Stem Cell Markers




Stem cells are primal cells common to all multi-cellular organisms that retain the ability to renew themselves through cell division and can differentiate into a wide range of specialized cell types. The three broad categories of mammalian stem cells exist: embryonic stem cells, derived from blastocytes, adult stem cells, which are found in adult tissues, and cord blood stem cells, which are found in the umbilical cord. In a developing embryo, stem cells are able to differentiate into all of the specialized embryonic tissues. In adult organisms, stem cells and progenitor cells act as a repair system for the body, replenishing specialized cells.

What are stem cells? (Stem Cell Information - NIH resource for stem cell research)



  • a biochemical and immunological marker of limbal basal cells, hypothesized to be corneal epithelial stem cells. PMID: 1730535


  • the fetal stem cell marker, is expressed in three major cell types: vascular endothelial cells, aorta-associated hematopoietic clusters, and primitive fetal liver hematopoietic progenitors. PMID: 10403644


  • a novel marker for human hematopoietic stem and progenitor cells. PMID: 9389720



  • thrombopoietin receptor, c-Mpl, is a selective surface marker for human hematopoietic stem cells. PMID: 16480521


  • a surface marker on mouse and rat male germline stem cells. PMID: 12954725


  • the main marker of the hematopoietic stem cell population. PMID: 10494177, PMID: 7519070

  • a marker for pluripotent stem cells also present on lineage-committed hematopoietic progenitors from bone marrow and a subpopulation of immature thymocytes. PMID: 7505122

CD133 (Prominin-1)

  • a neural stem cell surface marker. PMID: 16302851, PMID: 15976444

  • a plasma membrane marker found in several types of somatic stem cells, including hematopoietic and neural stem cells. PMID: 15917475

  • a neural and hematopoietic stem cell marker, is expressed in adult human differentiated cells and certain types of kidney cancer. PMID: 15558321

  • a novel marker for human prostatic epithelial stem cells. PMID: 15226377

  • the surrogate stem cell marker. PMID: 17332245

  • a plasma membrane marker found in several types of somatic stem cells, including hematopoietic and neural stem cells. PMID: 15917475


Connexin 43

  • a negative cell surface marker for the stem cell-containing population of human limbal epithelial cells. PMID: 16424398


  • a functional marker that defines long-term repopulating hematopoietic stem cells. PMID: 12438646


  • a positive marker for the isolation of murine long-term in vitro repopulating stem cells. PMID: 7635179

Fibroblast growth factor receptor-3



  • as a positive and negative selectable marker in embryonal stem cells. PMID: 8018715

Human Rex-1 (hRex-1)

  • also referred to as zinc-finger protein-42, Zfp42, encodes a zinc finger protein expression of which is believed to be characteristic of pluripotent stem cells. PMID: 16865673

  • highly expressed in mouse and human embryonic stem cells and one of several gene markers used to identify human stem cells. PMID: 16344273

Interleukin-2 receptors

Interleukin-3 receptor alpha chain

  • a unique marker for human acute myelogenous leukemia stem cells. PMID: 11021753


  • a positive functional marker defining stem cells and distinguishing them from progenitors. PMID: 10477517

Keratin 19

Lamin A/C

  • a marker of mouse and human embryonic stem cell differentiation. PMID: 16179429

Macromolecular insoluble cold globulin (MICG)


  • in human normal colon crypt cells: a possible stem cell marker of human colon epithelium. PMID: 12924647

  • a marker of stem and early lineage progenitor cells in murine intestinal tissue. PMID: 12558601

  • an evolutionally conserved marker for CNS progenitor cells including neural stem cells. PMID: 10657706


  • a putative neural stem cell marker that is expressed in different areas of the adult mammalian brain that are known to support mitotic activity. PMID: 16343784

  • a neuroectodermal stem cell marker molecule, is expressed in Leydig cells of the human testis and in some specific cell types from human testicular tumours. PMID: 15127288


Oct4 (Oct-4)



  • a marker of embryonic hematopoietic stem cells (HSCs) and erythroid cells and of adult HSCs and that it may be a valuable marker for the purification of these cells for transplantation. PMID: 15701716


  • present on a subset of bone marrow (BM) hematopoietic stem cells. PMID: 7860091

PSCA (Prostate stem cell antigen)

  • a homologue of the Ly-6/Thy-1 family of cell surface antigens. PMID: 12771726


  • a transcription factor from the SoxB1 subgroup and widely used marker of neural stem cells. PMID: 16797497


  • a persistent marker for multipotential neural stem cells derived from embryonic stem cells, the embryo or the adult. PMID: 15711057

Stem cell Antigen 1 and 2 (Sca-1 and Sca-2)


  • a promising marker of biological immortality of germ, stem, and cancer cells. PMID: 9467857


  • a cell surface marker used in conjunction with CD34 and lineage-specific markers to identify hematopoietic stem cells. PMID: 9462642

  • Thy-1-specific antibody 5E10 is an attractive tool for further studies on the biology and purification of human stem cells. PMID: 7683034

Transcription factor Stat5

  • an early marker of differentiation of murine embryonic stem cells. PMID: 9566306


  • defines a novel molecule that is expressed on CD34+ as well as on CD34- stem cell subsets. PMID: 11458505

How Do Researchers Use Markers to Identify Stem Cells? 

In recent years, scientists have discovered a wide array of stem cells that have unique capabilities to self-renew, grow indefinitely, and differentiate or develop into multiple types of cells and tissues. Researchers now know that many different types of stem cells exist but they all are found in very small populations in the human body, in some cases 1 stem cell in 100,000 cells in circulating blood. And, when scientists examine these cells under a microscope, they look just like any other cell in the tissue where they are found. So, how do scientists identify these rare type of cells found in many different cells and tissues—a process that is much akin to finding a needle in a haystack? The answer is rather simple thanks to stem cell "markers." This feature describes stem cell marker technology and how it is used in the research laboratory.


Following this is a listing of some of the commonly used stem cell markers.