Cell annotation

Last updated on Jul 13, 2021
Schematic outline of annotation of leukocyte, endothelial and non-endothelial/leukocyte cell susbsets.

Manual annotation of cell populations are performed by querying expression levels of specific genes within clusters of cells. For example, endothelial cell populations are generally enriched for transcripts corresponding Cadherin 5 (Cdh5; also known as vascular-endothelial cadherin) or Pecam (also known as CD31). Query of the genes shown in the schematic above, or those listed below, enables systematic annotation of major cell populations within a single-cell dataset.

Marker genes

Note: Genes displayed in bold indicate those that are present in multiple cell types, but are still useful for classifying the cell type the gene is listed for.

  • Leukocytes: Ptprc (also known as CD45).

  • Macrophages: Csf1r, Adgre1, Mrc1, H2-Aa, Fcgr1.

  • NK cells: Ncr1, Klb1, Nkg7.

  • Granulocytes: Csf3r, S100a8/9.

  • T cells: Cd3e, Cd3g.

  • B cells: Ms4a1, H2-Aa, Cd79a, Cd79b.

  • Fibroblasts: Col1a1, Pdgfra.

  • Mural cells: Mcam, Itga7, Pdgfrb, Cspg4.

  • Pericytes: Vtn, Kcnj8.

  • Smooth muscle cells: Tagln, Myh11.

  • Schwann cells: Mbp, Plp1.

  • Endothelial cells: Cadh5, Pecam, Emcn.

  • Endocardial cells: Npr3.

  • Lymphatic endothelial cells: Lyve1, Prox1, Pdpn.

  • Cardiomyocytes: Myh6, Tnnt2, Ttn.