Human and mouse immune cell marker genes

Chun-Jie Liu · 2022-06-27

Human immune cell and marker genes

Cell type	Marker genes
CD4_naive	9-Sep , CD2 , CD3G , CD4 , GIMAP6, GLG1 , HMOX2 , IL7R , ITK , LIMD2 , LY9 , NAA16 , OBSCN , PACS1 , PLCL1 , RPL14 , SNPH , TPP2 , TRAF1 , ZBTB40, CD40LG
CD8_naive	MAN1C1 , CRTAM , BLNK , CCR7 , KERA , ZNF208 , TREM1 , CD8A , CD8B , GPR15 , HTR1B , SMCP , NKTR , PSG11 , SLC17A4, RRH , SMR3B , CA14 , FXYD7 , CCDC87 , LIN28A , MOGAT2 , TNKS2 , GJB4 , KRT1 , CALY
Cytotoxic	KNG1 , PSORS1C2 , BLNK , SCN3A , TNFRSF10C, ITGAM , KLRK1 , CD8A , GNLY , GZMH , PTGDR2 , CD8B , GZMA , PRF1
Exhausted	ADGRG1 , AFAP1L2, CCND2 , CD38 , CD8A , CD8B , CHST12 , CTLA4 , DFNB31 , EOMES , FUT8 , ITM2A , LAG3 , MYO1E , NDFIP2 , PARK7 , PDCD1 , SIRPG , SNX9
Tr1	ATG2B , CCR4 , CD5 , CTLA4 , HS3ST3B1, ICOS , IL10RA , IPCEF1 , CD4
nTreg	FOXP3 , STAT5A , DUSP4 , CD4 , CTLA4 , TNFRSF9, IL10RA , IL2RA , CD5 , SIT1
iTreg	FOXP3 , STAT5A , CCR8 , CD5 , HS3ST3B1, TTN , CTLA4 , FASLG , ICOS , CCR3 , GALNT8 , NFATC3 , SIT1 , CD28 , IL10RA , PPM1B , ATG2B , CCR4 , ZFYVE9
Th1	IFNG , IL2 , MNAT1 , SLAMF1, STAT1 , EIF2B2, APBB2 , CCL4 , CTLA4 , GGT1 , LTA , SYNGR3, TACO1
Th2	GZMK , IL4 , GATA3 , GSTA4 , SLC25A44
Th17	IL1R1 , RORC , CD4 , IL21 , IL17RA
Tfh	CA8 , CD2 , CD3G , GZMM , ITK , KLRB1 , LTA , MAP4K1 , ST8SIA1, TRAC , TRAV9-2, TRIB2 , UBASH3A
Central_memory	CORO7 , ATM , GMEB2 , SNRPN , ADSL , ITK , TFAP4 , NAA16 , LY9 , CYLD , GIMAP4 , PURA , DVL1 , RPP38 , LRIG2 , IL7R , CDKN2AIP, APBB1 , IPCEF1 , CD247 , CD40LG , TRADD , CD3E , TPR , ARID5B , UBASH3A , NCK1 , SPTAN1 , GPR171 , CD5
Effector_memory	APBA3 , CD160 , CD2 , CD8B , CDK10 , CDKN2AIP, CHST12 , COG4 , CX3CR1 , DHX16 , EWSR1 , GIMAP6 , GPR171 , GZMK , HMOX2 , IKZF3 , ITK , KLRD1 , KLRG1 , MAPKAPK5, MORC2 , MRFAP1L1, PLCG1 , PSMC5 , RNF167 , SBF1 , SF3B2 , SLAMF1 , TBCD , USP47 , ZFYVE9 , ZNF549
NKT	CASP5 , DOLK , GMIP , PRR5L , SGCA , SLAMF1, TCOF1 , TGFBR2
MAIT	CD8A , CD8B , CERK , FLT4 , TBC1D31, DKK3 , GPR171 , NR1D1 , SLAMF1 , TC2N
DC	BLVRB , C1QA , C1QB , CSF1R , CXCR3 , FGL2 , GZMB , IL21R , KCNA5 , KCNC3 , KCTD5 , LILRB4 , LMAN2L , NFKB1 , PLD2 , PTCRA , PTGIR , SIGLEC1 , SLAMF8 , SLC15A3 , SYT17 , VAV2 , CA8 , CALY , CRTAM , CYP4F3 , GATA3 , ITIH4 , PRR5L , ST8SIA1 , TNFRSF10C
Bcell	AFTPH , AHSP , ANXA3 , CNOT1 , HLA-DPB1, HLA-DQA1, LSM6 , MEFV , MS4A1 , NMUR1 , PADI4 , PYGM , STRN4 , TRAF3 , TCL6 , BLK , WNT16 , CD37 , CD19 , HRH4 , CA1 , COL19A1 , GNG3 , PLIN1 , SGCA , CD79A , CD79B
Monocyte	IL7R , APOC3 , ADCY8 , CLCA4 , CPA2 , DPP6 , HSPB6 , KNG1 , KLRK1 , GZMH , KLRB1 , SGCA , CA1 , TLR8 , CYBB , IGSF6 , KLRF1 , CYP4F3 , CLEC10A, FOLR2 , LTBR , MAP3K2 , NUP214 , OSBPL11, RTN3 , SERP1 , TBK1 , SOCS3
Macrophage	ARPC4 , ATP6V0E1, BPI , C1QA , C1QB , CAMP , CHIT1 , CLEC5A , CLIP1 , CSF1R , CYBB , FGR , GGA1 , GRB2 , IFNAR1 , IGSF6 , IL17RA , LILRA2 , MARCO , MMP8 , MS4A6A , OTUD4 , PSME1 , RENBP
NK	DNAJB14, IL18RAP, IL2RB , KIR2DL3, KIR3DL2, NCR1 , NCR3 , PSMD4 , SPON2 , XCL1 , C1QB , CALY , CD37 , CLEC10A, CRTAM , CSF2RB , CX3CR1 , GZMB , IL7R , KNG1 , MAN1C1 , PRR5L , SYT17
Neutrophil	IL18RAP, BMX , BTNL8 , CASP5 , CLC , CXCR1 , CXCR2 , FCGR3B , FPR2 , HSPA6 , MEFV , PADI4 , S100A12, TREML2 , TRPM6 , SIGLEC5, CREB5 , ALPL , AATK , CEACAM3, CSF2RB , CSF3R , FBXO38 , MAK , PAK2 , TOP1 , UBXN2B , VNN3
Gamma_delta	KLRG1 , CYP4A11, CCR5 , GZMH , ACD , CHST12 , GZMA , GZMB , LAG3 , NKG7 , PRF1 , PVRIG , TINF2 , ZMAT5 , C1orf61, GNLY , LCP2 , PSTPIP1, PTPN4 , RALY , TAB2 , TDP1
CD4_T	SELL , NT5E , ITK , TRMT2B , AAK1 , CD4 , GPR183 , KLHL3 , CCR4 , ITIH4 , DLEC1 , ZAP70 , PLXDC1 , CD40LG , LAX1 , TNFRSF4, GPR171 , LY9 , NCK2 , PLCG1
CD8_T	CD27 , CD8B , CLUAP1 , CRTAM , FKTN , KLRG1 , LY9 , PLCG1 , RING1 , SF1 , SIRPG , TSPAN32, ARHGEF1, EEF1D , PPP1R2 , CTSW , FBXW4 , ZNF611 , GZMH , CD8A , TTN , CD7 , CX3CR1

Mouse immune cell and marker genes

Level 1

Cell type	Marker genes
B_cell	Btla , Lyl1 , Tnfrsf13c, Cd79b , Gm8369 , Cd81 , Cd24a , Kmo , Cd22 , B3gnt5
Dendritic_cells	Kynu , H2-DMb2, Il12b , Ccl17 , Htra4 , Ccr7 , Itgax , Slamf8 , Ccl22 , Asgr2
Granulocytes	Mgst1 , 4921507P07Rik, Kcnj2 , Vps4b , Siglece , Snapc5 , Dppa2 , Senp6 , Chil3 , Camp
Macrophage	Cd5l , Clec4d , Atp6v0d2, Hk3 , C3ar1 , Cd300ld , Msr1 , Tfec , Hpgds , Ms4a6d
Monocytes	Bex6 , Tlr7 , Gpr35 , Pirb , Cd209a , C130050O18Rik, Cd300a , Apoc2 , Treml4 , Igsf6
NK	Klrb1b , Klre1 , Il18rap, Clnk , Klrg1 , Klrd1 , Gimap5 , Bcl2 , S1pr5 , Khdc1b
T_cell	Cd3e , Cd6 , Cd5 , Cd8a , Cd3d , Thy1 , Cd3g , Sell , Cd4 , Cd69 , Gstm1

Level 2

Cell type	Marker genes
CD4_T_cell	Trat1 , Tspan32 , A630023P12Rik, Tnfrsf25 , Bach2 , St8sia1 , Slc16a5 , Gimap3 , Sit1 , Cd5 , Cd28 , Gm11346 , Cd4
CD8_T_cell	Cd8b1 , Eomes , Gzmb , Cxcr3 , Klrc1 , Tbx21 , Nmrk1 , Gzmk , Gzmm , Crtam , Fam71b, Xcl1
NKT	Klra5, Cd160, Nkg7 , Ccl5 , Il2rb, Ctsw , Rgs1 , Fasl , Cd7 , Ccr9
Tgd	Cd8a , Cd163l1, Itgae
B1_cell	Cxcr5 , Cd79a , Gimap3 , Blk , Hepacam2, Fcmr , Cd2 , Cd19 , Ly86 , Il5ra
Follicular_B	Ms4a4c, Ccr6 , Fcer2a, B3gnt5, Cd72 , Cd55 , Clec2i, Cr2 , Pgap1 , Tlr1
Germinal_center_B	Aicda , Gm11810, H2ac8 , Rgs13 , Mki67 , Gm8290 , Tes3-ps, H2ac4 , Cd83 , Gm7931
Marginal_Zone_B	Tsga13 , Angptl1, Cr2 , Cdh17 , Prp2 , Cnr2 , Tlr1 , Fam167a, Phxr4 , Cd22
Memory_B	Btla , Sspn , Ccr6 , Rsl1 , Cdh17 , Tlr1 , Zbtb20, B3gnt5, Fcrl1 , Pax5
Plasma_cell	Slpi , Jchain , Ighv1-62-3, Iglv1 , Oosp1 , Mzb1 , Tnfrsf17 , Ndufa1 , Endou , Slamf7
cDC1	Treml4 , Tbc1d9 , Dnase1l3 , Gm6377 , Slco3a1 , Parvg , Adam19 , C530030P08Rik, Cxcl9 , Tbc1d8
cDC2	Mmp12 , Tgm2 , Nlrp3 , Clec7a, Kit , H2-Eb2, Ptgs2 , Fam49a, Arap2 , Itgax
MoDC	Dcn , Retnla, Cxcl2 , Fn1 , Lyz1 , Pf4 , S100a6, Wfdc17, S100a4, Ifi207
pDC	Klk1 , Atp1b1, Ctsl , Rnase6, Tcf4 , Kmo , Tlr7 , Bcl11a, Cd180 , Cd209d
Basophil	Mcpt8, Anpep, Itga2, Il2ra, Ccr2
Eosinophil	Epx , Ccr3 , Prg2 , Alox15, Gata1 , Prg3 , Il4 , Abcc2 , P2rx1 , Il5ra
mast_cell	Tpsb2 , Mcpt2 , Il1rl1 , Spink2 , Gp1ba , Cd200r4, Poln , Pga5 , Fosb , Cma1
Neutrophils	Cd177 , Ifitm6, Mmp8 , Fpr1 , Clec5a, Cxcr2 , Trem3 , Ngp , Csf3r , Mmp9
M1_macrophage	Cxcl11 , Ms4a4c , Slfn4 , Fcgr1 , Ccl12 , Marco , Cysltr2, Il18bp , Spic , Ms4a6d
M2_macrophage	Egr2 , Tfec , Cd300lb , Atp6v0d2, Cd300ld , Lipn , Tmem202 , Tbxas1 , Plau , Tlr8

Level 3

Cell type	Marker genes
CD4_Tm	Cxcr5 , Sostdc1, Btla , Atp8a2 , Il21 , Gpm6b , Stfa3
Naive_CD4_T	Pfdn5 , Atp5g2 , Eif3h , N4bp2l2, Prrc2c , Ampd1 , Tspan32, Tap1 , Mbnl1 , Slc16a5
T_helper_cell	Ccl3 , Il3 , Ccl4 , Il24 , Il2ra , Il2 , Il13 , Zbtb32 , Lif , Il12rb2
Treg	H4c1 , Hist1h4m, Eno1b , Foxp3 , Trp53 , Tmem59 , St8sia6 , Cd2
CD8_Tc	H2ac8 , Prnp , Batf3 , Gzmb , Zfp979
CD8_Tcm	Lypla1 , Rgs3 , Il12rb2 , Ncoa4 , Fkbp8 , Gorasp2 , Ctdnep1 , Pcgf1 , Hist1h2ao, Pip4k2c
CD8_Tem	Dmrta1 , Cd163l1 , Lax1 , Gzmk , Fam169b , Il7r , Cd27 , Gzmm , Tbx21 , 5830411N06Rik
CD8_Tex	Gzmk , Cd3e , Klrc1 , Cd160 , Ndufa13, Ociad2 , Gm5797 , Tox , Xist , Cd8a
Naive_CD8_T	Gm13777 , Rpl18a , Zswim4 , Rps29 , Gm13212 , Slco4a1 , Rps11 , Rps8 , Rpl23 , 3000002C10Rik

Read object in to R

human <- readr::read_rds(file = "https://chunjie-sam-liu.life/data/human_immune_cell_marker_genes.rds.gz")
mouse <- readr::read_rds(file = "https://chunjie-sam-liu.life/data/mouse_immune_cell_marker_genes.rds.gz")