Stem Cell Marker Atlas
Quick Facts
| Feature | Information |
|---|---|
| Purpose | Cell Identification and Validation |
| Applications | ICC, IF, Flow Cytometry, Western Blot, qPCR, scRNA-seq |
| Marker Categories | Lineage, Surface, Functional, Maturation, Transcription Factors |
| Best Practice | Use Marker Panels Rather Than Single Markers |
Overview
The Stem Cell Marker Atlas is a consolidated reference guide for commonly used markers in stem cell biology, developmental biology, neuroscience, regenerative medicine, and disease modeling.
Markers are used to identify specific cell types, assess differentiation status, validate experimental outcomes, and annotate transcriptomic datasets.
Because no individual marker is completely specific, cell identity should always be confirmed using multiple complementary markers.
Marker Categories
| Category | Purpose |
|---|---|
| Lineage Markers | Identify cell type |
| Transcription Factors | Cell identity and fate specification |
| Surface Markers | Cell sorting and flow cytometry |
| Functional Markers | Specialized cellular function |
| Maturation Markers | Developmental stage |
Pluripotent Stem Cells
| Marker | Type | Function |
|---|---|---|
| OCT4 (POU5F1) | TF | Pluripotency |
| SOX2 | TF | Stemness |
| NANOG | TF | Self-renewal |
| LIN28A | RNA-binding | Stem cell maintenance |
| TRA-1-60 | Surface | Undifferentiated cells |
| TRA-1-81 | Surface | Undifferentiated cells |
| SSEA-4 | Surface | Human PSC marker |
| EPCAM | Surface | Epithelial marker |
Recommended Panel
- OCT4
- SOX2
- NANOG
- TRA-1-60
Neural Stem Cells (NSCs)
| Marker | Function |
|---|---|
| Nestin | Neural stem cell marker |
| SOX2 | Stemness |
| PAX6 | Neural commitment |
| Musashi-1 (MSI1) | Neural progenitor marker |
| FABP7 (BLBP) | Radial glia-like cells |
| Vimentin | Immature neural cells |
Recommended Panel
- Nestin
- SOX2
- PAX6
Neural Progenitor Cells (NPCs)
| Marker | Function |
|---|---|
| Nestin | Neural progenitor |
| SOX2 | Stemness |
| PAX6 | Neuroectoderm |
| Musashi-1 | Neural progenitor |
| ZO-1 | Neural rosettes |
| N-Cadherin | Neural epithelium |
| PLZF | Rosette marker |
| Ki67 | Proliferation |
Recommended Panel
- Nestin
- SOX2
- PAX6
- Ki67
Neurons
Pan-Neuronal
| Marker | Function |
|---|---|
| βIII-Tubulin (Tuj1) | Early neuron |
| MAP2 | Dendrites |
| NeuN (RBFOX3) | Mature neurons |
| Synaptophysin | Presynaptic protein |
| PSD95 | Postsynaptic protein |
Recommended Panel
- Tuj1
- MAP2
- NeuN
Cortical Neurons
TBR1 • CTIP2 (BCL11B) • SATB2 • BRN2
Dopaminergic Neurons
FOXA2 • LMX1A • NURR1 • TH • DAT • VMAT2
Motor Neurons
HB9 (MNX1) • ISL1 • ChAT • SMI32
GABAergic Neurons
GAD65 • GAD67 • VGAT
Astrocytes
| Marker | Function |
|---|---|
| GFAP | Intermediate filament |
| S100β | Calcium-binding protein |
| ALDH1L1 | Pan-astrocyte marker |
| AQP4 | Water channel |
| EAAT1 (GLAST) | Glutamate transporter |
| EAAT2 (GLT-1) | Glutamate transporter |
| Connexin-43 | Gap junction protein |
Recommended Panel
- GFAP
- ALDH1L1
- S100β
Microglia
| Marker | Function |
|---|---|
| TMEM119 | Homeostatic microglia |
| P2RY12 | CNS-specific microglia |
| CX3CR1 | Chemokine receptor |
| TREM2 | Phagocytosis regulation |
| IBA1 (AIF1) | Pan-microglial marker |
| CD11b | Myeloid marker |
| CD68 | Activated microglia |
Recommended Panel
- IBA1
- TMEM119
- P2RY12
Disease-Associated Microglia (DAM)
APOE • TREM2 • CST7 • LPL • ITGAX (CD11c)
Oligodendrocyte Lineage
OPCs
NG2 (CSPG4) • PDGFRα • Olig2 • NKX2.2
Recommended Panel
- NG2
- PDGFRα
- Olig2
Mature Oligodendrocytes
MBP • PLP1 • MOG • MAG
Recommended Panel
- MBP
- PLP1
- MOG
Schwann Cells
SOX10 • S100β • MPZ • PMP22
Recommended Panel
- SOX10
- MPZ
Endothelial Cells
CD31 (PECAM1) • VE-Cadherin (CDH5) • vWF • KDR (VEGFR2)
Blood-Brain Barrier
Claudin-5 • Occludin • ZO-1 • GLUT1
Recommended Panel
- CD31
- VE-Cadherin
- vWF
Pericytes
PDGFRβ • NG2 • CD146 • Desmin
Recommended Panel
- PDGFRβ
- NG2
- CD146
Hepatocytes
Albumin (ALB) • HNF4α • CYP3A4 • CYP2E1 • SERPINA1 (AAT)
Recommended Panel
- Albumin
- HNF4α
- CYP3A4
Mesenchymal Stem Cells (MSCs)
Positive Markers
CD73 • CD90 • CD105
Negative Markers
CD34 • CD45 • CD14 • HLA-DR
ISCT Recommended Panel
- CD73+
- CD90+
- CD105+
- CD34−
- CD45−
Hematopoietic Stem Cells (HSCs)
CD34 • CD90 • CD49f • CD38^low
Recommended Panel
- CD34
- CD90
- CD49f
Common Flow Cytometry Panels
| Cell Type | Suggested Panel |
|---|---|
| Human PSCs | TRA-1-60, TRA-1-81, SSEA-4 |
| NSCs | Nestin, SOX2, PAX6 |
| NPCs | Nestin, SOX2, Ki67 |
| Astrocytes | GFAP, ALDH1L1, S100β |
| Microglia | CD11b, TMEM119, P2RY12 |
| OPCs | PDGFRα, NG2, O4 |
| Endothelial Cells | CD31, VE-Cadherin, vWF |
| MSCs | CD73, CD90, CD105 |
Common scRNA-seq Marker Sets
| Cell Type | Representative Genes |
|---|---|
| Neurons | RBFOX3, MAP2, SNAP25, SYT1 |
| Astrocytes | GFAP, AQP4, ALDH1L1, SLC1A3 |
| Microglia | TMEM119, P2RY12, CX3CR1, AIF1 |
| Oligodendrocytes | MBP, PLP1, MOG, MOBP |
| OPCs | PDGFRA, CSPG4, OLIG1, OLIG2 |
Important Marker Caveats
| Marker | Limitation |
|---|---|
| GFAP | Also expressed in radial glia, reactive astrocytes and some NSCs |
| IBA1 | Also labels macrophages and activated monocytes |
| Nestin | Present in multiple neural progenitor populations |
| SOX2 | Shared by pluripotent stem cells and neural stem cells |
| CD11b | Not specific for microglia |
Always validate cell identity using multiple complementary markers and, where appropriate, functional assays.
References
- Zhang Y et al. Purification and characterization of progenitor and mature human astrocytes. Neuron (2016).
- Abud EM et al. iPSC-derived microglia models. Neuron (2017).
- Sloan SA et al. Human astrocyte maturation. Neuron (2017).
- Darmanis S et al. A survey of human brain transcriptome diversity. PNAS (2015).