Marker Name Cell Type
Blood Vessel Fetal liver kinase-1 (Flk1) Endothelial Cell-surface receptor protein that identifies endothelial cell progenitor;
marker of cell-cell contacts
Smooth muscle cell-specific Smooth muscle
myosin heavy chain
Vascular endothelial cell cadherin
Bone
Bone-specific alkaline
phosphatase (BAP)
Hydroxyapatite Osteoblast Minerlized bone matrix that provides structural integrity; marker of bone formation
Osteocalcin (OC) Osteoblast Mineral-binding protein uniquely synthesized by osteoblast; marker of
bone formation
Bone Marrow and Blood
Bone morphogenetic
protein receptor (BMPR) Mesenchymal stem and progenitor cells Important for the differentiation of committed mesenchymal cell types from mesenchymal stem and progenitor cells; BMPR identifies early
mesenchymal lineages (stem and progenitor cells)
CD4 and CD8 White blood cell (WBC) Cell-surface protein markers specific for mature T lymphocyte (WBC
subtype)
CD34 Hematopoietic stem cell Cell-surface protein on bone marrow cell, indicative of a HSC and
(HSC), satellite,
endothelial progenitor
CD34+Sca1+ Lin- profile Mesencyhmal stem cell
(MSC)
CD38 Absent on HSC Present on WBC lineages
CD44 Mesenchymal A type of cell-adhesion molecule used to identify specific types of
mesenchymal cells
c-Kit HSC, MSC Cell-surface receptor on BM cell types that identifies HSC and MSC;
binding by fetal calf serum (FCS) enhances proliferation of ES cells,
HSCs, MSCs, and hematopoietic progenitor cells
Colony-forming unit (CFU) HSC, MSC progenitor CFU assay detects the ability of a single stem cell or progenitor cell to
give rise to one or more cell lineages, such as red blood cell (RBC)
and/or white blood cell (WBC) lineages endothelial progenitor; CD34 also identifies muscle satellite, a muscle stem cell Identifies MSCs, which can differentiate into adipocyte, osteocyte, chondrocyte, and myocyte Cell-surface molecule that identifies WBC lineages. Selection of CD34+/CD38- cells allows for purification of HSC populations Osteoblast Enzyme expressed in osteoblast; activity indicates bone formation Smooth muscle Identifies smooth muscle cells in the wall of blood vessels Identifies smooth muscle cells in the wall of blood vessels Significance
Marker Name
Fibroblast colony-forming unit (CFU-F) Cell Type Bone marrow fibroblast Significance An individual bone marrow cell that has given rise to a colony of multipotent fibroblastic cells; such identified cells are precursors of
differentiated mesenchymal lineages
Hoechst dye Absent on HSC Fluorescent dye that binds DNA; HSC extrudes the dye and stains
lightly compared with other cell types
Leukocyte common antigen WBC
(CD45)
Lineage surface antigen
(Lin)
Differentiated RBC and
WBC lineages
Mac-1 WBC Cell-surface protein specific for mature granulocyte and macrophage
(WBC subtypes)
Muc-18 (CD146) Bone marrow fibroblasts, Cell-surface protein (immunoglobulin superfamily) found on bone
endothelial marrow fibroblasts, which may be important in hematopoiesis; a
subpopulation of Muc-18+ cells are mesenchymal precursors
Stem cell antigen (Sca-1) HSC, MSC Cell-surface protein on bone marrow (BM) cell, indicative of HSC and
MSC Bone Marrow and Blood cont.
Stro-1 antigen Stromal (mesenchymal) Cell-surface glycoprotein on subsets of bone marrow stromal
precursor cells,
hematopoietic cells (mesenchymal) cells; selection of Stro-1+ cells assists in isolating mesenchymal precursor cells, which are multipotent cells that give rise to adipocytes, osteocytes, smooth myocytes, fibroblasts,
chondrocytes, and blood cells
Thy-1 HSC, MSC Cell-surface protein; negative or low detection is suggestive of HSC
Cartilage
Collagen types II and IV
Keratin
Sulfated proteoglycan Chondrocyte Keratinocyte Chondrocyte Structural proteins produced specifically by chondrocyte Principal protein of skin; identifies differentiated keratinocyte Molecule found in connective tissues; synthesized by chondrocyte
Fat Adipocyte lipid-binding
protein (ALBP)
Fatty acid transporter (FAT) Adipocyte
Adipocyte lipid-binding
protein (ALBP)
General Adipocyte Transport molecule located specifically in adipocyte Lipid-binding protein located specifically in adipocyte Adipocyte Lipid-binding protein located specifically in adipocyte HSC, MSC Thirteen to 14 different cell-surface proteins that are markers of mature blood cell lineages; detection of Lin-negative cells assists in the purification of HSC and hematopoietic progenitor populations Cell-surface protein on WBC progenitor
Marker Name
Y chromosome Cell Type Male cells Significance Male-specific chromosome used in labeling and detecting donor cells in female transplant recipients
Karyotype Most cell types Analysis of chromosome structure and number in a cell
Liver
Albumin Hepatocyte Principal protein produced by the liver; indicates functioning of
maturing and fully differentiated hepatocytes B-1 integrin Hepatocyte Cell-adhesion molecule important in cell-cell interactions; marker
expressed during development of liver
Nervous System
CD133 Neural stem cell, HSC Cell-surface protein that identifies neural stem cells, which give rise to neurons and glial cells
Glial fibrillary acidic protein Astrocyte
(GFAP)
Microtubule-associated
protein-2 (MAP-2)
Myelin basic protein (MPB) Oligodendrocyte Neuron Dendrite-specific MAP; protein found specifically in dendritic branching of neuron Protein produced by mature oligodendrocytes; located in the myelin
sheath surrounding neuronal structures
Nestin Neural progenitor Intermediate filament structural protein expressed in primitive neural tissue
Neural tubulin Neuron Important structural protein for neuron; identifies differentiated
neuron
Neurofilament (NF) Neuron Important structural protein for neuron; identifies differentiated neuron
Neurosphere Embryoid body (EB), ES Cluster of primitive neural cells in culture of differentiating ES cells;
indicates presence of early neurons and glia
Noggin O4
O1
Synaptophysin Neuron Oligodendrocyte Oligodendrocyte Neuron A neuron-specific gene expressed during the development of neurons Cell-surface marker on immature, developing oligodendrocyte Cell-surface marker that characterizes mature oligodendrocyte Neuronal protein located in synapses; indicates connections between
neurons
Tau Neuron Type of MAP; helps maintain structure of the axon Pancreas
Cytokeratin 19 (CK19) Pancreatic epithelium CK19 identifies specific pancreatic epithelial cells that are progenitors
for islet cells and ductal cells Protein specifically produced by astrocyte
Marker Name Cell Type Significance
Glucagon Pancreatic islet Expressed by alpha-islet cell of pancreas
Insulin Pancreatic islet Expressed by beta-islet cell of pancreas Pancreas
Transcription factor expressed by beta-islet cell of pancreas Insulin-promoting factor-1 Pancreatic islet (PDX-1)
Nestin Pancreatic progenitor Structural filament protein indicative of progenitor cell lines including
pancreatic
Pancreatic polypeptide
Somatostatin Pancreatic islet Pancreatic islet Expressed by gamma-islet cell of pancreas Expressed by delta-islet cell of pancreas
Pluripotent Stem Cells
Alkaline phosphatase Embryonic stem (ES),
embryonal carcinoma
(EC) Elevated expression of this enzyme is associated with undifferentiated pluripotent stem cell (PSC)
Alpha-fetoprotein (AFP) Endoderm Protein expressed during development of primitive endoderm; reflects
endodermal differentiation Pluripotent Stem Cells
Bone morphogenetic
protein-4
Brachyury Mesoderm Growth and differentiation factor expressed during early mesoderm formation and differentiation Mesoderm Transcription factor important in the earliest phases of mesoderm
formation and differentiation; used as the earliest indicator of
mesoderm formation
Cluster designation 30
(CD30)
Cripto (TDGF-1) ES, EC Surface receptor molecule found specifically on PSC ES, cardiomyocyte Gene for growth factor expressed by ES cells, primitive ectoderm, and
developing cardiomyocyte
GATA-4 gene
GCTM-2 Endoderm ES, EC Expression increases as ES differentiates into endoderm Antibody to a specific extracellular-matrix molecule that is synthesized
by undifferentiated PSCs
Genesis ES, EC Transcription factor uniquely expressed by ES cells either in or during
the undifferentiated state of PSCs
Germ cell nuclear factor ES, EC Transcription factor expressed by PSCs
Transcription factor expressed early in endoderm formation Hepatocyte nuclear factor-4 Endoderm
(HNF-4)
Nestin Ectoderm, neural and
pancreatic progenitor
Neuronal cell-adhesion
molecule (N-CAM) Ectoderm Intermediate filaments within cells; characteristic of primitive neuroectoderm formation Cell-surface molecule that promotes cell-cell interaction; indicates primitive neuroectoderm formation
Marker Name
Oct-4 ES, EC Cell Type Significance Transcription factor unique to PSCs; essential for establishment and
maintenance of undifferentiated PSCs
Pax6 Ectoderm Transcription factor expressed as ES cell differentiates into
neuroepithelium
Stage-specific embryonic
antigen-3 (SSEA-3)
Stage-specific embryonic
antigen-4 (SSEA-4)
Stem cell factor (SCF or
c-Kit ligand) ES, EC, HSC, MSC ES, EC ES, EC Glycoprotein specifically expressed in early embryonic development and by undifferentiated PSCs Glycoprotein specifically expressed in early embryonic development and by undifferentiated PSCs Membrane protein that enhances proliferation of ES and EC cells, hematopoietic stem cell (HSCs), and mesenchymal stem cells (MSCs);
binds the receptor c-Kit
Telomerase ES, EC An enzyme uniquely associated with immortal cell lines; useful for
identifying undifferentiated PSCs
TRA-1-60 ES, EC Antibody to a specific extracellular matrix molecule is synthesized by
undifferentiated PSCs
TRA-1-81 ES, EC Antibody to a specific extracellular matrix molecule normally
synthesized by undifferentiated PSCs
Vimentin Ectoderm, neural and pancreatic progenitor Intermediate filaments within cells; characteristic of primitive neuroectoderm formation
Skeletal Muscle/Cardiac/Smooth Muscle
MyoD and Pax7 Myoblast, myocyte Transcription factors that direct differentiation of myoblasts into
mature myocytes Myogenin and MR4 Skeletal myocyte Secondary transcription factors required for differentiation of
myoblasts from muscle stem cells
Myosin heavy chain Cardiomyocyte A component of structural and contractile protein found in
cardiomyocyte
Myosin light chain Skeletal myocyte A component of structural and contractile protein found in skeletal
myocyte
Marker Name Cell Type
Blood Vessel Fetal liver kinase-1 (Flk1) Endothelial Cell-surface receptor protein that identifies endothelial cell progenitor;
marker of cell-cell contacts
Smooth muscle cell-specific Smooth muscle
myosin heavy chain
Vascular endothelial cell cadherin
Bone
Bone-specific alkaline
phosphatase (BAP)
Hydroxyapatite Osteoblast Minerlized bone matrix that provides structural integrity; marker of bone formation
Osteocalcin (OC) Osteoblast Mineral-binding protein uniquely synthesized by osteoblast; marker of
bone formation
Bone Marrow and Blood
Bone morphogenetic
protein receptor (BMPR) Mesenchymal stem and progenitor cells Important for the differentiation of committed mesenchymal cell types from mesenchymal stem and progenitor cells; BMPR identifies early
mesenchymal lineages (stem and progenitor cells)
CD4 and CD8 White blood cell (WBC) Cell-surface protein markers specific for mature T lymphocyte (WBC
subtype)
CD34 Hematopoietic stem cell Cell-surface protein on bone marrow cell, indicative of a HSC and
(HSC), satellite,
endothelial progenitor
CD34+Sca1+ Lin- profile Mesencyhmal stem cell
(MSC)
CD38 Absent on HSC Present on WBC lineages
CD44 Mesenchymal A type of cell-adhesion molecule used to identify specific types of
mesenchymal cells
c-Kit HSC, MSC Cell-surface receptor on BM cell types that identifies HSC and MSC;
binding by fetal calf serum (FCS) enhances proliferation of ES cells,
HSCs, MSCs, and hematopoietic progenitor cells
Colony-forming unit (CFU) HSC, MSC progenitor CFU assay detects the ability of a single stem cell or progenitor cell to
give rise to one or more cell lineages, such as red blood cell (RBC)
and/or white blood cell (WBC) lineages endothelial progenitor; CD34 also identifies muscle satellite, a muscle stem cell Identifies MSCs, which can differentiate into adipocyte, osteocyte, chondrocyte, and myocyte Cell-surface molecule that identifies WBC lineages. Selection of CD34+/CD38- cells allows for purification of HSC populations Osteoblast Enzyme expressed in osteoblast; activity indicates bone formation Smooth muscle Identifies smooth muscle cells in the wall of blood vessels Identifies smooth muscle cells in the wall of blood vessels Significance
Marker Name
Fibroblast colony-forming unit (CFU-F) Cell Type Bone marrow fibroblast Significance An individual bone marrow cell that has given rise to a colony of multipotent fibroblastic cells; such identified cells are precursors of
differentiated mesenchymal lineages
Hoechst dye Absent on HSC Fluorescent dye that binds DNA; HSC extrudes the dye and stains
lightly compared with other cell types
Leukocyte common antigen WBC
(CD45)
Lineage surface antigen
(Lin)
Differentiated RBC and
WBC lineages
Mac-1 WBC Cell-surface protein specific for mature granulocyte and macrophage
(WBC subtypes)
Muc-18 (CD146) Bone marrow fibroblasts, Cell-surface protein (immunoglobulin superfamily) found on bone
endothelial marrow fibroblasts, which may be important in hematopoiesis; a
subpopulation of Muc-18+ cells are mesenchymal precursors
Stem cell antigen (Sca-1) HSC, MSC Cell-surface protein on bone marrow (BM) cell, indicative of HSC and
MSC Bone Marrow and Blood cont.
Stro-1 antigen Stromal (mesenchymal) Cell-surface glycoprotein on subsets of bone marrow stromal
precursor cells,
hematopoietic cells (mesenchymal) cells; selection of Stro-1+ cells assists in isolating mesenchymal precursor cells, which are multipotent cells that give rise to adipocytes, osteocytes, smooth myocytes, fibroblasts,
chondrocytes, and blood cells
Thy-1 HSC, MSC Cell-surface protein; negative or low detection is suggestive of HSC
Cartilage
Collagen types II and IV
Keratin
Sulfated proteoglycan Chondrocyte Keratinocyte Chondrocyte Structural proteins produced specifically by chondrocyte Principal protein of skin; identifies differentiated keratinocyte Molecule found in connective tissues; synthesized by chondrocyte
Fat Adipocyte lipid-binding
protein (ALBP)
Fatty acid transporter (FAT) Adipocyte
Adipocyte lipid-binding
protein (ALBP)
General Adipocyte Transport molecule located specifically in adipocyte Lipid-binding protein located specifically in adipocyte Adipocyte Lipid-binding protein located specifically in adipocyte HSC, MSC Thirteen to 14 different cell-surface proteins that are markers of mature blood cell lineages; detection of Lin-negative cells assists in the purification of HSC and hematopoietic progenitor populations Cell-surface protein on WBC progenitor
Marker Name
Y chromosome Cell Type Male cells Significance Male-specific chromosome used in labeling and detecting donor cells in female transplant recipients
Karyotype Most cell types Analysis of chromosome structure and number in a cell
Liver
Albumin Hepatocyte Principal protein produced by the liver; indicates functioning of
maturing and fully differentiated hepatocytes B-1 integrin Hepatocyte Cell-adhesion molecule important in cell-cell interactions; marker
expressed during development of liver
Nervous System
CD133 Neural stem cell, HSC Cell-surface protein that identifies neural stem cells, which give rise to neurons and glial cells
Glial fibrillary acidic protein Astrocyte
(GFAP)
Microtubule-associated
protein-2 (MAP-2)
Myelin basic protein (MPB) Oligodendrocyte Neuron Dendrite-specific MAP; protein found specifically in dendritic branching of neuron Protein produced by mature oligodendrocytes; located in the myelin
sheath surrounding neuronal structures
Nestin Neural progenitor Intermediate filament structural protein expressed in primitive neural tissue
Neural tubulin Neuron Important structural protein for neuron; identifies differentiated
neuron
Neurofilament (NF) Neuron Important structural protein for neuron; identifies differentiated neuron
Neurosphere Embryoid body (EB), ES Cluster of primitive neural cells in culture of differentiating ES cells;
indicates presence of early neurons and glia
Noggin O4
O1
Synaptophysin Neuron Oligodendrocyte Oligodendrocyte Neuron A neuron-specific gene expressed during the development of neurons Cell-surface marker on immature, developing oligodendrocyte Cell-surface marker that characterizes mature oligodendrocyte Neuronal protein located in synapses; indicates connections between
neurons
Tau Neuron Type of MAP; helps maintain structure of the axon Pancreas
Cytokeratin 19 (CK19) Pancreatic epithelium CK19 identifies specific pancreatic epithelial cells that are progenitors
for islet cells and ductal cells Protein specifically produced by astrocyte
Marker Name Cell Type Significance
Glucagon Pancreatic islet Expressed by alpha-islet cell of pancreas
Insulin Pancreatic islet Expressed by beta-islet cell of pancreas Pancreas
Transcription factor expressed by beta-islet cell of pancreas Insulin-promoting factor-1 Pancreatic islet (PDX-1)
Nestin Pancreatic progenitor Structural filament protein indicative of progenitor cell lines including
pancreatic
Pancreatic polypeptide
Somatostatin Pancreatic islet Pancreatic islet Expressed by gamma-islet cell of pancreas Expressed by delta-islet cell of pancreas
Pluripotent Stem Cells
Alkaline phosphatase Embryonic stem (ES),
embryonal carcinoma
(EC) Elevated expression of this enzyme is associated with undifferentiated pluripotent stem cell (PSC)
Alpha-fetoprotein (AFP) Endoderm Protein expressed during development of primitive endoderm; reflects
endodermal differentiation Pluripotent Stem Cells
Bone morphogenetic
protein-4
Brachyury Mesoderm Growth and differentiation factor expressed during early mesoderm formation and differentiation Mesoderm Transcription factor important in the earliest phases of mesoderm
formation and differentiation; used as the earliest indicator of
mesoderm formation
Cluster designation 30
(CD30)
Cripto (TDGF-1) ES, EC Surface receptor molecule found specifically on PSC ES, cardiomyocyte Gene for growth factor expressed by ES cells, primitive ectoderm, and
developing cardiomyocyte
GATA-4 gene
GCTM-2 Endoderm ES, EC Expression increases as ES differentiates into endoderm Antibody to a specific extracellular-matrix molecule that is synthesized
by undifferentiated PSCs
Genesis ES, EC Transcription factor uniquely expressed by ES cells either in or during
the undifferentiated state of PSCs
Germ cell nuclear factor ES, EC Transcription factor expressed by PSCs
Transcription factor expressed early in endoderm formation Hepatocyte nuclear factor-4 Endoderm
(HNF-4)
Nestin Ectoderm, neural and
pancreatic progenitor
Neuronal cell-adhesion
molecule (N-CAM) Ectoderm Intermediate filaments within cells; characteristic of primitive neuroectoderm formation Cell-surface molecule that promotes cell-cell interaction; indicates primitive neuroectoderm formation
Marker Name
Oct-4 ES, EC Cell Type Significance Transcription factor unique to PSCs; essential for establishment and
maintenance of undifferentiated PSCs
Pax6 Ectoderm Transcription factor expressed as ES cell differentiates into
neuroepithelium
Stage-specific embryonic
antigen-3 (SSEA-3)
Stage-specific embryonic
antigen-4 (SSEA-4)
Stem cell factor (SCF or
c-Kit ligand) ES, EC, HSC, MSC ES, EC ES, EC Glycoprotein specifically expressed in early embryonic development and by undifferentiated PSCs Glycoprotein specifically expressed in early embryonic development and by undifferentiated PSCs Membrane protein that enhances proliferation of ES and EC cells, hematopoietic stem cell (HSCs), and mesenchymal stem cells (MSCs);
binds the receptor c-Kit
Telomerase ES, EC An enzyme uniquely associated with immortal cell lines; useful for
identifying undifferentiated PSCs
TRA-1-60 ES, EC Antibody to a specific extracellular matrix molecule is synthesized by
undifferentiated PSCs
TRA-1-81 ES, EC Antibody to a specific extracellular matrix molecule normally
synthesized by undifferentiated PSCs
Vimentin Ectoderm, neural and pancreatic progenitor Intermediate filaments within cells; characteristic of primitive neuroectoderm formation
Skeletal Muscle/Cardiac/Smooth Muscle
MyoD and Pax7 Myoblast, myocyte Transcription factors that direct differentiation of myoblasts into
mature myocytes Myogenin and MR4 Skeletal myocyte Secondary transcription factors required for differentiation of
myoblasts from muscle stem cells
Myosin heavy chain Cardiomyocyte A component of structural and contractile protein found in
cardiomyocyte
Myosin light chain Skeletal myocyte A component of structural and contractile protein found in skeletal
myocyte