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Microglia markers

We've pulled together the most common markers for astrocytes from recent literature, so you can quickly identify the suitable marker for your experiment.
Last edited Mon 10 Oct 2022

What are microglia?

Microglia are specialized macrophages in the brain and spinal cord. They play various roles in brain development and aging but most commonly function as the innate immune cells of the central nervous system (CNS). 

Due to the shared lineage of microglia and macrophages, many markers are common to both cell types. 


TMEM119 is a cell-surface protein, which is a specific microglial marker in both mouse and human samples. This marker isn’t expressed by macrophages or any other immune or neural cell types, so it has a huge advantage over other microglial markers. Browse all TMEM119 antibodies.

Mouse brain tissue sections stained with anti-TMEM119 (green) (ab209064).

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View 2 references for TMEM119

CD11b and CD45

A combination of CD11b and CD45 labeling can be used to distinguish microglia from macrophages. Resting microglia are CD11bhi, CD45low, whereas macrophages are CD11bhi, CD45hi.

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Mouse tissue (Eo771 breast cancer) stained with anti-CD11b (green) (ab133357).

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View 4 references for CD11b and CD45


Ionized calcium-binding adaptor molecule 1 (Iba1) is a microglial and macrophage-specific calcium-binding protein involved with membrane ruffling and phagocytosis in activated microglia.

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Mouse cerebral cortex tissue sections stained with anti-Iba1 (green) (ab178846).

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CX3CR1 is the fractalkine receptor found on the surface of both microglia and macrophages in the CNS, where it responds to CX3CL1 (fractalkine) secreted by neurons.

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Flow cytometric analysis of human peripheral blood mononuclear cells stained with anti-CX3CR1 (right) (ab245248) compared with a Rabbit monoclonal IgG (ab172730) isotype control (left).

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F4/80 is a 160 KDa glycoprotein found on the surface of macrophages and resting microglia.

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Mouse liver tissue sections stained with anti-F4/80 [SP115] (ab111101).

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CD68 is a lysosomal protein expressed in high levels by macrophages and activated microglia and in low levels by resting microglia.

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Human cervical carcinoma tissue sections stained with anti-CD68 (ab213363).

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CD40 is a cell surface molecule necessary for antigen presentation and is expressed by activated microglia and macrophages.

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Human diffuse large B-cell lymphoma tissue sections stained with anti-CD40 (ab224639).

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View 2 references for CD40