Curated markers for annotating single-cell clusters: 3–5 core markers per cell type, supporting markers, and negative markers to rule out look-alikes, given separately for human and mouse. Paste the top genes of a cluster to find the most likely cell types.
Everything runs locally in your browser. Pasted data is never uploaded to any server.
Reverse lookup: what could this cluster be?
Paste the top markers of one cluster (e.g. the top 20–50 genes of FindAllMarkers sorted by log2FC), one per line or separated by spaces/commas. You can also paste the result table with its header; the gene column is picked automatically.
When a tissue is chosen, general immune, stromal/vascular and common states are included too.
The examples are illustrative gene lists, not real data.
Score = core hits × 3 + supporting hits × 1 − negative hits × 2 + fraction of core markers hit × 2 (the fraction term slightly favors types whose core markers are all hit). Ties put tissue-specific types before general ones. The score is a hint, not a verdict: check these genes across clusters with DotPlot / FeaturePlot.
Paste some genes first, or try one of the examples above.
Browse by tissue
Immune cells (blood / PBMC and tissue-resident) 28 types
Immune cells found in every tissue. Confirm PTPRC (CD45) first, then refine with the types below.
Copy whole tissue (R list / Python dict)
T cells (all)
T · pan-T · T cell
Human
Core
CD3DCD3ECD3GCD2
Supporting
TRACTRBC2CD247LCKIL7R
Negative
KLRF1MS4A1CD14
Copy
Mouse
Core
Cd3dCd3eCd3gTrac
Supporting
Trbc2Cd247LckCd2Thy1
Negative
Ncr1Cd79aLyz2
Copy
How to tell apartNK cells are essentially CD3D/CD3E-negative; separate them with KLRF1/NCR1, then split by CD4 vs CD8A/CD8B. Mouse B cells also express Cd2, so it is not a core marker in mouse.
CD4+ T cells
CD4 T · Th · helper T · CD4
Human
Core
CD3ECD3DCD4CD40LG
Supporting
IL7RMALLTBTCF7CCR7ICOS
Negative
CD8ACD8BCD14
Copy
Mouse
Core
Cd3eCd3dCd4Cd40lg
Supporting
Il7rTcf7Ccr7IcosCd28
Negative
Cd8aCd8b1
Copy
How to tell apartCD4 mRNA is poorly detected, so CD3E+ CD8A/CD8B− is often the practical call. Human monocytes/macrophages also express CD4; if CD14/LYZ are high it is not a T cell.
Naive T cells
Tn · naive · naive T · TN
Human
Core
CCR7SELLTCF7LEF1
Supporting
CD3EIL7RCD27CD28MAL
Negative
GZMKCCL5NKG7MS4A1
Copy
Mouse
Core
Ccr7SellTcf7Lef1
Supporting
Cd3eIl7rSatb1Cd27Cd28
Negative
GzmkCcl5Nkg7Cd79a
Copy
How to tell apartCentral memory T cells (TCM) are also CCR7+ SELL+ but have lower LEF1 and higher IL7R. B cells are CCR7+ SELL+ too, so check CD3E first. Use CD4 vs CD8A/CD8B to split naive CD4/CD8.
CD8+ T cells
CD8 T · CTL · Tc · cytotoxic T · CD8
Human
Core
CD3ECD3DCD8ACD8B
Supporting
GZMKCCL5NKG7GZMACST7GZMHPRF1
Negative
CD4CD40LGKLRF1
Copy
Mouse
Core
Cd3eCd3dCd8aCd8b1
Supporting
GzmkCcl5Nkg7GzmaGzmbCxcr3
Negative
Cd4Cd40lgNcr1
Human CD8B is Cd8b1 in mouse.
Copy
How to tell apartNK and some γδ T cells express CD8A (CD8αα); CD8B is more specific. Separate from NK with CD3E and KLRF1/NCR1. Naive CD8 T: see "Naive T cells"; exhausted CD8 T: see tumor microenvironment.
Regulatory T cells (Treg)
Treg · Tregs · regulatory T
Human
Core
FOXP3IL2RACTLA4IKZF2
Supporting
CD4TIGITTNFRSF4TNFRSF18RTKN2BATF
Negative
CD8ACD8B
Copy
Mouse
Core
Foxp3Il2raCtla4Ikzf2
Supporting
Cd4Tnfrsf4Tnfrsf18Izumo1rNrp1Tigit
Negative
Cd8aCd8b1
Mouse FR4 (folate receptor 4) is now officially Izumo1r.
Copy
How to tell apartActivated conventional CD4 T cells also up-regulate IL2RA and CTLA4; FOXP3 is the key gene. FOXP3 is detected in only part of the cluster, which is normal.
T follicular helper cells (Tfh)
Tfh · TFH · Tph · follicular helper
Human
Core
CXCR5PDCD1CXCL13ICOSTOX2
Supporting
CD4BCL6MAFSH2D1AIL21CD200
Negative
FOXP3CCR7
Copy
Mouse
Core
Cxcr5Pdcd1Bcl6IcosIl21
Supporting
Cd4Tox2MafSh2d1aCd200
Negative
Foxp3Ccr7
Mouse Tfh cells hardly make Cxcl13 (a human Tfh feature), so it is not used here.
Copy
How to tell apartHuman tissues also contain peripheral helper T cells (Tph: PD-1 high, CXCR5−) that are CXCL13-high; exhausted CD8 T cells in tumors express CXCL13 too, so check CD4/CD8 first. Follicular regulatory T cells (Tfr) are also FOXP3+.
Th17 cells
Th17 · TH17 · IL-17
Human
Core
RORCIL17AIL23RCCR6
Supporting
IL17FKLRB1IL22CTSHRORACD4
Negative
FOXP3CD8BTRDC
Copy
Mouse
Core
RorcIl17aIl23rCcr6
Supporting
Il17fIl22Il1r1Tmem176aTmem176bCd4
Negative
Foxp3Cd8b1Trdc
Copy
How to tell apartRORC/IL17A are shared with γδT17, MAIT and ILC3: Th17 cells are CD4+ and TRDC− (and TRAV1-2− in human); ILC3 lack CD3.
Mouse TCRγ constant genes are now Trgc1/Trgc2/Trgc4 (formerly Tcrg-C1 etc.). IL-17-producing γδ T cells (γδT17) also express Scart1 (formerly Cd163l1), Sox13, Blk and Rorc.
Copy
How to tell apartHuman blood γδ T cells are mostly Vδ2Vγ9 (TRDV2/TRGV9); tissues are richer in Vδ1 (TRDV1). If TCR genes are poorly detected, use VDJ sequencing.
MAIT cells
MAIT · mucosal-associated invariant T
Human
Core
TRAV1-2SLC4A10KLRB1ZBTB16
Supporting
IL7RGZMKCXCR6NCR3RORCIL23RIL18R1PRSS35
Negative
TRDCCCR7
Copy
Mouse
No specific marker; the genes below are the best available combination (see note)
Core
Trav1Zbtb16RorcIl18r1
Supporting
Il7rIl23rCcr6Cxcr6Il17a
Negative
Trdc
MAIT cells are very rare in standard SPF C57BL/6 mice and rarely form their own cluster; these genes overlap with γδT17 and iNKT cells, and confirmation needs MR1 tetramer.
Copy
How to tell apartKLRB1 (CD161) and RORC are shared with Th17 and γδ T cells; TRAV1-2 together with SLC4A10 is the most useful combination.
NK cells
NK · natural killer · CD56dim · CD56bright
Human
Core
KLRF1NCR1NCAM1KLRD1GNLY
Supporting
NKG7PRF1GZMBFCGR3ASPON2FGFBP2TYROBPXCL1
Negative
CD3DCD3E
Copy
Mouse
Core
Ncr1Klrb1cGzmaKlrd1Eomes
Supporting
Nkg7Prf1Klra4Klra7Klra8Klrk1Itga2Fcer1g
Negative
Cd3dCd3e
Mouse has no GNLY ortholog. The Ly49 family (Klra*) differs between strains; Klra8 (Ly49H) is typical of C57BL/6. Mouse NK cells carry CD16 as Fcgr3 (Fcgr4, the sequence homolog of human FCGR3A, is mainly on monocytes/macrophages).
Copy
How to tell apartShares NKG7, GZMB and PRF1 with CD8 T cells; separate by CD3D/CD3E negativity and KLRF1/NCR1. Human CD56bright NK: NCAM1, XCL1, GZMK, SELL high and FCGR3A low; CD56dim NK: FCGR3A, FGFBP2, SPON2 high. Mouse ILC1 are also Ncr1+ but Eomes-low.
Group 2 innate lymphoid cells (ILC2)
ILC2 · ILC · innate lymphoid
Human
Core
PTGDR2IL1RL1GATA3HPGDS
Supporting
IL7RKLRB1KLRG1IL17RBAREGIL13IL5
Negative
CD3DCD3ETPSAB1
Copy
Mouse
Core
Gata3Il1rl1Klrg1Il17rb
Supporting
Il7rAregIl13Il5Arg1Rora
Negative
Cd3dCd3e
Copy
How to tell apartILCs lack CD3 and B/myeloid markers. ILC2 share GATA3 and IL13 with Th2 cells, which are CD3+ CD4+. Human HPGDS is also high in mast cells; rule them out with TPSAB1.
Group 3 innate lymphoid cells (ILC3)
ILC3 · LTi · NCR+ ILC3
Human
Core
RORCKITIL23RIL1R1
Supporting
NCR2IL22AHRIL7RLTBCCR6
Negative
CD3DCD3E
Copy
Mouse
Core
RorcIl22Il23rIl7r
Supporting
Ncr1Ccr6KitIl17aAhr
Negative
Cd3dCd3e
Human NCR2 (NKp44) has no mouse ortholog; mouse NCR+ ILC3 are marked by Ncr1 and LTi-like cells by Ccr6.
Copy
How to tell apartTh17 and γδT17 cells are also RORC+/IL23R+, but ILC3 lack CD3. Mostly found in mucosal tissues such as gut and tonsil.
B cells
B · naive B · memory B · B cell
Human
Core
MS4A1CD79ACD79BCD19
Supporting
PAX5BANK1CD22TCL1AIGHDIGHMFCER2CR2
Negative
CD3EJCHAINLYZ
Copy
Mouse
Core
Cd79aCd79bCd19Ms4a1
Supporting
Pax5Ebf1IghdFcer2aCr2Bank1Cd22H2-Ab1
Negative
Cd3eJchain
Human FCER2 (CD23) is Fcer2a in mouse.
Copy
How to tell apartNaive B: IGHD, TCL1A, FCER2 high. Memory B: CD27 and class-switched IGHG/IGHA. Plasma cells lose MS4A1/CD19 and gain JCHAIN, MZB1, SDC1.
Germinal center B cells
GC B · GCB · germinal center
Human
Core
RGS13AICDAMEF2BLMO2
Supporting
BCL6GCSAMELL3S1PR2SERPINA9MKI67MS4A1
Negative
FCER2IGHDCCR7
Copy
Mouse
Core
AicdaS1pr2Rgs13Mef2b
Supporting
Bcl6GcsamFasMki67Cd79aMs4a1
Negative
Fcer2aIghdCcr7
Copy
How to tell apartFound in lymph nodes, spleen, tonsil and tertiary lymphoid structures. Dark-zone cells are proliferative (MKI67, AICDA); light-zone cells have higher CD83.
Plasma cells
plasma · plasmablast · ASC · PB
Human
Core
JCHAINMZB1TNFRSF17SDC1PRDM1
Supporting
XBP1DERL3CD38FKBP11TXNDC5IGHG1IGHA1IGKC
Negative
MS4A1LILRA4
Copy
Mouse
Core
JchainMzb1Sdc1Prdm1Tnfrsf17
Supporting
Xbp1Derl3Fkbp11Txndc5IgkcIghaIghg1
Negative
Ms4a1Siglech
Copy
How to tell apartIg transcripts (IGKC, IGHG1, …) are so abundant that they contaminate other clusters as ambient RNA; do not call plasma cells on Ig genes alone. Human pDCs also express JCHAIN and MZB1; rule them out with LILRA4/IL3RA. Proliferating plasmablasts are also MKI67+.
Human LYZ corresponds to mouse Lyz2 (Lyz1 is mainly Paneth cells). In mouse, classical monocytes are identified by Ly6c2 and Ccr2 rather than Cd14. The Ly6C protein is encoded by two genes, Ly6c1 and Ly6c2; monocytes mainly express Ly6c2 (Ly6c1 is more endothelial and T-cell).
Copy
How to tell apartShares S100A8/S100A9 with neutrophils: neutrophils are FCGR3B/CSF3R/CXCR2-high, monocytes CD14/LYZ/HLA-DR-high. In tissues they gradually become macrophages (C1QA/B/C rise).
The mouse homolog of human FCGR3A is Fcgr4, expressed on non-classical monocytes and some macrophages. Nr4a1 is required for non-classical monocytes but is also an immediate-early / dissociation-stress gene, so it is only a supporting marker.
Copy
How to tell apartNK cells are FCGR3A+ too: non-classical monocytes also have high LST1, MS4A7, CDKN1C and low NKG7/GNLY.
Conventional type 1 dendritic cells (cDC1)
cDC1 · DC1 · CD141 DC · BDCA3 · XCR1 DC · CD8a DC · CD103 DC · DC
Human
Core
CLEC9AXCR1CADM1IDO1
Supporting
IRF8BATF3WDFY4DNASE1L3CLNKC1orf54
Negative
CD1CCLEC10ALILRA4
Copy
Mouse
Core
Xcr1Clec9aCadm1Irf8
Supporting
ItgaeWdfy4NaaaTlr3Batf3
Negative
Cd209aSirpaSiglech
Copy
How to tell apartcDC1 are rare and often sit next to cDC2/mregDC; CLEC9A plus XCR1 together are the most reliable.
Conventional type 2 dendritic cells (cDC2)
cDC2 · DC2 · CD1c DC · BDCA1 · DC3 · DC
Human
Core
CD1CFCER1ACLEC10ACD1E
Supporting
HLA-DQA1HLA-DRAPKIBCLEC4AIRF4
Negative
CLEC9AXCR1LILRA4
Copy
Mouse
Core
Cd209aClec4a4Irf4Mgl2
Supporting
SirpaItgamClec10aH2-Ab1
Negative
Xcr1Clec9aSiglech
Human CD1C has no mouse ortholog (mice only have CD1d: Cd1d1/Cd1d2). Mouse cDC2 are identified by Clec4a4 (DCIR2, the 33D1 antigen), Cd209a, Irf4 and Mgl2; Sirpa (CD172a) is also on monocytes, macrophages and neutrophils, so it is only supporting.
Copy
How to tell apartDC3 (CD14+ CD1C+) and monocyte-derived DCs carry monocyte features (CD14, S100A8) and are easily mixed up with monocytes; the cDC2 signature is CD1C, FCER1A, CLEC10A.
Plasmacytoid dendritic cells (pDC)
pDC · plasmacytoid DC · BDCA2 · DC
Human
Core
LILRA4CLEC4CIL3RAPLD4
Supporting
TCF4IRF7GZMBJCHAINSERPINF1ITM2CPTCRAIRF8
Negative
TNFRSF17CD1CCD14
Copy
Mouse
Core
SiglechBst2Ccr9Ly6d
Supporting
Tcf4Irf7Irf8Cox6a2Pacsin1
Negative
Xcr1Cd209a
Human LILRA4 and CLEC4C have no mouse orthologs; mouse pDCs are identified by Siglech, Bst2 (PDCA-1), Ccr9 and Ly6d. Siglech is also high in microglia, and Bst2 is interferon-inducible in many cells.
Copy
How to tell apartHuman pDCs also express JCHAIN, MZB1 and GZMB; do not mistake them for plasma cells or cytotoxic T cells. pDCs lack TNFRSF17 and SDC1.
Mature regulatory DCs (mregDC / LAMP3+ DC)
mregDC · LAMP3 DC · CCR7 DC · mature DC · DC
Human
Core
LAMP3CCR7FSCN1CCL19CCL22
Supporting
CD274IDO1CD83BIRC3IL4I1CCL17MARCKSL1
Copy
Mouse
Core
Ccr7Fscn1Ccl22Il4i1Cacnb3
Supporting
Cd274Cd200Socs2Ccl17Cd40Cd83
Copy
How to tell apartDerived from activated cDC1 or cDC2, so they may retain some CLEC9A or CD1C. Common in tumors and lymph nodes.
Macrophages (general)
Mac · Mφ · macrophage · TRM
Human
Core
C1QAC1QBC1QCCD163CD68
Supporting
MRC1APOEMS4A7MAFSELENOPFOLR2LYVE1CSF1R
Negative
FCN1S100A8CD3E
Copy
Mouse
Core
C1qaC1qbC1qcAdgre1Cd68
Supporting
Mrc1Fcgr1MertkCsf1rApoeMs4a7Lyve1Folr2
Negative
Ly6c2S100a8
Mouse F4/80 is encoded by Adgre1.
Copy
How to tell apartTissue-resident macrophages have tissue-specific markers (Kupffer cells, alveolar macrophages, microglia, …; see the tissue sections). Monocyte-derived macrophages keep monocyte features such as FCN1, S100A8 or CCR2.
Neutrophils
Neu · PMN · neutrophil · granulocyte
Human
Core
FCGR3BCSF3RCXCR2CMTM2
Supporting
S100A8S100A9S100A12MNDAG0S2PROK2FPR1
Negative
CD14HLA-DRACD3E
Copy
Mouse
Core
RetnlgS100a8S100a9Cxcr2Csf3r
Supporting
Ly6gMmp8Mmp9Il1bClec4dWfdc21
Negative
H2-Ab1Csf1r
Mouse Ly6g mRNA is detected inconsistently; S100a8/S100a9 and Retnlg are more reliable.
Copy
How to tell apartNeutrophils have little RNA and are often removed by gene-count filters; in 10x data only a small cluster may remain. Precursors (MPO, ELANE, LTF, CAMP): see bone marrow.
Mast cells
Mast · MC · mast cell
Human
Core
TPSAB1TPSB2CPA3KITMS4A2
Supporting
HDCGATA2HPGDSCMA1CTSGIL1RL1SIGLEC6
Negative
CLCCD3E
Copy
Mouse
Core
Cpa3Cma1Mcpt4Tpsb2Kit
Supporting
Fcer1aMs4a2HdcGata2Mcpt1Mcpt2
Negative
Mcpt8Prss34
Mouse connective-tissue mast cells are Cma1/Mcpt4/Tpsb2-high; mucosal (gut) mast cells mainly express Mcpt1 and Mcpt2.
Copy
How to tell apartBasophils also express HDC, MS4A2 and CPA3 but are KIT/TPSAB1-low and CLC-high (mouse: Mcpt8/Prss34-high).
Basophils
Baso · basophil
Human
Core
CLCHDCGATA2CCR3
Supporting
MS4A2CPA3FCER1AIL3RAENPP3
Negative
KITTPSB2
Copy
Mouse
Core
Mcpt8Prss34Cd200r3
Supporting
Fcer1aHdcGata2Il4Ms4a2
Negative
KitCma1
Copy
How to tell apartRare and often next to mast cells or eosinophils. Human eosinophils are also CLC/CCR3-high but lack HDC.
Eosinophils
Eos · eosinophil
Human
Core
CLCSIGLEC8IL5RACCR3
Supporting
EPXPRG2RNASE2RNASE3ADGRE1ALOX15
Negative
HDCKIT
Copy
Mouse
Core
SiglecfCcr3Il5ra
Supporting
Prg2EpxEar1Ear2Alox15Cebpe
Negative
MarcoC1qa
Mouse alveolar macrophages are Siglecf+ too; rule them out with macrophage genes such as Marco and C1qa. Granule genes Prg2/Epx are high in immature bone-marrow eosinophils but often low in mature tissue eosinophils, so they are only supporting.
Copy
How to tell apartLow RNA content and fragile; often missing or very few in standard scRNA-seq.
Megakaryocytes / platelets
Mk · MK · platelet · PLT · megakaryocyte
Human
Core
PPBPPF4GP9ITGA2BTUBB1
Supporting
GP1BANRGNCAVIN2TREML1CLU
Copy
Mouse
Core
PpbpPf4Gp9Itga2bTubb1
Supporting
Gp1bbGp5Treml1Clec1b
Some mouse tissue macrophages (e.g. brain border-associated and lung interstitial macrophages) also express Pf4.
Copy
How to tell apartPBMC data often contain a small platelet cluster, or platelet–monocyte doublets (CD14 and PPBP both high).
Erythrocytes
RBC · erythrocyte · red blood cell
Human
Core
HBBHBA1HBA2HBD
Supporting
ALAS2CA1SLC4A1AHSPGYPA
Copy
Mouse
Core
Hba-a1Hba-a2Hbb-bsHbb-bt
Supporting
Alas2Car2SncaBpgmSlc4a1
Copy
How to tell apartHemoglobin genes appear in every cluster as ambient RNA; a true erythrocyte cluster expresses little besides hemoglobin. Erythroblasts: see bone marrow.
Stromal and vascular cells 11 types
Fibroblasts, smooth muscle, pericytes, endothelium and mesothelium occur in every organ; tissue-specific subsets are listed in the tissue sections.
Copy whole tissue (R list / Python dict)
Fibroblasts
Fib · FB · fibroblast
Human
Core
DCNLUMCOL1A1COL1A2PDGFRA
Supporting
COL3A1FBLN1MFAP5PI16CFDSERPINF1
Negative
MYH11KCNJ8PECAM1
Copy
Mouse
Core
DcnLumCol1a1Col1a2Pdgfra
Supporting
Col3a1Fbln1Mfap5Pi16CfdGsn
Negative
Myh11Kcnj8Pecam1
Copy
How to tell apartSmooth muscle cells and pericytes also make collagen. Fibroblasts are PDGFRA/DCN/LUM-high, smooth muscle MYH11/DES-high, pericytes RGS5/KCNJ8-high. PI16+ fibroblasts are a "universal" subset shared across tissues (Buechler 2021).
Smooth muscle cells
SMC · VSMC · vSMC · smooth muscle
Human
Core
MYH11ACTA2CNN1DES
Supporting
TAGLNMYL9ACTG2LMOD1SYNPO2MYOCD
Negative
KCNJ8PDGFRA
Copy
Mouse
Core
Myh11Acta2Cnn1Des
Supporting
TaglnMyl9Actg2Lmod1Synpo2Myocd
Negative
Kcnj8Pdgfra
Copy
How to tell apartACTG2 favors visceral smooth muscle (gut, bladder, uterus). Myofibroblasts are ACTA2-high but MYH11/DES-low. Testicular peritubular myoid cells also match this entry.
Pericytes
pericyte · mural cell
Human
Core
RGS5PDGFRBKCNJ8ABCC9HIGD1B
Supporting
NOTCH3CSPG4MCAMCOX4I2NDUFA4L2
Negative
MYH11PDGFRA
Copy
Mouse
Core
Rgs5PdgfrbKcnj8Abcc9Higd1b
Supporting
Notch3Cspg4McamVtnCox4i2Ndufa4l2
Negative
Myh11Pdgfra
Copy
How to tell apartPericytes and smooth muscle form a continuum: pericytes are KCNJ8/ABCC9/HIGD1B-high and MYH11/DES-low. Mouse brain pericytes also express Vtn.
Blood vessel endothelial cells (all)
EC · BEC · endothelial · endothelium
Human
Core
PECAM1VWFCDH5CLDN5EMCN
Supporting
FLT1KDRRAMP2EGFL7ENGTIE1ERG
Negative
PROX1PTPRC
Copy
Mouse
Core
Pecam1Cdh5Cldn5EmcnKdr
Supporting
Flt1Ramp2Egfl7EngTie1ErgVwf
Negative
Prox1Ptprc
Copy
How to tell apartLymphatic endothelium is also PECAM1+ CDH5+; check PROX1 and CCL21. Blood cells stuck to endothelium form doublets. Arterial, venous and capillary subtypes follow.
How to tell apartInflammation induces SELE, SELP and VCAM1 in other endothelial cells too; ACKR1 best marks postcapillary venules.
Capillary endothelial cells
capEC · capillary · cEC
Human
Core
CA4RGCCCD300LG
Supporting
CD36KDRFABP4PLVAPSPARCPECAM1CDH5
Negative
GJA5ACKR1
Copy
Mouse
Core
Car4RgccCd300lg
Supporting
Cd36KdrFabp4PlvapPecam1Cdh5
Negative
Gja5Ackr1
Copy
How to tell apartCapillary endothelium differs greatly between organs (lung aCap/gCap, liver sinusoidal EC, brain BBB EC); these general markers are only for a first pass. CD36 is also high in monocytes/macrophages and adipocytes, so it is only supporting.
Lymphatic endothelial cells
LEC · lymphatic
Human
Core
PROX1CCL21LYVE1PDPNTFF3
Supporting
FLT4MMRN1RELNPECAM1CDH5
Negative
C1QACD68
Copy
Mouse
Core
Prox1Ccl21aLyve1PdpnMmrn1
Supporting
Flt4RelnTbx1Pecam1Cdh5
Negative
C1qaCd68
Human CCL21 has several copies in mouse; Ccl21a is the one usually present in annotations.
Copy
How to tell apartLYVE1 is also on some macrophages and liver sinusoidal EC, PDPN on fibroblastic reticular cells and mesothelium; PROX1 is the most reliable but lowly expressed.
Mesothelial cells
Meso · mesothelium · mesothelial
Human
Core
MSLNUPK3BCALB2WT1KRT19
Supporting
ITLN1LRRN4KRT8KRT18BNC1
Negative
EPCAM
Copy
Mouse
Core
MslnUpk3bLrrn4Wt1Krt19
Supporting
Calb2Krt8Krt18Bnc1Upk1b
Negative
Epcam
Copy
How to tell apartLines pleura, peritoneum and epicardium (epicardial cells are also WT1+ UPK3B+). Unlike epithelium, EPCAM is low and WT1 is present.
Adipocytes
adipocyte · fat cell · ADI
Human
Core
ADIPOQPLIN1PLIN4LEP
Supporting
CIDEACIDECLPLPPARGFABP4GPAM
Copy
Mouse
Core
AdipoqPlin1CidecLep
Supporting
Plin4LplPpargFabp4Car3Retn
Brown/beige adipocytes additionally express Ucp1.
Copy
How to tell apartMature adipocytes are large and fragile and are rarely captured by standard scRNA-seq; they mostly appear in snRNA-seq.
Schwann cells
Schwann · SC · peripheral glia
Human
Core
MPZS100BSOX10PLP1CDH19
Supporting
NGFRPMP22GFRA3L1CAMMBPPRX
Negative
PMELMLANA
Copy
Mouse
Core
MpzS100bSox10Plp1Cdh19
Supporting
NgfrPmp22Gfra3L1camMbpPrx
Negative
PmelMlana
Copy
How to tell apartMelanocytes are also SOX10+ S100B+; rule them out with PMEL/MLANA. Myelinating Schwann cells are MPZ/PRX/MBP-high, non-myelinating ones NGFR/L1CAM-high.
Lung 14 types
Copy whole tissue (R list / Python dict)
Alveolar type 1 cells (AT1)
AT1 · ATI · AEC1 · type I pneumocyte
Human
Core
AGERRTKN2CLIC5EMP2
Supporting
HOPXCAV1PDPNSPOCK2GPRC5A
Negative
SFTPCLAMP3
Copy
Mouse
Core
AgerRtkn2Akap5Hopx
Supporting
Clic5PdpnCav1Emp2Spock2Gprc5a
Negative
SftpcLamp3
Copy
How to tell apartDuring injury repair, KRT8-high transitional cells between AT2 and AT1 appear (called ADI / DATP / PATS in mouse studies).
Alveolar type 2 cells (AT2)
AT2 · ATII · AEC2 · type II pneumocyte
Human
Core
SFTPCSFTPA1SFTPA2NAPSALAMP3
Supporting
SFTPBSFTPDABCA3LPCAT1SLC34A2PGC
Negative
AGERSCGB1A1
Copy
Mouse
Core
SftpcSftpa1NapsaLamp3Abca3
Supporting
SftpbSftpdLyz1Lyz2Slc34a2Lpcat1Etv5
Negative
AgerScgb1a1
Mouse AT2 cells express high Lyz1/Lyz2; do not call them macrophages because of it.
Copy
How to tell apartSFTPC is so high that it shows up in other clusters as ambient RNA. Mouse bronchioalveolar stem cells (BASC) are both Sftpc+ and Scgb1a1+.
Club cells
Club · Clara · secretory
Human
Core
SCGB1A1SCGB3A1SCGB3A2
Supporting
CYP2F1BPIFA1MSMBWFDC2SLPI
Negative
FOXJ1
Copy
Mouse
Core
Scgb1a1Scgb3a2Cyp2f2Cbr2
Supporting
Scgb3a1Bpifa1Cyp4b1
Negative
Foxj1
Copy
How to tell apartSecretory cells form a club-to-goblet continuum: higher MUC5AC/MUC5B means more goblet-like.
Ciliated cells (airway)
ciliated · multiciliated · cilia
Human
Core
FOXJ1CAPSTPPP3DYNLRB2RSPH1
Supporting
CIMAP3TMEM190CCDC78SNTNCDHR3DNAH5
Copy
Mouse
Core
Foxj1Ccdc153Tppp3Dynlrb2Rsph1
Supporting
Cimap3Cdhr3Dnah5SntnTmem212
Copy
How to tell apartAirway, oviduct and brain ependyma all have multiciliated cells with similar genes; see brain "Ependymal cells". PIFO is now officially CIMAP3.
Airway basal cells
basal · airway basal
Human
Core
KRT5TP63KRT15
Supporting
KRT17S100A2KRT14BCAM
Negative
SCGB1A1FOXJ1
Copy
Mouse
Core
Krt5Trp63Krt15
Supporting
Krt17Krt14NgfrAqp3
Negative
Scgb1a1Foxj1
Human TP63 is Trp63 in mouse. In mouse, basal cells are confined to the trachea and main bronchi.
Copy
How to tell apartBasal cells of skin, breast and prostate are also KRT5+ TP63+; tissue origin must come from other markers.
Airway goblet / mucous cells
goblet · mucous · airway goblet
Human
Core
MUC5ACMUC5BBPIFB1
Supporting
TFF1TFF3SPDEFAGR2SCGB1A1
Negative
FOXJ1
Copy
Mouse
Core
Muc5acMuc5bAgr2Spdef
Supporting
Tff2Bpifb1Clca1
Negative
Foxj1
Mouse airways have few goblet cells at baseline; Muc5ac rises markedly after allergen/IL-13 challenge.
Copy
Pulmonary neuroendocrine cells (PNEC)
PNEC · NE · neuroendocrine
Human
Core
CHGACALCAASCL1GRP
Supporting
SCG5SCG2PCSK1NSYPCHGB
Copy
Mouse
Core
CalcaChgaAscl1Scg5
Supporting
ChgbResp18Pcsk1nSypScg2
Copy
Pulmonary ionocytes
ionocyte
Human
Core
FOXI1CFTRASCL3
Supporting
ATP6V1G3BSND
Copy
Mouse
Core
Foxi1CftrAscl3
Supporting
Atp6v1g3Bsnd
Copy
How to tell apartVery rare; FOXI1 is also expressed by kidney intercalated cells.
Alveolar macrophages
AM · AMs · alveolar macrophage
Human
Core
MARCOFABP4INHBAPPARG
Supporting
MSR1MCEMP1APOC1CD68MRC1GPNMB
Negative
FCN1LYVE1
Copy
Mouse
Core
SiglecfCar4Krt79Itgax
Supporting
Chil3Ear2Ear1PpargMarcoMrc1
Negative
Lyve1Ly6c2
Mouse Siglecf and Ear2 are also high in eosinophils; use Car4, Krt79 and Itgax to separate them (eosinophils are Ccr3/Il5ra-high and lack Car4/Krt79).
Copy
Lung interstitial macrophages
IM · IMs · interstitial macrophage
Human
Core
LYVE1F13A1FOLR2CD163
Supporting
C1QAC1QBMRC1SELENOPSTAB1
Negative
MARCOFABP4
Copy
Mouse
Core
C1qaMrc1Lyve1Folr2
Supporting
C1qbCx3cr1Cd163Pf4H2-Ab1
Negative
SiglecfCar4
Copy
How to tell apartLung macrophages are alveolar or interstitial; interstitial ones split into LYVE1-high/MHC-II-low and LYVE1-low/MHC-II-high subsets (Chakarov 2019).
Aerocytes (aCap)
aCap · aerocyte · CAP2
Human
Core
APLNEDNRBHPGDCA4
Supporting
TBX2SOSTDC1KDRCDH5PECAM1
Negative
APLNRFCN3
Copy
Mouse
Core
Car4AplnEdnrbTbx2
Supporting
KdrCdh5Pecam1
Negative
AplnrGpihbp1
Copy
How to tell apartLung capillary endothelium splits into aCap and gCap (Gillich 2020): aCap for gas exchange, gCap with progenitor-like features.
General capillary cells (gCap)
gCap · CAP1 · general capillary
Human
Core
FCN3APLNRIL7RGPIHBP1
Supporting
PLVAPKDRCDH5PECAM1
Negative
APLNEDNRBHPGD
Copy
Mouse
Core
Gpihbp1AplnrPlvapIl7r
Supporting
KitCdh5Pecam1
Negative
AplnCar4Ednrb
Copy
Alveolar fibroblasts
AF · alveolar fibroblast · lipofibroblast
Human
Core
NPNTITGA8FGFR4SCN7A
Supporting
GPC3LIMCH1SLIT2COL1A1PDGFRA
Negative
PI16SFRP2
Copy
Mouse
Core
NpntInmtCes1dTcf21
Supporting
Itga8Fgfr4Plin2Col13a1Pdgfra
Negative
Pi16Serpinf1
Copy
Adventitial fibroblasts (lung)
adventitial fibroblast
Human
Core
PI16SFRP2SERPINF1MFAP5
Supporting
DPTCD34SCARA5PDGFRACOL1A1
Negative
NPNTFGFR4
Copy
Mouse
Core
Pi16Serpinf1DptMfap5
Supporting
Cd34Scara5PdgfraCol1a1
Negative
NpntInmt
Copy
How to tell apartSame as the cross-tissue PI16+ universal fibroblasts, located around vessels and airways.
Liver 7 types
Hepatocyte transcripts (ALB, APOA1, …) are abundant and appear as ambient RNA in every cluster, especially in snRNA-seq; judge non-parenchymal cells by their own markers.
Copy whole tissue (R list / Python dict)
Hepatocytes
Hep · hepatocyte · PH
Human
Core
ALBAPOA1SERPINA1TTRHP
Supporting
TFAPOC3APOHFGBFGACYP3A4AHSG
Negative
KRT19KRT7
Copy
Mouse
Core
AlbApoa1TtrSerpina1aApoc3
Supporting
TrfApohFgbFgaAhsgHp
Negative
Krt19Krt7
Mouse α1-antitrypsin has several copies (Serpina1a–e); transferrin is Trf in mouse.
Copy
Pericentral hepatocytes (zone 3)
zone 3 · pericentral · central hepatocyte · PC hepatocyte
Human
Core
CYP2E1GLULCYP1A2OAT
Supporting
CYP3A4RHBGALB
Negative
HALSDS
Copy
Mouse
Core
GlulCyp2e1OatCyp1a2
Supporting
RhbgLect2Axin2Slc1a2Alb
Negative
Cyp2f2HalSds
Copy
How to tell apartHepatocytes form a continuous portal-to-central gradient; mid-lobular (zone 2) cells share features of both ends.
Periportal hepatocytes (zone 1)
zone 1 · periportal · portal hepatocyte · PP hepatocyte
Human
Core
HALSDSCPS1ASS1
Supporting
PCK1HAMPARG1ALB
Negative
CYP2E1GLUL
Copy
Mouse
Core
Cyp2f2HalSdsPck1
Supporting
Cps1Ass1HampAlb
Negative
GlulCyp2e1
Copy
How to tell apartZonation genes differ somewhat between species; e.g. Cyp2f2 is a classic periportal marker in mouse.
Cholangiocytes
cholangiocyte · biliary epithelial · BEC · bile duct
Human
Core
KRT19KRT7EPCAMSOX9
Supporting
CFTRSPP1ANXA4TACSTD2ONECUT1HNF1B
Negative
ALBAPOA1
Copy
Mouse
Core
Krt19Krt7EpcamSox9
Supporting
Spp1CftrHnf1bClu
Negative
AlbApoa1
Copy
Kupffer cells
KC · Kupffer
Human
Core
CD5LVSIG4MARCOTIMD4
Supporting
C1QACD163SLC40A1HMOX1FOLR2
Negative
FCN1S100A8
Copy
Mouse
Core
Clec4fVsig4Cd5lTimd4
Supporting
C1qaMarcoSlc40a1Hmox1Folr2Cd163Adgre1
Negative
Ly6c2Ccr2
Clec4f is the classic mouse Kupffer cell marker; in human, CD5L, VSIG4, MARCO and TIMD4 are used.
Copy
How to tell apartThe liver also has monocyte-derived macrophages (FCN1, S100A8 or CCR2-high) and lipid-associated macrophages (TREM2, GPNMB, SPP1; common in steatosis/fibrosis).
Liver sinusoidal endothelial cells
LSEC · LSECs · sinusoidal endothelial
Human
Core
CLEC4GCLEC4MSTAB2CRHBP
Supporting
FCN2FCN3OIT3DNASE1L3LYVE1STAB1
Negative
VWF
Copy
Mouse
Core
Stab2Clec4gOit3Dnase1l3
Supporting
KdrLyve1Fcgr2bStab1Mrc1Bmp2
Negative
Vwf
Human CLEC4M (L-SIGN) has no one-to-one mouse ortholog.
Copy
How to tell apartLarge-vessel endothelium (portal and central veins) is VWF-high; sinusoidal endothelium is VWF-low.
Hepatic stellate cells
HSC · HSCs · stellate · Ito cell
Human
Core
RELNLRATCOLEC11HGF
Supporting
DCNPDGFRBRGS5NGFRECM1
Negative
MYH11
Copy
Mouse
Core
LratRelnColec11Hgf
Supporting
DcnDesPdgfrbRgs5NgfrEcm1
Negative
Myh11
Copy
How to tell apartWhen activated (fibrosis) COL1A1, ACTA2, TIMP1 and LUM go up and LRAT/RELN go down (myofibroblast-like). Note that "HSC" also means hematopoietic stem cell (see bone marrow).
Kidney 7 types
Copy whole tissue (R list / Python dict)
Podocytes
POD · podocyte
Human
Core
NPHS1NPHS2PODXLPTPRO
Supporting
WT1CLIC5SYNPOMAFBPLA2R1
Negative
LRP2
Copy
Mouse
Core
Nphs1Nphs2PodxlPtpro
Supporting
Wt1Clic5SynpoMafb
Negative
Lrp2
Copy
Proximal tubule cells
PT · PTC · proximal tubule · S1 · S2 · S3
Human
Core
LRP2CUBNSLC34A1SLC5A12
Supporting
ALDOBHNF4ASLC22A6SLC22A8GATMMIOX
Negative
UMODAQP2
Copy
Mouse
Core
Lrp2Slc34a1Slc5a12Cubn
Supporting
AldobHnf4aSlc22a6KapMioxGatmSlc5a2Slc7a13
Negative
UmodAqp2
In mouse, S1/S2 segments are Slc5a2-high and S3 is Slc7a13-high; Kap is higher in males.
Copy
How to tell apartThe most abundant and most dissociation-sensitive kidney cells. Injured / failed-repair states up-regulate HAVCR1 (KIM-1) and VCAM1 and lose LRP2/SLC34A1.
Thick ascending limb (TAL)
TAL · LOH · loop of Henle · mTAL · cTAL
Human
Core
UMODSLC12A1CLDN16CASR
Supporting
EGFKCNJ1CLDN10
Negative
LRP2SLC12A3
Copy
Mouse
Core
UmodSlc12a1Cldn16Casr
Supporting
EgfKcnj1Cldn10Ptger3
Negative
Lrp2Slc12a3
Copy
Distal convoluted tubule (DCT)
DCT · distal tubule
Human
Core
SLC12A3TRPM6CALB1
Supporting
EGFCNNM2SLC8A1
Negative
UMODAQP2
Copy
Mouse
Core
Slc12a3PvalbTrpm6Calb1
Supporting
EgfSlc8a1Cnnm2
Negative
UmodAqp2
Copy
How to tell apartCALB1 is also high in the connecting tubule (CNT); mouse DCT1 is Pvalb-high.
Collecting duct principal cells
PC · principal cell · CD-PC · CNT · collecting duct
Human
Core
AQP2SCNN1GFXYD4GATA3
Supporting
AQP3HSD11B2SCNN1BAVPR2CALB1
Negative
ATP6V1G3FOXI1
Copy
Mouse
Core
Aqp2Scnn1gFxyd4Hsd11b2
Supporting
Aqp3Scnn1bAvpr2Gata3Calb1
Negative
Atp6v1g3Foxi1
Copy
Intercalated cells
IC · IC-A · IC-B · intercalated
Human
Core
ATP6V1G3ATP6V0D2FOXI1ATP6V1B1
Supporting
SLC4A1SLC26A4SLC4A9
Negative
AQP2
Copy
Mouse
Core
Atp6v1g3Atp6v0d2Foxi1Atp6v1b1
Supporting
Slc4a1Slc26a4Slc4a9
Negative
Aqp2
Copy
How to tell apartType A intercalated cells are SLC4A1-high, type B SLC26A4-high; FOXI1 is also in airway ionocytes.
Mesangial cells
MC · mesangial
Human
No specific marker; the genes below are the best available combination (see note)
Core
ITGA8PDGFRBPIEZO2GATA3
Supporting
POSTNDESACTA2
Negative
MYH11
Mesangial cells share many genes with vascular smooth muscle and pericytes and have no single specific gene; verify with tissue location.
Copy
Mouse
No specific marker; the genes below are the best available combination (see note)
Core
Itga8PdgfrbGata3Des
Supporting
Piezo2Acta2Ren1
Negative
Myh11
Same caveat as human; Ren1-high cells are juxtaglomerular (JG) cells.
How to tell apartContinuous with transit-amplifying (TA) cells, which are MKI67/TOP2A-high with fading LGR5. In human, OLFM4 is a good crypt-base marker.
Enterocytes (small intestine)
enterocyte · absorptive · SI enterocyte
Human
Core
FABP2APOA4RBP2ALPI
Supporting
APOBSIFABP1MTTPAPOA1FABP6
Negative
MUC2LGR5
Copy
Mouse
Core
Fabp2Apoa4Rbp2Alpi
Supporting
ApobSisFabp1MttpApoa1Fabp6
Negative
Muc2Lgr5
Copy
How to tell apartDuodenum and ileum differ: the ileum is FABP6/SLC10A2-high. Mouse sucrase-isomaltase is Sis (human SI).
Colonocytes
colonocyte · colon epithelium
Human
Core
CA1SLC26A3AQP8CEACAM7
Supporting
CA2GUCA2AGUCA2BCA4SLC26A2KRT20MS4A12
Negative
FABP2APOA4
Copy
Mouse
Core
Car1Slc26a3Aqp8Car4
Supporting
Car2Guca2aGuca2bKrt20Slc26a2
Negative
Fabp2Apoa4
Human CA1/CA2/CA4 are Car1/Car2/Car4 in mouse.
Copy
BEST4+ epithelial cells
BEST4 · BEST4+ enterocyte · OTOP2
Human
Core
BEST4OTOP2CA7SPIB
Supporting
GUCA2BCFTR
Copy
Mouse
No entry for this speciesMouse has no BEST4 ortholog and no corresponding intestinal population has been described.
How to tell apartSPIB is also expressed by M cells and pDCs.
Goblet cells (intestine)
goblet · GC
Human
Core
MUC2TFF3SPDEFFCGBPZG16
Supporting
CLCA1REG4SPINK4AGR2
Copy
Mouse
Core
Muc2Tff3Clca1Zg16Fcgbp
Supporting
SpdefAgr2Reg4Spink4Retnlb
Copy
Paneth cells
Paneth
Human
Core
DEFA5DEFA6REG3APLA2G2A
Supporting
LYZPRSS2ITLN2
Copy
Mouse
Core
Lyz1Defa24Mptx2Ang4
Supporting
Itln1Pnliprp2Defa22Reg3g
Negative
Lyz2
Human LYZ corresponds to Lyz1 in mouse Paneth cells (macrophages use Lyz2). Mouse α-defensins (Defa*) have dozens of copies with no one-to-one match to human DEFA5/DEFA6.
Copy
How to tell apartMainly in the small intestine; nearly absent from normal colon (Paneth cell metaplasia can occur in inflammation).
Tuft cells
tuft · brush cell · Dclk1
Human
Core
POU2F3IRAG2SH2D6AVIL
Supporting
TRPM5HCKPTGS1IL25DCLK1
Copy
Mouse
Core
Dclk1Pou2f3Trpm5Il25
Supporting
AvilSh2d6Irag2Ptgs1Alox5apGnat3
Copy
How to tell apartLRMP is now officially IRAG2. Airways and bile ducts also contain tuft cells with similar genes.
Enteroendocrine cells
EEC · EE · enteroendocrine · EC cell · L cell · K cell
Human
Core
CHGACHGBNEUROD1SCGN
Supporting
TPH1PYYGCGGIPCCKSST
Copy
Mouse
Core
ChgaChgbNeurod1
Supporting
Tph1PyyGcgGipCckSstScg5
Copy
How to tell apartEC cells: TPH1; L cells: GCG/PYY; K cells: GIP; I cells: CCK; D cells: SST.
Microfold (M) cells
M cell · microfold
Human
Core
SPIBGP2CCL20
Supporting
TNFRSF11ASOX8MARCKSL1
Copy
Mouse
Core
Gp2SpibSox8Tnfaip2
Supporting
Ccl20Ccl9Marcksl1
Copy
How to tell apartOnly in follicle-associated epithelium (e.g. Peyer’s patches); rare in standard intestinal epithelium data.
Stomach 5 types
Copy whole tissue (R list / Python dict)
Pit (surface mucous) cells
pit · foveolar · surface mucous
Human
Core
MUC5ACTFF1GKN1GKN2
Supporting
TFF2VSIG1CLDN18
Negative
MUC6PGC
Copy
Mouse
Core
Gkn1Gkn2Tff1Muc5ac
Supporting
Vsig1Cldn18
Negative
Muc6Pgc
Copy
Mucous neck cells
MNC · neck · mucous neck
Human
Core
MUC6TFF2PGC
Negative
MUC5ACGKN1ATP4B
Copy
Mouse
Core
Muc6Tff2Gkn3
Supporting
Pgc
Negative
Muc5acGkn1Atp4b
Copy
How to tell apartNeck cells differentiate continuously into chief cells; intermediates are MUC6- and PGC/LIPF-high. Antral gland mucous cells are also MUC6+ TFF2+.
Chief cells
chief · zymogenic · peptic
Human
Core
PGA3PGA4LIPFPGC
Supporting
PGA5CHIA
Negative
MUC5ACATP4B
Copy
Mouse
Core
Pga5Chia1CblifPgc
Supporting
ClpsBhlha15
Negative
Muc5acAtp4b
Intrinsic factor is made by parietal cells in human (CBLIF, formerly GIF) but by chief cells in mouse (Cblif).
Copy
How to tell apartPGA3/PGA4/PGA5 are nearly identical, so reads may be split between them.
Parietal cells
parietal · oxyntic
Human
Core
ATP4AATP4BCBLIFKCNE2
Supporting
CA2
Copy
Mouse
Core
Atp4aAtp4bKcne2
Supporting
Car2
Copy
How to tell apartParietal cells are found only in the corpus/fundus, not in the antrum.
Gastric enteroendocrine cells
EEC · G cell · D cell · ECL · X/A cell
Human
Core
CHGAGASTSSTGHRL
Supporting
CHGBHDCNEUROD1
Copy
Mouse
Core
ChgaGastSstGhrl
Supporting
ChgbHdcNeurod1
Copy
How to tell apartG cells: GAST (antrum); D cells: SST; ECL cells: HDC (corpus; mast cells are HDC+ too); X/A cells: GHRL.
Brain 11 types
Brain is usually profiled by snRNA-seq; high nuclear transcripts (MALAT1, …) and low mitochondrial reads are normal.
Copy whole tissue (R list / Python dict)
Neurons (all)
neuron · Neu
Human
Core
RBFOX3SNAP25SYT1STMN2
Supporting
RBFOX1CELF4NEFLSYP
Negative
AQP4MBP
Copy
Mouse
Core
Rbfox3Snap25Syt1Stmn2
Supporting
Rbfox1Celf4NeflSyp
Negative
Aqp4Mbp
Copy
Excitatory neurons
Ex · ExN · excitatory · glutamatergic
Human
Core
SLC17A7SATB2NEUROD6
Supporting
SLC17A6CAMK2ATBR1CUX2RORBFEZF2
Negative
GAD1GAD2
Copy
Mouse
Core
Slc17a7Satb2Neurod6
Supporting
Slc17a6Camk2aTbr1Cux2RorbFezf2
Negative
Gad1Gad2
Copy
How to tell apartCortical layers: CUX2 ≈ L2/3, RORB ≈ L4, FEZF2 ≈ L5; subcortical excitatory neurons mostly use SLC17A6.
Inhibitory neurons
In · InN · inhibitory · GABAergic · interneuron
Human
Core
GAD1GAD2SLC32A1
Supporting
SSTPVALBVIPLAMP5ADARB2LHX6
Negative
SLC17A7SATB2
Copy
Mouse
Core
Gad1Gad2Slc32a1
Supporting
SstPvalbVipLamp5Adarb2Lhx6
Negative
Slc17a7Satb2
Copy
How to tell apartCortical interneurons split into PVALB, SST, VIP and LAMP5 classes (MGE-derived LHX6+, CGE-derived ADARB2+).
Astrocytes
Astro · AST · astrocyte
Human
Core
AQP4GFAPSLC1A2SLC1A3ALDH1L1
Supporting
GJA1ALDOCGLULSLC4A4FGFR3
Negative
PDGFRAMBP
Copy
Mouse
Core
Aqp4Slc1a3Slc1a2Aldh1l1Gja1
Supporting
GfapAldocGlulSlc4a4Fgfr3Sparcl1
Negative
PdgfraMbp
Copy
How to tell apartCortical protoplasmic astrocytes may be GFAP-low (fibrous and reactive astrocytes are GFAP-high); AQP4, SLC1A3 and ALDH1L1 are more universal.
Oligodendrocytes
Oligo · OL · ODC · oligodendrocyte
Human
Core
MBPPLP1MOGMOBPMAG
Supporting
ST18CNPOPALINCLDN11ERMN
Negative
PDGFRACSPG4
Copy
Mouse
Core
MbpPlp1MogMobpMag
Supporting
Cldn11CnpOpalinErmnSt18
Negative
PdgfraCspg4
Copy
How to tell apartPLP1 and MBP are abundant and appear in other clusters as ambient RNA; peripheral Schwann cells are PLP1+/MBP+ too.
Oligodendrocyte precursor cells (OPC)
OPC · NG2 glia · oligodendrocyte precursor
Human
Core
PDGFRACSPG4VCANPTPRZ1
Supporting
OLIG1OLIG2SOX10BCANGPR17
Negative
MOGMOBP
Copy
Mouse
Core
PdgfraCspg4VcanPtprz1
Supporting
Olig1Olig2Sox10C1ql1BcanGpr17
Negative
MogMobp
Copy
How to tell apartDifferentiating intermediates (COP / newly formed oligodendrocytes) are GPR17-high, plus Bmp4 and Neu4 in mouse.
Microglia
MG · microglia
Human
Core
P2RY12TMEM119CX3CR1SALL1
Supporting
CSF1RC1QAHEXBGPR34OLFML3
Negative
MRC1LYVE1CD163
Copy
Mouse
Core
P2ry12Tmem119Sall1HexbFcrl2
Supporting
Cx3cr1Csf1rC1qaGpr34Olfml3Siglech
Negative
Mrc1Lyve1Cd163
Mouse Fcrls is now officially Fcrl2. Mouse microglia also express Siglech (do not confuse with pDCs).
Copy
How to tell apartDisease-associated microglia (DAM) lose P2RY12/TMEM119 and gain APOE, TREM2, LPL, CST7 (Keren-Shaul 2017). Infiltrating monocyte-derived macrophages lack TMEM119 and SALL1.
Border-associated macrophages (BAM)
BAM · PVM · perivascular macrophage · CAM
Human
Core
MRC1LYVE1CD163F13A1
Supporting
SIGLEC1MS4A7STAB1C1QA
Negative
P2RY12TMEM119
Copy
Mouse
Core
Mrc1Pf4Lyve1Cd163Ms4a7
Supporting
F13a1Siglec1Stab1C1qa
Negative
P2ry12Tmem119Sall1
Copy
How to tell apartLocated around vessels, in the meninges and in the choroid plexus.
Brain endothelial cells (blood–brain barrier)
BBB · brain EC · brain endothelial
Human
Core
CLDN5FLT1SLC2A1ABCB1
Supporting
MFSD2APECAM1CDH5ESAM
Negative
PLVAP
Copy
Mouse
Core
Cldn5Flt1Slc2a1Abcb1a
Supporting
Mfsd2aSlco1a4Pecam1Cdh5Ly6c1Itm2a
Negative
Plvap
Human ABCB1 has two mouse genes, Abcb1a and Abcb1b; the blood–brain barrier mainly uses Abcb1a.
Copy
How to tell apartBBB endothelium is PLVAP-low; PLVAP-high cells are fenestrated endothelium (choroid plexus, circumventricular organs).
Ependymal cells
ependymal · EPEN
Human
Core
FOXJ1DRC12TMEM212DYNLRB2
Supporting
CAPSRSPH1CIMAP3S100B
Copy
Mouse
Core
Foxj1Ccdc153Tmem212Dynlrb2
Supporting
Rarres2Rsph1Cimap3
Copy
How to tell apartHuman CCDC153 is now officially DRC12 (still Ccdc153 in mouse).
Choroid plexus epithelial cells
CP · CPE · choroid plexus
Human
Core
TTRKLCLIC6FOLR1
Supporting
KCNE2OTX2HTR2CAQP1
Copy
Mouse
Core
TtrKlClic6Folr1
Supporting
Kcne2Otx2Htr2cAqp1
Copy
How to tell apartTTR is extremely abundant and contaminates other clusters; it is also expressed by hepatocytes and pancreatic alpha cells.
Skin 6 types
Copy whole tissue (R list / Python dict)
Basal keratinocytes
KC · basal KC · BAS · keratinocyte
Human
Core
KRT5KRT14KRT15COL17A1
Supporting
TP63CXCL14ITGB4DST
Negative
KRT1KRT10
Copy
Mouse
Core
Krt5Krt14Krt15Col17a1
Supporting
Trp63Itgb4DstCxcl14
Negative
Krt1Krt10
Copy
Differentiated keratinocytes (spinous / granular)
SPN · GRN · spinous · granular · suprabasal · KC
Human
Core
KRT1KRT10KRTDAPDMKN
Supporting
SBSNLORICRINFLGIVLKRT2CALML5
Negative
KRT15COL17A1
Copy
Mouse
Core
Krt1Krt10KrtdapDmkn
Supporting
SbsnLoricrinFlgIvl
Negative
Krt15Col17a1
Copy
How to tell apartLoricrin is now officially LORICRIN (mouse Loricrin), formerly LOR.
Melanocytes
MEL · melanocyte
Human
Core
PMELMLANATYRP1DCTTYR
Supporting
MITFSOX10S100BKIT
Negative
MPZ
Copy
Mouse
Core
PmelMlanaTyrp1DctTyr
Supporting
MitfSox10Kit
Negative
Mpz
Copy
Langerhans cells
LC · Langerhans
Human
Core
CD207CD1AS100B
Supporting
HLA-DRAHLA-DQB2CD74EPCAM
Negative
C1QACD14
Copy
Mouse
Core
Cd207EpcamH2-Ab1
Supporting
Cd74H2-AaItgax
Negative
C1qa
Mouse lacks CD1A (only CD1d exists). In mouse, epidermal Cd207+ Epcam+ myeloid cells are Langerhans cells; dermal Cd207+ cDC1 are Epcam−.
Copy
Hair follicle bulge stem cells
HFSC · bulge · hair follicle stem cell
Human
Core
KRT15SOX9LHX2CD200
Supporting
KRT19LGR5KRT5
Negative
KRT1KRT10
Copy
Mouse
Core
Cd34Krt15Sox9Lhx2
Supporting
Lgr5Krt24Nfatc1Krt5
Negative
Krt1Krt10
Mouse bulge stem cells are Cd34+, whereas the human bulge is CD34− (use CD200 and KRT15 in human).
Copy
Sweat gland cells
sweat gland · eccrine · SG
Human
Core
DCDSCGB2A2MUCL1PIP
Supporting
SCGB1D2KRT19KRT7AQP5
Copy
Mouse
No entry for this speciesMice have sweat glands only in the paw pads, so back/ear skin samples usually contain none; mouse also lacks a DCD ortholog.
Heart 4 types
Cardiomyocytes are too large for standard scRNA-seq and are usually profiled by snRNA-seq; cardiomyocyte transcripts (TTN, MB, …) appear in other cells as ambient RNA. Judge epicardium with "Mesothelial cells".
How to tell apartAfter injury such as infarction they become POSTN/ACTA2-high myofibroblasts.
Sinoatrial node pacemaker cells
SAN · pacemaker · conduction
Human
Core
HCN4SHOX2TBX3ISL1
Copy
Mouse
Core
Hcn4Shox2Tbx3Isl1
Copy
How to tell apartExtremely rare; usually absent unless the sinoatrial node is dissected specifically.
Pancreas 5 types
INS and acinar enzymes are so abundant that they appear in every pancreatic cluster as ambient RNA; judge by relative levels. PP cells express PPY and epsilon cells GHRL; both are rare. Judge pancreatic stellate cells with the general pericyte/fibroblast entries.
Copy whole tissue (R list / Python dict)
Alpha cells (glucagon)
alpha · α cell · A cell · islet
Human
Core
GCGIRX2ARXTTR
Supporting
CHGAPCSK2GCTM4SF4FEV
Negative
INSSST
Copy
Mouse
Core
GcgArxIrx2Ttr
Supporting
ChgaPcsk2GcMafbIrx1
Negative
Ins1Ins2
Copy
Beta cells (insulin)
beta · β cell · B cell islet · islet
Human
Core
INSIAPPMAFANKX6-1
Supporting
PDX1HADHADCYAP1DLK1G6PC2
Negative
GCGSST
Copy
Mouse
Core
Ins1Ins2IappMafaNkx6-1
Supporting
Pdx1G6pc2Slc2a2Ucn3
Negative
GcgSst
Mouse has two insulin genes, Ins1 and Ins2. Mouse beta cells are Slc2a2 (GLUT2)-high, human beta cells SLC2A2-low.
Copy
Delta cells (somatostatin)
delta · δ cell · D cell · islet
Human
Core
SSTHHEXRBP4
Supporting
LEPRBCHECHGA
Negative
INSGCG
Copy
Mouse
Core
SstHhexRbp4
Supporting
LeprChgaGhsr
Negative
Ins1Gcg
Copy
Acinar cells
acinar · ACC
Human
Core
PRSS1CPA1CELA3ACTRB1PNLIP
Supporting
CPB1CELCTRB2REG1ASPINK1CPA2
Negative
KRT19
Copy
Mouse
Core
Cpa1Cela3bCtrb1Pnlip
Supporting
Cpb1CelPrss2Reg1Spink1Cela2a
Negative
Krt19
Copy
How to tell apartMouse trypsinogen genes do not map one-to-one to human (e.g. Prss2); use Cela3b for elastase.
Pancreatic ductal cells
duct · ductal
Human
Core
KRT19CFTRSOX9KRT7
Supporting
MMP7SPP1SLC4A4CA2
Negative
PRSS1CPA1
Copy
Mouse
Core
Krt19CftrSox9Spp1
Supporting
Krt7Slc4a4Car2
Negative
Cpa1Cela3b
Copy
Mammary gland / breast 3 types
Mammary epithelium has three main classes: hormone-sensing mature luminal, luminal progenitor and basal/myoepithelial cells; stroma, fat and immune cells follow the general entries.
Copy whole tissue (R list / Python dict)
Hormone-sensing luminal cells (mature luminal)
LumHR · HS · mature luminal · ML · LHS
Human
Core
ESR1PGRANKRD30AAR
Supporting
FOXA1PRLRTBX3KRT18KRT8
Negative
KRT14ELF5
Copy
Mouse
Core
Esr1PgrPrlrFoxa1
Supporting
ArCited1Krt18Krt8
Negative
Krt14Elf5
Human ANKRD30A has no mouse ortholog.
Copy
Luminal progenitor (secretory luminal) cells
LP · LumSec · luminal progenitor · alveolar
Human
Core
KITELF5SLPILTF
Supporting
MMP7KRT15PIGRCCL28ALDH1A3
Negative
ESR1PGR
Copy
Mouse
Core
Elf5KitAldh1a3Cd14
Supporting
Csn3Krt8Krt18
Negative
Esr1Pgr
Copy
Basal / myoepithelial cells (breast)
BMYO · basal · myoepithelial · ME
Human
Core
KRT5KRT14ACTA2OXTRTP63
Supporting
KRT17MYLKMYH11CNN1
Negative
ESR1KIT
Copy
Mouse
Core
Krt5Krt14Acta2OxtrTrp63
Supporting
Krt17MylkMyh11Cnn1
Negative
Esr1Kit
Copy
Bone marrow and hematopoiesis 8 types
Hematopoiesis is a continuum and progenitor boundaries are fuzzy; mature blood cells are in "Immune cells".
How to tell apartCTSK and MMP9 are also in some macrophages; osteoclasts are large multinucleated cells and hard to capture.
Testis 7 types
Germ cells change continuously along differentiation; spermatid PRM/TNP transcripts are so abundant that they contaminate every cluster. Judge peritubular myoid cells with "Smooth muscle cells".
How to tell apartAMH falls after puberty; immature (prepubertal) Sertoli cells are AMH-high.
Leydig cells
Leydig · LC
Human
Core
INSL3CYP17A1STARCYP11A1
Supporting
HSD3B2LHCGRDLK1HSD17B3
Negative
SOX9ACTA2
Copy
Mouse
Core
Insl3Cyp17a1StarCyp11a1
Supporting
Hsd3b1Hsd3b6LhcgrHsd17b3
Negative
Sox9Acta2
The 3β-HSD family does not map one-to-one: human testis uses HSD3B2, mouse Hsd3b1/Hsd3b6 and others.
Copy
Tumor microenvironment 10 types
Malignant cells have no universal marker: find epithelial cells with lineage markers (e.g. EPCAM, KRT) and separate malignant from normal by inferred copy-number changes (inferCNV, copyKAT, …). CAF and TAM subsets form continua with intermediate states.
Copy whole tissue (R list / Python dict)
Myofibroblastic CAFs (myCAF)
myCAF · CAF · myofibroblast
Human
Core
ACTA2TAGLNMYL9POSTN
Supporting
COL1A1COL1A2TPM2MMP11FAP
Negative
MYH11KCNJ8
Copy
Mouse
Core
Acta2TaglnMyl9Postn
Supporting
Col1a1Col1a2Tpm2Fap
Negative
Myh11Kcnj8
Copy
How to tell apartTumor pericytes are also ACTA2/MYL9-high and are easily mistaken for myCAF: RGS5/KCNJ8/PDGFRB-high, collagen-low clusters are pericytes.
Inflammatory CAFs (iCAF)
iCAF · inflammatory CAF · CAF
Human
Core
IL6CXCL12PDGFRAC3
Supporting
CFDHAS1LIFCXCL1CXCL14DPT
Copy
Mouse
Core
Il6Cxcl12Ly6c1Has1
Supporting
Cxcl1DptClec3bC3PdgfraLif
Copy
How to tell apartThe myCAF/iCAF split comes from pancreatic cancer studies (Öhlund 2017, Elyada 2019) and broadly applies to other cancers.
Antigen-presenting CAFs (apCAF)
apCAF · antigen-presenting CAF · CAF
Human
Core
CD74HLA-DRAHLA-DPA1SLPI
Supporting
HLA-DRB1COL1A1DCN
Negative
PTPRCLYZC1QA
Copy
Mouse
Core
Cd74H2-Ab1H2-AaSaa3
Supporting
SlpiH2-Eb1Col1a1Msln
Negative
PtprcLyz2C1qa
Human HLA-DR corresponds to mouse H2-Ab1 / H2-Aa / H2-Eb1.
Copy
How to tell apartRare; always rule out doublets with macrophages/DCs (PTPRC, LYZ, C1QA should be low).
Matrix CAFs (COL11A1+)
mCAF · matrix CAF · COL11A1 CAF · ECM-CAF · CAF
Human
Core
COL11A1COMPMMP11FAPCTHRC1
Supporting
POSTNCOL10A1SULF1INHBACOL1A1
Copy
Mouse
Core
Col11a1FapCthrc1Comp
Supporting
PostnSulf1InhbaCol1a1
Copy
How to tell apartPartly overlaps with myCAF; normal-tissue fibroblasts hardly express COL11A1.
SPP1+ tumor-associated macrophages
TAM · SPP1 TAM · SPP1+ macrophage
Human
Core
SPP1FN1GPNMBAPOC1
Supporting
APOETREM2CD68CTSBVEGFA
Negative
FCN1S100A8
Copy
Mouse
Core
Spp1Arg1GpnmbFn1
Supporting
ApoeTrem2Cd68CtsbVegfaMmp12
Negative
Ly6c2S100a8
Copy
How to tell apartSPP1+ and C1QC+ TAMs are the two common TAM types across cancers (Zhang 2020); most tumors contain both, with intermediates.
How to tell apartThis is terminal exhaustion; their precursors (Tpex) are TCF7/SLAMF6-high and HAVCR2-low. Activated T cells transiently up-regulate PDCD1, so PDCD1 alone is not enough.
Progenitor exhausted T cells (Tpex)
Tpex · progenitor exhausted · stem-like
Human
Core
TCF7PDCD1SLAMF6TOX
Supporting
GZMKCD8ACXCR5IL7R
Negative
HAVCR2ENTPD1
Copy
Mouse
Core
Tcf7Pdcd1Slamf6Tox
Supporting
Cxcr5Xcl1Id3Cd8a
Negative
Havcr2Entpd1
Copy
Tumor-infiltrating Tregs
ti-Treg · tumor Treg · CCR8 Treg · Treg
Human
Core
FOXP3CCR8TNFRSF9TNFRSF4
Supporting
IL2RACTLA4IKZF2TNFRSF18LAYNBATF
Negative
CD8A
Copy
Mouse
Core
Foxp3Ccr8Tnfrsf9Tnfrsf4
Supporting
Il2raCtla4Ikzf2Tnfrsf18Batf
Negative
Cd8a
Copy
How to tell apartCompared with blood Tregs, CCR8, TNFRSF9 and TNFRSF4 are clearly higher.
Tip-like tumor endothelial cells
tip cell · TEC · angiogenic EC
Human
Core
ESM1ANGPT2APLNPGF
Supporting
KDRCOL4A1COL4A2PECAM1CDH5
Copy
Mouse
Core
Esm1Angpt2AplnPgf
Supporting
KdrCol4a1Col4a2Pecam1Cdh5
Copy
How to tell apartMouse lung aCap cells also express Apln; in lung tumors interpret with context.
Common states (not cell types) 3 types
These genes define states or technical artifacts that can occur in any cell type; if they top the reverse lookup, the cluster is mostly state-driven.
Copy whole tissue (R list / Python dict)
Cycling cells
cycling · proliferating · proliferation · S phase · G2M
Human
Core
MKI67TOP2ACENPFNUSAP1
Supporting
STMN1TYMSUBE2CBIRC5CDK1PCLAF
Copy
Mouse
Core
Mki67Top2aCenpfNusap1
Supporting
Stmn1TymsUbe2cBirc5Cdk1Pclaf
Copy
How to tell apartDetermine the lineage with other markers (cycling T, B, epithelium, …), or regress out cell-cycle scores before clustering.
Dissociation stress signature
stress · dissociation · IEG · heat shock
Human
Core
FOSJUNHSPA1AHSPA1B
Supporting
FOSBJUNBEGR1ATF3IER2DUSP1
Copy
Mouse
Core
FosJunHspa1aHspa1b
Supporting
FosbJunbEgr1Atf3Ier2Dusp1
Copy
How to tell apartTissue dissociation (especially 37 °C enzymatic digestion) induces immediate-early and heat-shock genes (van den Brink 2017); clusters separated only by these genes are usually artifacts.
Low-quality cells (high mitochondrial reads)
low quality · mito · mitochondrial · dying
Human
Core
MT-CO1MT-ND1MT-CYBMT-ATP6
Supporting
MT-CO2MT-CO3MT-ND2MT-ND4
Copy
Mouse
Core
mt-Co1mt-Nd1mt-Cytbmt-Atp6
Supporting
mt-Co2mt-Co3mt-Nd2mt-Nd4
Copy
How to tell apartUsually broken or dying cells that should be removed by a mitochondrial-fraction filter; metabolically active tissues (heart, kidney) are naturally higher, so set thresholds per tissue.
Core markers are specific and reliably detected: check first whether they are high together in the cluster. Supporting markers back the call but are less specific. Negative markers are high in look-alike types and should be low here; use them to rule out confusion.
Human and mouse are curated separately: the mouse column lists mouse markers, not human symbols with lower-case letters (e.g. human FCGR3A corresponds to mouse Fcgr4; human pDC marker CLEC4C is replaced by Siglech / Bst2 in mouse). Where mouse lacks good markers or the cell type, this is stated.
All gene names are current official symbols (NCBI Gene, the same data as our Gene ID Converter); search and reverse lookup also recognize common aliases and old names (e.g. CD45 → PTPRC, PIFO → CIMAP3). An alias that maps to several genes in the table counts all of them (human CD16 → FCGR3A / FCGR3B); mouse Ly6C maps to the monocyte gene Ly6c2 first.
This is our own curation based on public resources and classic papers, for annotation guidance only: markers vary with tissue, disease state and protocol (single-cell vs single-nucleus), so validate annotations in your own data.
Copied R vectors / Python lists can go straight into Seurat DotPlot(features = …) or scanpy.pl.dotplot; “Copy whole tissue” gives a named list / dict grouped by cell type, keeping each gene only under its first cell type.
Main references
CellMarker 2.0 (Hu et al., Nucleic Acids Research, 2023)
PanglaoDB (Franzén et al., Database, 2019)
Human Protein Atlas single cell type atlas (Karlsson et al., Science Advances, 2021)
Tabula Sapiens (Tabula Sapiens Consortium, Science, 2022); Tabula Muris (Tabula Muris Consortium, Nature, 2018)
Azimuth human PBMC reference (Hao et al., Cell, 2021)
Human lung cell atlas (Travaglini et al., Nature, 2020); lung aCap / gCap (Gillich et al., Nature, 2020); lung interstitial macrophages (Chakarov et al., Science, 2019)
Human liver (MacParland et al., Nature Communications, 2018); mouse liver zonation (Halpern et al., Nature, 2017)
Mouse small intestinal epithelium (Haber et al., Nature, 2017); mouse endothelial atlas (Kalucka et al., Cell, 2020); cross-tissue fibroblasts (Buechler et al., Nature, 2021)
Disease-associated microglia (Keren-Shaul et al., Cell, 2017); dissociation stress genes (van den Brink et al., Nature Methods, 2017)
CAF subtypes (Öhlund et al., Journal of Experimental Medicine, 2017; Elyada et al., Cancer Discovery, 2019); TAM subtypes (Zhang et al., Cell, 2020)