Table 3 Adipose cell-type annotations and proposed marker genes in mouse single-cell data

From: Towards a consensus atlas of human and mouse adipose tissue at single-cell resolution

Cell types

Mouse cell-type markers

Cell subtypes

Mouse cell-subtype markers

Adipocytes

Adipoq5,133,136, Plin4 (ref. 3)

White

Retn194

Brown/beige

Ucp1 (refs. 81,82,136,147,194), Ppargc1a81,82, Cidea81,82,194, Adrb3 (ref. 81), Clstn3 (ref. 81), Atp5k136, Cox7a1 (refs. 136,194)

ASPCs

Pdgfra3,5,84,147,177,195, Dcn3,81,147,196

Early preadipocytes

Dpp4 (refs. 84,88,89,131,176,196), Cd55 (refs. 88,89,195), Pi16 (refs. 84,88,90,133,195,196,197), Aldh1a3 (ref. 5), Ebf2 (refs. 3,90)

Committed preadipocytes

Pparg3,88,90,129,196,198, Icam88, Cd36 (refs. 3,129)

Areg cells in inguinal WAT

Cd142 (refs. 89,90,91,195), Clec11a84,89,91,195, Fmo2 (refs. 89,90,91,195), Meox2 (refs. 90,91), Epha3 (ref. 5)

Pericytes

Steap4 (ref. 5), Enpep5

  

SMCs

Myocd5, Myh11 (refs. 120,133,147,177,195), Acta2 (refs. 8,120,133,147,195,197,199)

  

ECs

Pecam5,120,147,195, Cdh5 (refs. 84,120,147,195)

Lymphatic ECs

Prox1 (refs. 5,120,177), Lyve1 (refs. 5,120,147)

Arterial ECs

Hey1 (ref. 120), Gkn3 (ref. 120)

Venous ECs

Vcam1 (ref. 120), Vwf120, Ackr1 (ref. 120)

Capillary ECs

Car4 (ref. 120), Rgcc120

Mesothelial cells

Msln3,5,133,195, Krt19 (refs. 5,195)

  

B cells

Ms4a1 (refs. 3,5,188), Cd79a3,103,188,193, Cd79b3,113

Naive B cells

Ighd188

  

Memory B cells

Zbtb32 (ref. 188)

Plasmablast

Jchain188

  

T cells

Cd3d103,113,188,193, Cd3e103,188

Treg cells

Cd4 (refs. 103,186,188), Foxp3 (refs. 103,113,186,188)

CD4+ cells

Cd4 (ref. 188), Cxcr3 (ref. 188)

CD8+ effector memory cells

Cd8b1 (ref. 188), Cxcr3 (ref. 188)

CD8+ central memory cells

Cd8b1 (ref. 188), Ccr7 (ref. 188), Sell188

Cycling CD8+ T cells

Cd8b1 (ref. 188), Cxcr3 (ref. 188), Stmn1 (ref. 188), Pclaf188

CD8+ γδ T cells

Il7r188, Trdv4 (ref. 188), Cd163l1 (refs. 103,188), Cxcr6 (ref. 188), Trdc188

NK cells

Klrd1 (ref. 5), Xcl1 (ref. 188)

Mature NK cells

Ncr1 (ref. 188), Klrb1b188, Klrb1c188

NK-like cells

Ly6c2 (ref. 188), Klrb1c188, Cd3d188, Cd3e188

Invariant NK T cells

Tbx21 (ref. 200)

ILCs

Il7r188, Gata3 (refs. 188,193), Arg1 (ref. 103)

ILC2

Klrg1 (ref. 188), Ccdc184 (ref. 188)

DCs

Flt3 (refs. 3,5,103)

cDC1

Xcr1 (refs. 103,186,188), Clec9a5,186,188

Activated cDC1s

Ccr7 (ref. 188), Mreg188, Il12b188

Cycling cDC1

Xcr1 (ref. 188), Clec9a188, Stmn1 (ref. 188), Pclaf188

cDC2

Sirpa103,188, Cd209a104,113,188

Activated cDC2

Sirpa188, Ccr7 (ref. 188), Mreg188

Cycling cDC2

Sirpa188, Cd209a188,193, Ear2 (ref. 188), Stmn1 (ref. 188), Pclaf188

Plasmacytoid DCs

Siglech113,188, Cd209a188, Cox6a2 (ref. 188) Clec9a188

Migratory DCs

Ccr7 (ref. 103), Ccl22 (ref. 103), Nudt17 (ref. 103)

Neutrophils

S100a8 (ref. 188), Csf3r5, S100a9 (refs. 113,188)

  

Monocytes

Plac8 (refs. 188,193) Lyz1 (ref. 113), Lyz2 (ref. 188)

Classical monocytes

Socs6 (ref. 5), Fcgr1 (ref. 188), Ly6c2 (ref. 188), Ccr2 (ref. 188)

Non-classical monocytes

Ace188, Dgkg5

Macrophages

Mrc1 (refs. 103,113,188), Adgre1 (refs. 3,103,177,188)

PVMs

Lyve1 (refs. 3,104,113,177,186), Cd163 (refs. 3,104,113,177), Cd209f113,186

LAMs

Cd9 (refs. 3,113,186), Trem2 (refs. 3,5,104,113,177,186), Lpl3,104,113

Nerve-associated macrophages

Maoa104, St3gal6 (ref. 104), Lilra5 (ref. 104)

Mast cells

Kit188, Cpa3 (refs. 5,177,188), Mcpt4 (ref. 188)

  

Schwann cells

Mpz133,147,197

  
  1. A summary of commonly used cell-type and subtype marker genes reported in mouse scRNA-seq/snRNA-seq studies to date. Distinguishing closely related cellular subtypes often requires a combination of marker genes. Moreover, subtype markers may not effectively separate subtypes from other cell types in the tissue and are typically only useful for distinguishing subtypes within a specific cell type or a small subset of related types.
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