspan="2">Cell Atlas Markers</th>
</tr>
<tr>
<td class="label">Cell Type</td>
<td>Primary Markers</td>
</tr>
<tr>
<td class="label">Layer 2/3 pyramidal</td>
<td>CUX2, SATB2</td>
</tr>
<tr>
<td class="label">Layer 5 pyramidal</td>
<td>CTIP2, TLE4</td>
</tr>
<tr>
<td class="label">CA1 pyramidal</td>
<td>PROX1, SLC17A6</td>
</tr>
<tr>
<td class="label">CA3 pyramidal</td>
<td>WNT2, GRIK1</td>
</tr>
<tr>
<td class="label">Dentate granule</td>
<td>PROX1, SLC17A7</td>
</tr>
<tr>
<td class="label">Subiculum</td>
<td>CUX2, FOXP2</td>
</tr>
<tr>
<td class="label">Cell Type</td>
<td>Primary Markers</td>
</tr>
<tr>
<td class="label">Parvalbumin (PV)</td>
<td>PVALB, GAD1</td>
</tr>
<tr>
<td class="label">Somatostatin (SST)</td>
<td>SST, GAD1</td>
</tr>
<tr>
<td class="label">VIP</td>
<td>VIP, GAD2</td>
</tr>
<tr>
<td class="label">Cholecystokinin (CCK)</td>
<td>CCK, GAD1</td>
</tr>
<tr>
<td class="label">Chandelier</td>
<td>PAX6, SLC6A1</td>
</tr>
<tr>
<td class="label">Cell Type</td>
<td>Markers</td>
</tr>
<tr>
<td class="label">Dopaminergic (SNc)</td>
<td>TH, DAT, GIRK2</td>
</tr>
<tr>
<td class="label">Dopaminergic (VTA)</td>
<td>TH, DAT, CALB1</td>
</tr>
<tr>
<td class="label">Noradrenergic (LC)</td>
<td>DBH, NET, PHOX2A</td>
</tr>
<tr>
<td class="label">Serotonergi

Cell Atlas Markers

Overview

<table class="infobox infobox-cell">
<tr>
<th class="infobox-header" colspan="2">Cell Atlas Markers</th>
</tr>
<tr>
<td class="label">Cell Type</td>
<td>Primary Markers</td>
</tr>
<tr>
<td class="label">Layer 2/3 pyramidal</td>
<td>CUX2, SATB2</td>
</tr>
<tr>
<td class="label">Layer 5 pyramidal</td>
<td>CTIP2, TLE4</td>
</tr>
<tr>
<td class="label">CA1 pyramidal</td>
<td>PROX1, SLC17A6</td>
</tr>
<tr>
<td class="label">CA3 pyramidal</td>
<td>WNT2, GRIK1</td>
</tr>
<tr>
<td class="label">Dentate granule</td>
<td>PROX1, SLC17A7</td>
</tr>
<tr>
<td class="label">Subiculum</td>
<td>CUX2, FOXP2</td>
</tr>
<tr>
<td class="label">Cell Type</td>
<td>Primary Markers</td>
</tr>
<tr>
<td class="label">Parvalbumin (PV)</td>
<td>PVALB, GAD1</td>
</tr>
<tr>
<td class="label">Somatostatin (SST)</td>
<td>SST, GAD1</td>
</tr>
<tr>
<td class="label">VIP</td>
<td>VIP, GAD2</td>
</tr>
<tr>
<td class="label">Cholecystokinin (CCK)</td>
<td>CCK, GAD1</td>
</tr>
<tr>
<td class="label">Chandelier</td>
<td>PAX6, SLC6A1</td>
</tr>
<tr>
<td class="label">Cell Type</td>
<td>Markers</td>
</tr>
<tr>
<td class="label">Dopaminergic (SNc)</td>
<td>TH, DAT, GIRK2</td>
</tr>
<tr>
<td class="label">Dopaminergic (VTA)</td>
<td>TH, DAT, CALB1</td>
</tr>
<tr>
<td class="label">Noradrenergic (LC)</td>
<td>DBH, NET, PHOX2A</td>
</tr>
<tr>
<td class="label">Serotonergic (Raphe)</td>
<td>TPH2, SERT, PET1</td>
</tr>
<tr>
<td class="label">Cell Type</td>
<td>Markers</td>
</tr>
<tr>
<td class="label">Basal forebrain</td>
<td>CHAT, VAChT, p75NTR</td>
</tr>
<tr>
<td class="label">Brainstem</td>
<td>CHAT, VAChT</td>
</tr>
<tr>
<td class="label">Striatal interneurons</td>
<td>CHAT, SST, Calb1</td>
</tr>
<tr>
<td class="label">Marker</td>
<td>Expression</td>
</tr>
<tr>
<td class="label">GFAP</td>
<td>High</td>
</tr>
<tr>
<td class="label">ALDH1L1</td>
<td>High</td>
</tr>
<tr>
<td class="label">AQP4</td>
<td>High</td>
</tr>
<tr>
<td class="label">EAAT1 (GLAST)</td>
<td>High</td>
</tr>
<tr>
<td class="label">EAAT2 (GLT1)</td>
<td>High</td>
</tr>
<tr>
<td class="label">S100B</td>
<td>Medium</td>
</tr>
<tr>
<td class="label">Marker</td>
<td>Expression</td>
</tr>
<tr>
<td class="label">P2RY12</td>
<td>High</td>
</tr>
<tr>
<td class="label">TMEM119</td>
<td>High</td>
</tr>
<tr>
<td class="label">CX3CR1</td>
<td>High</td>
</tr>
<tr>
<td class="label">IBA1 (AIF1)</td>
<td>Medium</td>
</tr>
<tr>
<td class="label">CD68</td>
<td>Low</td>
</tr>
<tr>
<td class="label">TREM2</td>
<td>Low</td>
</tr>
<tr>
<td class="label">Stage</td>
<td>Markers</td>
</tr>
<tr>
<td class="label">OPC</td>
<td>PDGFRA, CSPG4</td>
</tr>
<tr>
<td class="label">Pre-OL</td>
<td>OLIG2, NKX2.2</td>
</tr>
<tr>
<td class="label">Mature OL</td>
<td>MBP, PLP, CNP</td>
</tr>
<tr>
<td class="label">Marker</td>
<td>Expression Change</td>
</tr>
<tr>
<td class="label">TREM2</td>
<td>Upregulated</td>
</tr>
<tr>
<td class="label">APOE</td>
<td>Upregulated</td>
</tr>
<tr>
<td class="label">CD9</td>
<td>Upregulated</td>
</tr>
<tr>
<td class="label">TYROBP</td>
<td>Upregulated</td>
</tr>
<tr>
<td class="label">CST3</td>
<td>Upregulated</td>
</tr>
<tr>
<td class="label">Marker</td>
<td>Change</td>
</tr>
<tr>
<td class="label">C3</td>
<td>Upregulated</td>
</tr>
<tr>
<td class="label">Serping1</td>
<td>Upregulated</td>
</tr>
<tr>
<td class="label">Ligp1</td>
<td>Upregulated</td>
</tr>
<tr>
<td class="label">Marker</td>
<td>Change</td>
</tr>
<tr>
<td class="label">S100A10</td>
<td>Upregulated</td>
</tr>
<tr>
<td class="label">Ptx3</td>
<td>Upregulated</td>
</tr>
<tr>
<td class="label">Marker</td>
<td>Change</td>
</tr>
<tr>
<td class="label">GFAP</td>
<td>Increased</td>
</tr>
<tr>
<td class="label">YKL-40</td>
<td>Increased</td>
</tr>
<tr>
<td class="label">S100B</td>
<td>Increased</td>
</tr>
<tr>
<td class="label">Resource</td>
<td>Cell Types</td>
</tr>
<tr>
<td class="label">Allen Brain Cell Atlas</td>
<td>~100+</td>
</tr>
<tr>
<td class="label">SEA-AD</td>
<td>~80</td>
</tr>
<tr>
<td class="label">Human Cell Atlas</td>
<td>Multiple</td>
</tr>
<tr>
<td class="label">BICCN</td>
<td>~100+</td>
</tr>
<tr>
<td class="label">Resource</td>
<td>Cell Types</td>
</tr>
<tr>
<td class="label">Allen Mouse Brain Cell Atlas</td>
<td>~500+</td>
</tr>
<tr>
<td class="label">Tabula Muris</td>
<td>~100+</td>
</tr>
</table>

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. [@allen2024]

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. [@cell2021]

--- [@human2022]

Neuronal Markers

Excitatory Neuron Markers

Inhibitory Neuron Markers

Monoaminergic Neurons

Cholinergic Neurons

Glial Markers

Astrocyte Markers

Microglia Markers

Oligodendrocyte Markers

Disease-Associated Marker States

Disease-Associated Microglia (DAM)

Reactive Astrocytes (A1/A2)

A1 (Neurotoxic)

A2 (Neuroprotective)

ALS Astrocytes

Cell Type Atlas Resources

Human Cell Type Atlases

Mouse Cell Type Atlases

Marker Validation Considerations

RNA vs Protein

• RNA markers indicate transcription but not protein levels
• Protein markers confirm functional expression
• Post-translational modifications affect activity

Species Differences

• Many markers conserved between mouse and human
• Some markers species-specific
• Need to validate in relevant species
• [Alzheimer's Disease](/diseases/alzheimers-disease)
• [Parkinson's Disease](/diseases/parkinsons-disease)

External Links

• [PubMed](https://pubmed.ncbi.nlm.nih.gov/)
• [KEGG Pathways](https://www.genome.jp/kegg/pathway.html)

See Also

• [Neurodegeneration](/wiki/diseases-neurodegeneration) — cell_type_involved_in