Adipocytes differentiate from mesenchymal stem cells and compose adipose tissue. Three classes of transcription factor are known to directly influence adipocyte development. These include PPARγ, C/EBPs, and the basic helix–loop–helix family (ADD1/SREBP1c) [1]. There are two types of adipocytes: white, beige and brown adipose tissue. White adipose tissue maintains energy metabolism by storing energy as lipids. Brown adipose tissue (BAT) is a key site of thermogenesis in mammals. Mitochondria in brown adipocytes contain uncoupling protein-1 (UCP1). UCP1-expressing adipocytes, developed in white adipose tissue (WAT), have been named beige adipocytes [2].

Adipose tissue can be stained by perilipin [3]. A number of specific marker genes have been identified for different types of adipocytes. Gene markers such as leptin, HOXC8 and HOXC9 are specific for white adipocytes [4]. Brown adipocytes express Ucp1 [2]. Other important markers of brown adipocytes include CIDEA, and PRDM16 [4], Zic1 [5], Lhx8 [5], Eva1 [6] and Epsti1 [7] and the beige markers include Cd137 [6], Tmem26 [6], Tbx1 [6], Cited1 [7] and Shox2 [8].

Beige adipocytes express a unique gene expression profile. Beige adipocytes express the following markers: Cd137 [6], Tmem26 [6], Tbx1 [6], Cited1 [7] and Shox2 [8], TBX1 and TMEM26 [4]. Beige cell surface proteins CD137 or TMEM26 can be used to identify primary beige fat cell precursors [6].

A recent article reports that amino acid transporter ASC-1, amino acid transporter PAT2, and purinergic receptor P2RX5 are cell surface markers for white, beige, and brown adipocytes, respectively [9]. Flaherty SE et al used ATGL and FABP4 as adipocyte markers [10].

Endothelial cells form the interior surface of all blood vessels, from largest arterias and veins to capillaries. A large number of exclusive and non-exclusive endothelial markers have been identified.

Exclusive endothelial cell markers include von Willebrand factor [11], vascular endothelial cadherin (VE-cadherin, CD144) [12], thrombomodulin (CD141) [13] and Pathologische Anatomie Leiden-endothelium (PAL-E) [14]. Importantly, PAL-E as a specific marker for vascular endothelium, is used to distinguish between vascular and lymphatic endothelium. Other markers distinguishing lymphatic endothelial cells from vascular ones include Lyve-1 [15], Prox1 [15], podoplanin (also a marker for mesothelia [16] ), and vascular endothelial growth factor receptor 3 (VEGFR3) [15, 17, 18]. Double immunostaining for D2-40 podoplanin/CD31 and for PROX1/CD31 was found to distinguishing lymphatic vs. venous blood vessels in dura samples [19]. Besides, MECA-79 and the Daffy antigen receptor for chemokines (DARC) were shown to be highly specific for endothelial cells [11]. H Hu et al stained endothelial cells in human mature arteriovenous fistulae with the Abcam antibody against VWF ( ab11713). Gur-Cohen S et al used endomucin as the marker for blood capillaries [15]. Gifford CA et al labeled endothelial cells in mouse hearts with endomucin [20].

Non-exclusive endothelial specific markers include CLEC4G [21], platelet/EC adhesion molecule-1 (PECAM-1, CD31) [22, 23], transglutaminase 2 / tissue transglutaminase / TG2 [24], vascular endothelial growth factor receptors (VEGFRs): VEGF R1 (Flt-1), VEGF R2 (KDR/Flk-1), and VEGF R3, CD146 (MUC-18, S-endo), UEA-1 (Ulex europaeus I agglutinin), eNOS (endothelial nitric oxide synthase), and Griffonia simplicifolia isolectin B4 (IsoB4). IsoB4 can be delivered in vivo to identify vascular endothelial cells [25, 26].

Other markers, which are important for the activation of endothelial cells, include CD146 (MUC-18, S-endo), thrombomodulin (CD141), ICAM-1 (intercellular adhesion molecule, CD54), E-selectin (CD62E) [27], and apelin [28].

Epithelial cells (EpC) originate from all embryonic germ layers (ectoderm, endoderm and mesoderm). Epidermal cells have ectodermal origin. Predominant epidermal cells are keratinocytes, which differentiate from epidermal stem cells. There are a large number of subtype-specific epithelial markers.

Keratines (K) are keratin-containing proteins detected in the cytoplasm of EpCs [31-33]. There are acidic type I and basic type II Ks. Keratins 1-3 are expressed by squamous EpCs. The expression of K5 and K6 are specific for mesothelial cells (also podoplanin [16] ) and K7 for ductal and glandular EpCs. K8 is expressed in EpCs of gastrointestinal tract (including stomach, colon, small intestine, gall bladder, liver, pancreas) and mammary gland ducts [34]. EpCs of skin, keratinocytes, express the following specific markers: keratins 1, 5, 10, 14, 15 and 16. K10 is expressed in suprabasal layer of squamous epithelia. K18 serves as a marker of proliferating malignant EpCs [35]. K Yoshida et al isolated bronchial epithelial cells through flow cytometry using EpCAM as a marker [36].

Other markers of EpCs include E-cadherin, epithelial membrane antigen (EMA, CD227, MUC-1) (expressed by most secretory EpCs), epithelial sodium channels α, β, γ, δ, prostate-specific antigen (PSA) (expressed by prostate EpCs), surfactant protein A-D (expressed by pulmonary epithelia, pro-surfactant protein C as a marker for type II alveolar epithelial cells [43] ), survivin (cells of epithelial carcinoma). Also, they express the receptors for the Fc part of the IgG (FcR), integrin molecules: VLA-1, 2, 3, 4, 5, 6, adhesion molecules LFA-1, LFA-2, ICAM-1 [1548035). The cells, forming the lining of the gastrointestinal tract, develop from endoderm. The lining of body cavities develops from mesoderm.

Tuft cells (also called brush cells) are a specialized type of epithelial cells able to use taste receptors and other surface proteins to detect pathogens. They are found in digestive and respiratory tracts. Both structural components (villin, fimbrin, α- or β-tubulin, Ac-tubulin, ankyrin, CK-18, neurofilaments, Dclk1) and taste cell-related proteins (α-gustducin, Trpm5, T1R1/T1R3) can serve as markers, in addition to Ptgs1, Ptgs2, H-Pgds, UEA1 lectin and Sox9 [44]. Wilen CB et al used DCLK1 and CK18 to identify Tuft cells in mouse ileum and colon [42]. Miller CN et al transcriptionally profiled a subset of thymic cells and found them to be similar to intestinal Tuft cells and confirmed the expression of KRT18/8 and DCLK1 among these thymic Tuft cells [37]. Nadjsombati MS et al used DCLK1 as a marker in the mouse small intestinal Tuft cells [38]. Lei W et al used DCLK1 staining as well to identify Tuft cells in mouse jejunum tissues [45].

Dendritic cells (DC) have the key role in adaptive immunity inducing antigen-specific immunity. Regarding both functions and localization, DCs can be classified into three subsets: conventional, plasmacytoid and dermal (skin located) DCs [46].

Conventional DCs reside in lymph nodes, spleen and thymus. In mice, conventional DCs can be divided into CD8+ (with phenotypes CD8+CD205+SIRPa-CD11b- in spleen and CD11chi MHCII+ CD8+ CD205+ in lymph nodes) and CD8- DCs [47]. These cells activate T cells toward Th1 and Th2 differentiation respectively.

Plasmacytoid DCs (pDC) belong to the second DC subset, which reside in lymph nodes, spleen, thymus and bone marrow. Human pDCs mature in the bone marrow and play specific role in anti-viral immunity by secreting anti-viral and pro-inflammatory cytokines including IFNs, TNFα, IL-6 and IL-12. These cells are composed of two subsets: CD2high and CD2low pDCs. Both human and murine pDCs express the following markers: B220/CD45R, CD11c [48], TLR7 and TLR9, IRF7, IRF8 [49] and BDCA2 [50].

The third subset of DCs is located in skin and develops from myeloid lineage. There are two distinct subgroups of the skin DCs: epidermal Langerhans cells (LCs) and dermal DCs. LCs are identified by the presence of Langerin-containing Birbeck granules and expression of the following markers: CD1a, CD45. In addition, among dermal DCs two subpopulations have been identified: CD103+ CD11blow Langerin+ and CD103- CD11bhi Langerin- DCs [51]. Dermal DCs also express CD14. Mature DCs also express CD1a, CD1b and CD1c molecules, which present lipid and glycolipid antigens to CD1/restricted T cells [52].

Several factors regulating differentiation of DCs have been identified. Human CD14+ monocytes differentiate into DCs when cultured with GMC-SF+ IL4 [53]. Also, human CD34+ cells can differentiate into DCs when cultured with GMC-SF + TNF [54]. Mouse bone marrow cells cultured with GMCSF+ TNF+ stem cell factor (SCF] can differentiate into DCs [55].

There are other DC markers which have different degree of specificity. CD83 is a specific marker of mature DCs [56]. CD21 and clusterin are markers of follicular DCs [57, 58]. In addition, DCs express: ADAM19 [59], CD86 [60], DC-LAMP (CD208] [61, 62], DC-SIGN (CD209) [63], DEC-205 [64], CLIP-170/restin [65], NLDC-145 [66]. MADDAM (metalloprotease and disintegrin dendritic antigen marker) is a marker of DC differentiation [67].

Glial cells are the cells located in the nervous system which provide protection and nutrition for the neurons, regulate migration of neurons in early development, communications between neurons and neurotransmitter release. The glial cell lineage includes microglia and macroglia. Microglia are extensively discussed in Labome's article Macrophage Markers.

Macroglia consists of astrocytes, oligodendrocytes, ependymal cells, radial glia, Schwann cells, satellite cells and enteric glial cells. Astrocytes are classified into type 1 astrocytes (Ran2+, GFAP+, FGFR3+, A2B5-) and type 2 astrocytes (A2B5+, GFAP+, FGFR3-, Ran 2-). There are two main groups of Schwann cells: myelinating (specific markers: proteins S-100, Myelin protein zero (P-Zero) and Myelin basic protein (MBP)) and non-myelinating (specific markers: S-100 and Glial fibrillary acidic protein (GFAP)). Precursors of oligodendrocytes express platelet-derived growth factor (PDGF) receptors, which bind PDGF [70]. Ependymal cells express S-100, vimentin, GFAP, BLBP, 3A7 and 3CB2 [71]. Schwann cells are the main glial cells of the peripheral nervous system. Specific markers for identification of Schwann cells are S-100, myelin basic protein (MBP) and myelin protein zero (MPZ). Satellite cells provide support for neurons in peripheral nervous system and express CD45 and markers of myeloid lineage CD14, CD68, and CD11b [72]. The specific markers for enteric glial cells include: S-100 protein, the neurofilament protein and the protein gene product 9.5 (PGP) [73]. Nott A et al isolated oligodendrocyte nuclei from human brain tissues through FANS with an antibody against OLIG2 and astrocyte nuclei with an antibody against LHX2 [74].

Bone marrow contains hematopoietic stem cells (HSC) which give raise to three main classes of blood cells: leukocytes, erythrocytes and thrombocytes. The main phenotype of human HSCs is: CD34+, CD38low/-, CD59+, Thy1+, c-Kit+, Lin-. Mouse HCSs can be identified as: CD34low/-, CD38+, Thy1+/low, SCA-1+, c-Kit+, Lin-. The other markers expressed by HSCs are: CD90, CD93, CD105, CD110, Ly-6A/E (Sca-1), CD111, CD135 (Flk-2), CD150 (SLAM), CD184 (CXCR4), CD202b, CD243 (MDR-1), CD271 (NFGR), CD309 (VEGFR2) and CD338 [75].

The main processes of differentiation in bone marrow include myelopoiesis, erythropoiesis and megakaryocyte lineage development. In the process of myelopoiesis the following cell types are generated: granulocytes, monocytes and mast cells. There are three different types of granulocytes generated in the bone marrow: eosinophils, basophils and neutrophils. Eosinophils differentiate from bone marrow in response to IL-3, IL-5 and GM-CSF [76-78]. Both mouse and human neutrophils express the following markers: Ly-6G [79, 80], CD11b [80], FcεRI, CD123, CD49b / DX-5, CD69, Thy-1.2, 2B4. Specific surface marker for monocytes is CD14 (CD14+ cells). ElTanbouly MA et al obtained mouse neutrophils as CD11b+ Ly6G+ Ly6C−, and monocytes as CD11b+ Ly6C+ Ly6G− [80]. Markers constantly expressed by bone marrow mast cells include: CD9, CD29, CD33, CD43, CD44, CD49d, CD49e, CD51, CD71, CD117, and Fc(epsilon)RI [81].

Natural Killer (NK) cells play the important role in immune response against malignant and infected cells. During NK lineage development, human NK cells pass through five main stages of differentiation. During these five stages NK cells express distinct sets of markers: 1) CD34+ CD45RA+ CD117− CD161− CD94−; 2) CD34+ CD45RA+ CD117+ CD161+/− CD94−; 3) CD34− CD117+ CD161+ NKp46− CD94−; 4) CD34− CD117+/− NKp46+ CD94+ CD16− CD56bright; 5) CD34− CD117− NKp46+ CD94+/− CD16+ CD56dim [82]. There are two major populations of human blood NK cells which are defined on the basis of the surface expression intensity of CD56 [83, 84] and the low-affinity Fc receptor CD16 [85]. A larger population of CD56dim NK cells (∼90%) expresses high levels of CD16, whereas a minor subset of CD56bright NK cells expresses limited CD16.

In contrast to human NK cells, murine NK cellular subsets can be distinguished from each other by the expression of CD27 and CD11b markers. These subsets include immature CD11b- NK cells, CD27+ NK cells and mature (terminal) CD27-CD11b+ NK cells. NK cells can be activated by several interleukins: IL-12, IL-2, IL-15, IL-18. Also, NK cells express receptors for CXC, CC and C chemokines, which are important for the regulation of NK functions [86]. In addition, NK cells express receptors recognizing MHC class I molecules (human KIRs, the rodent Ly49 and CD94/NKG2), NKp46, FcgRII and non-MHC-binding NK receptors (NKR-P1 (CD161)) [87], natural cytotoxicity receptors (NCR) and 2B4) [88], NKG2A and NKp80 [89], CD107a - a functional marker NK cell activity [90], CD69 - NK cell activation marker [87], CD335/NKp46 [91], BAT [92], CD57/HNK1 [93], NKH1 (N901) [94], DPIV (dipeptidyl peptidase IV) - a surface marker of NK cells [95], H25 [96].

The following discusses markers for less commonly studied cell types.

L Pellegrini et al used TTR / transthyretin, CLIC6 and HTR2C as markers for choroid plexus [98].

Pericentriolar material 1 (PCM1) and cTroponins I and T can be used to label cardiomyocyte nuclei [99, 100]. Connexin 43 (cx43) is also a good marker for cardiomyocytes [101]. Wheat germ agglutinin lectin can label cardiomyocyte fibrosis [99, 102]. MF20 from DSHB, an antibody against sarcomeric isoforms of myosin heavy chain, can stain cardiomyocyte differentiation [103].

Enterocytes, or intestinal absorptive cells, are a type of epithelial cells response for the absorption of water, ions, and other nutrients in the small intestines. AldolaseB is commonly used as their marker [104].

T Yokota et al labeled fibroblasts with vimentin [105]. H Qian et al, on the other hand, used fibronectin as a marker for fibroblasts [106].

Germ cells include specific cell types involved in reproduction. They include gametes (the sperm and eggs) and gonocytes regulating the production of gametes. The specific markers of germ cells include 4C9 [107], GCNA1 (germ cell nuclear antigen 1, GCNA-1) [108, 109], DAZ-like 1(DAZL1) [110], VASA [111], ZAR1 (zygotic arrest 1) [108], TEX101 [112]. In addition, RBM (RNA-binding motif) [113] and tesmin [114].

Granulosa cells form a barrier around ovarian oocyte follicles. As the follicles mature, the granulosa cells multiply to form many layers around the oocyte. Granulosa cells produce estradiol before ovulation and secrete progesterone after ovulation. The main markers of granulose cells are AMH (anti-mullerian hormone) [115], Follicle regulatory protein (FRP) [116], inhibin [117, 118], MCAM (Melanoma cell adhesion molecule, CD146) [119], fibronectin [120].

Hepatocytes are the parenchymal cells of liver. Aizarani N et al used HP and ASGR1 as markers for hepatocytes to build a human liver atlas using single-cell RNA-seq [21].

Jurkat cells are the cells of CD4+ T cell leukemia line. These cells express specific markers of T cells including CD3, CD4, CD45 [121] and produce interleukin-2 (IL-2). In addition, Jurkat cells express chemokine receptors CCR1-10 and CXCR4.

Large luteal cells are located in the corpus luteum and produce progesterone and oxytocin. They are derived from granulose cells. Markers of large luteal cells include CYP11A1 [122], luteinizing hormone receptor [123], phosphorylated Akt [124].

Mast cells are granulated cells of hematopoietic origin found in most tissues. Mast cells contain large amount of granules rich in histamine and heparin and play an important role in allergy and anaphylaxis. Specific markers of mast cells are tryptase [125], high affinity IgE receptor [126], CD25 [126], CD45 [127], CD23 [126], CD117 (c-Kit) [41, 127] and CD203c [126].

Neuroendocrine cells are activated by neurotransmitters and release hormones. Ouadah Y et al used CGRP as a marker for pulmonary neuroendocrine cell marker [128].

Paneth cells are one of the main cell type of the small intestine epithelium. They are part of the immune defence system, since they synthesize and secrete antimicrobial peptides and proteins and lysozyem. Lysozyme is commonly used as their marker [104].

Pericytes, located around the capillaries and venules, help maintain homeostatic and hemostatic functions. F Binet et al labeled mouse retinal vascular pericytes with NG2 [25]. Nortley R et al labeled pericytes with antibodies against platelet-derived growth factor receptor beta and NG2/CSPG4, and outlined the pericyte basement membrane with fluorescently-tagged isolectin B4 [129].

Purkinje cells are a subtype of neuronal cells located in cerebellar cortex. Specific markers of Purkinje cells include cGMP-dependent protein kinase [130], guanosine 3':5'-phosphate-dependent protein kinase [131], zebrin I and zebrin II - Purkinje cell-specific markers [132-134], Car8 [135], HFB-16 (KIAA0864 Protein) [136], inositol 1, 4, 5-triphosphate receptors (IP3R) [137-139].

Pyramidal cells are neurons located in several different regions of central nervous system such as cerebral cortex, hippocampus and amygdala. They are suggested to play an important role in cognitive functions. Specific markers of pyramidal cells include CaMK (calcium/calmodulin-dependent protein kinase II, CaMKII) [140], neurogranin/RC3 [141, 142], SMI-32 [143-145], MATH-2 [146], SCIP [146, 147], Emx1 [148].

Retinal ganglion cells are the output neurons in retina. Ganglion cells acquire information about the visual world and transfer it through optical nerve to brain visual centers. Specific markers of retinal ganglion cells include RBPMS [149], NGF, NSCL2 [150], PKC, Hu, and Brn3b [151].

Glial cells are the cells located in the nervous system which provide protection and nutrition for the neurons, regulate migration of neurons in early development, communications between neurons and neurotransmitter release. Schwann cells are the main glial cells of the peripheral nervous system. Schwann cells wrap themselves around neurve axons. In addition, Schwann cells play an important role in removing debris and in the regrowth of nerve axons. Specific markers for identification of Schwann cells are S-100 [152], myelin basic protein (MBP) [153] and myelin protein zero (MPZ).

Sertoli cell have an important role in the mechanisms of spermatogenesis. In addition, Sertoli cell control the transport of hormones into the seminiferous tubules. Specific markers of Sertoli cells include ABP (androgen-binding protein) [154], Dhh (Desert hedgehog) [155], GATA-1 [156].

Y Shwartz et al labelled the arrector pili muscle with integrin alpha 8 or smooth muscle actin [157]. H Hu et al stained smooth muscle cells in human mature arteriovenous fistulae with the Abcam antibody against alpha actin ( ab5694) [30].