annotuneagent 0.1.0__py3-none-any.whl

annotuneagent/markers.tsv

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+species	scope	cell_type	parent	positive	negative	note	cl_id	cl_label	evidence	confidence	support
+human	any	T cell		CD3D;CD3E;CD3G;TRAC	MS4A1;CD79A;CD14	lineage; CD3D/CD3E/TRAC transcripts are also detected at lower levels in NK cells and ILCs (HPA, Azimuth NK_1), so use relative thresholds; MAIT, gamma-delta T and NKT are T-cell subsets	CL:0000084	T cell	Azimuth(PBMC:CD4 T +5)=4/4; PanglaoDB(T cells)=4/4; HPA(t-cells;top10)=4/4; lit=PMID:34062119|PMID:35549404	high
+human	any	CD4-positive, alpha-beta T cell	T cell	CD3E;IL7R	CD8A;CD8B;MS4A1	CD4 mRNA is low/dropout-prone in T cells and is expressed at higher levels by monocytes, macrophages and DCs (HPA), so it adds to the score only when enriched and is not required; IL7R is shared with CD8 memory T, MAIT and ILCs	CL:0000624	CD4-positive, alpha-beta T cell	Azimuth(PBMC:CD4 T +11)=3/3; PanglaoDB(T helper cells)=1/3; HPA(t-cells;top10)=3/3; lit=PMID:34062119	high	CD4
+human	any	CD8-positive, alpha-beta T cell	T cell	CD3E;CD8A;CD8B	CD4;MS4A1	CD8A is also expressed by some NK cells, gamma-delta T cells and CD8aa intraepithelial T cells; CD8B is more specific for alpha-beta CD8 T cells	CL:0000625	CD8-positive, alpha-beta T cell	Azimuth(PBMC:CD8 T +14)=3/3; PanglaoDB(T cytotoxic cells)=1/3; HPA(t-cells;top10)=3/3; lit=PMID:34062119	high
+human	any	B cell		MS4A1;CD79A;CD79B;CD19;BANK1	CD3E;CD3D	CD79A/CD79B are retained in plasma cells while MS4A1/CD19 are lost; pDCs can carry low B-like transcripts (e.g. IRF8/SPIB/TCF4) but lack MS4A1	CL:0000236	B cell	Azimuth(PBMC:B +3)=4/5; PanglaoDB(B cells)=5/5; HPA(b-cells;top10)=5/5; lit=PMID:34062119|PMID:35549404	high
+human	any	plasma cell		JCHAIN;MZB1;XBP1;TNFRSF17;DERL3	MS4A1;CD3E;LILRA4	"MS4A1 is usually lost; pDCs also express MZB1/JCHAIN/ITM2C (hence LILRA4 as negative); immunoglobulin transcripts (IGKC/IGHG/IGHA) are strong ambient RNAs; in Cell Ontology plasma cell is an antibody secreting cell of the B lineage, not a subclass of ""B cell"""	CL:0000786	plasma cell	Azimuth(PBMC:Plasmablast +9)=5/5; PanglaoDB(Plasma cells)=3/5; HPA(plasma cells;top10)=5/5; lit=PMID:34062119	high
+human	any	NK cell		NKG7;GNLY;KLRD1;KLRF1	MS4A1;CD3D;CD3G;CD5	CD3E (and CD247/TRDC) mRNA is detectable in human NK cells (HPA nk-cells CD3E ~1/3 of T-cell level; CD3E listed among Azimuth NK_1 markers), so CD3E was replaced by CD3D/CD3G/CD5 as negatives; NKT-like and effector CD8/gamma-delta T cells share NKG7/GNLY/KLRD1 and must be excluded by T-cell genes, not by NK genes	CL:0000623	natural killer cell	Azimuth(PBMC:NK +11)=4/4; PanglaoDB(NK cells)=4/4; HPA(nk-cells;top10)=4/4; lit=PMID:34062119|PMID:30413361	high
+human	any	monocyte		LYZ;CD14;FCN1;CSF1R	CD3E;MS4A1;FCGR3B	CD14 is low in CD16+ monocytes; LYZ is one of the strongest ambient RNAs in blood/BALF samples; neutrophils also express LYZ/S100A8/S100A9/CD14 (exclude with FCGR3B/CSF3R/CXCR2)	CL:0000576	monocyte	Azimuth(PBMC:Mono +4)=3/4; PanglaoDB(Monocytes)=4/4; HPA(monocytes;top10)=4/4; lit=PMID:34062119|PMID:28428369	high
+human	any	CD14-positive monocyte	monocyte	CD14;LYZ;S100A8;VCAN;FCN1	FCGR3A;CD3E;FCGR3B	classical (CD14-high/CD16-low) monocytes; S100A8/S100A9 are also high in neutrophils (FCGR3B as negative); intermediate (CD14+CD16+) monocytes express both CD14 and FCGR3A, so FCGR3A negativity must be relative; CL term CL:0001054 also covers CD14+CD16+ monocytes, the strictly classical term is CL:0002057	CL:0001054	CD14-positive monocyte	Azimuth(PBMC:CD14 Mono +4)=5/5; PanglaoDB(Monocytes)=5/5; HPA(monocytes;top10)=5/5; lit=PMID:34062119|PMID:28428369	high
+human	any	CD16-positive monocyte	monocyte	FCGR3A;MS4A7;LST1;CDKN1C;HES4	CD14;CD3E;GNLY	"non-classical (CD14-low/CD16-high) monocytes; FCGR3A (CD16) is also high in CD56dim NK cells and neutrophils express FCGR3B, so GNLY is added as negative; mapped to CL ""CD14-low, CD16-positive monocyte"" (CL:0002396)"	CL:0002396	CD14-low, CD16-positive monocyte	Azimuth(PBMC:CD16 Mono +4)=5/5; PanglaoDB(Monocytes)=3/5; HPA(monocytes;top10)=3/5; lit=PMID:34062119|PMID:28428369	high
+human	any	platelet		PPBP;PF4;GP9;TUBB1	PTPRC;LYZ	anucleate; shares all markers with megakaryocytes; PTPRC is NOT fully absent from platelet transcriptomes (HPA platelets ~93 nCPM vs >900 in leukocytes) and platelet-monocyte/platelet-T aggregates or doublets co-express PPBP/PF4 with PTPRC/LYZ, so PTPRC and LYZ are relative negatives; platelet RNA also contributes ambient PPBP/PF4	CL:0000233	platelet	Azimuth(PBMC:Platelet +2)=4/4; PanglaoDB(Platelets)=4/4; HPA(platelets;top10)=4/4; lit=PMID:34062119	high
+human	any	erythrocyte		HBB;HBA1;HBA2;ALAS2;SLC4A1	PTPRC	HBB/HBA1/HBA2 are the most common ambient RNAs (blood, spleen, bone marrow, liver, lung); do not call erythrocytes from hemoglobin alone - require a very high hemoglobin UMI fraction plus ALAS2/SLC4A1 and low gene count, and consider SoupX/CellBender; cells retained after RBC lysis are mostly reticulocytes; PTPRC is genuinely low in erythrocytes (HPA ~10 nCPM)	CL:0000232	erythrocyte	Azimuth(PBMC:Eryth +2)=5/5; PanglaoDB(Erythroid-like and erythroid precursor cells)=4/5; HPA(erythrocytes;top10)=5/5; lit=PMID:34062119|PMID:33367645|PMID:37550580	high
+human	any	endothelial cell		PECAM1;VWF;CDH5;CLDN5;KDR	PTPRC;EPCAM	pan-endothelial incl. lymphatic EC; PECAM1 is also on leukocytes/platelets (hence PTPRC negative); VWF is low in capillary EC (e.g. lung gCap, brain) and high in platelets/megakaryocytes; CLDN5 is low in liver sinusoidal EC	CL:0000115	endothelial cell	Azimuth(Motor Cortex:Endo +4)=3/5; PanglaoDB(Endothelial cells)=5/5; HPA(vascular endothelial cells;top10)=5/5; lit=PMID:34030460|PMID:35549404	high
+human	lung	pulmonary alveolar type 2 cell		SFTPC;SFTPB;ABCA3;NAPSA;SLC34A2	AGER;PTPRC	SFTPC/SFTPB/SFTPA are among the strongest lung ambient RNAs and are also found in alveolar macrophages (ambient/phagocytosed), hence PTPRC negative; AGER is expressed at low level in AT2 and transitional AT2-AT1 states co-express both programs, so AGER negativity must be relative; SFTPB/NAPSA also in club/secretory cells	CL:0002063	pulmonary alveolar type 2 cell	Azimuth(Lung v1:Alveolar Epithelial Type 2 +3)=5/5; PanglaoDB(Pulmonary alveolar type II cells)=5/5; HPA(alveolar cells type 2;top10)=5/5; lit=PMID:33208946|PMID:37291214	high
+human	lung	pulmonary alveolar type 1 cell		AGER;PDPN;CLIC5;RTKN2;EMP2	SFTPC;PECAM1	PDPN is also expressed by lymphatic EC, mesothelium and some fibroblasts and AGER is low in AT2, so require the combination; AT1-capillary EC doublets are frequent (PECAM1 negative); AT1 often carry ambient SFTPC, so SFTPC negativity must be relative	CL:0002062	pulmonary alveolar type 1 cell	Azimuth(Lung v1:Alveolar Epithelial Type 1 +3)=3/5; PanglaoDB(Pulmonary alveolar type I cells)=5/5; HPA(alveolar cells type 1;top10)=5/5; lit=PMID:33208946|PMID:37291214	high
+human	lung	alveolar macrophage		FABP4;MARCO;MRC1;INHBA;PPARG	S100A8;CD3E	not blood monocyte; MRC1 is also expressed by interstitial/perivascular macrophages and FABP4 by some capillary EC and adipocytes, so use the combination; monocyte-derived AMs in disease have lower FABP4/MARCO	CL:0000583	alveolar macrophage	Azimuth(Lung v1:Macrophage +9)=3/5; PanglaoDB(Alveolar macrophages)=2/5; HPA(macrophages;top10)=4/5; lit=PMID:33208946|PMID:37291214|PMID:36103853	high
+human	liver	hepatocyte		ALB;APOB;TTR;APOC3;FGB	PTPRC;KRT19	ALB/APO*/SERPINA1/HP transcripts dominate liver ambient RNA; hepatocytes are fragile/large and under-represented in scRNA-seq (snRNA-seq recommended); zonation: CYP2E1/GLUL pericentral, HAL/SDS/CYP2F1-like periportal	CL:0000182	hepatocyte	Azimuth(Liver:Hepatocyte +1)=2/5; PanglaoDB(Hepatocytes)=5/5; HPA(hepatocytes;top10)=5/5; lit=PMID:30348985|PMID:31292543|PMID:35021063	high
+human	liver	Kupffer cell		VSIG4;CD5L;C1QA;MARCO;TIMD4	S100A8;CD3E	C1QA is pan-macrophage (kept for compatibility); CLEC4F is a mouse KC marker but is low in human scRNA; MARCO is also on alveolar and splenic macrophages	CL:0000091	Kupffer cell	Azimuth(Liver:Myeloid +1)=3/5; PanglaoDB(Kupffer cells)=4/5; HPA(kupffer cells;top10)=5/5; lit=PMID:30348985|PMID:35021063	high
+human	brain	microglial cell		P2RY12;TMEM119;CX3CR1;CSF1R	S100A8;CD3E;MRC1;LYVE1	MRC1/LYVE1 added as negatives to exclude border-associated macrophages; CX3CR1 is also on BAMs, monocytes and NK/effector T cells; P2RY12/TMEM119 are down-regulated in disease-associated/activated microglia; snRNA-seq under-detects microglial activation genes (Thrupp 2020) and dissociation induces artefactual activation genes (Marsh 2022)	CL:0000129	microglial cell	Azimuth(Motor Cortex:Micro-PVM +2)=3/4; PanglaoDB(Microglia)=4/4; HPA(microglia;top10)=4/4; lit=PMID:26884166|PMID:32997994|PMID:35260865	high
+human	brain	oligodendrocyte		PLP1;MBP;MOG;MOBP	AQP4;SLC17A7;PDGFRA	MBP (Golli-MBP isoforms) is broadly expressed by leukocytes (HPA: ~200-1800 nCPM in blood immune cells), so MBP is not oligodendrocyte-specific outside the CNS context; PLP1/MBP/MOBP/MOG are major brain (especially white matter, snRNA-seq) ambient RNAs and contaminate other clusters; PDGFRA added to exclude OPCs	CL:0000128	oligodendrocyte	Azimuth(Motor Cortex:Oligo +7)=4/4; PanglaoDB(Oligodendrocytes)=3/4; HPA(oligodendrocytes;top10)=4/4; lit=PMID:34616062	high
+human	brain	astrocyte		AQP4;GFAP;SLC1A3;SLC1A2;ALDH1L1	PLP1;SLC17A7	GFAP is high in fibrous/reactive astrocytes and also in Bergmann glia, ependymal and neural stem cells; SLC1A3 is also expressed by radial glia/progenitors	CL:0000127	astrocyte	Azimuth(Motor Cortex:Astro +5)=4/5; PanglaoDB(Astrocytes)=5/5; HPA(astrocytes;top10)=5/5; lit=PMID:34616062	high
+human	brain	excitatory neuron		SLC17A7;SATB2	GAD1;GAD2	CL term: glutamatergic neuron; SLC17A7 marks cortical/hippocampal, SLC17A6 thalamic/subcortical glutamatergic neurons; SATB2 is mostly cortical (IT-type); a cell need not express all positives	CL:0000679	glutamatergic neuron	Azimuth(Motor Cortex:Glutamatergic)=1/3; PanglaoDB(Glutaminergic neurons)=2/3; HPA(brain excitatory neurons;top10)=3/3; lit=PMID:34616062	high
+human	brain	inhibitory neuron		GAD1;GAD2;SLC32A1	SLC17A7;SLC17A6	CL term: GABAergic neuron; includes cortical interneurons, striatal medium spiny neurons and cerebellar Purkinje cells	CL:0000617	GABAergic neuron	Azimuth(Motor Cortex:GABAergic)=2/3; PanglaoDB(GABAergic neurons)=3/3; HPA(brain inhibitory neurons;top10)=3/3; lit=PMID:34616062	high
+human	any	regulatory T cell	CD4-positive, alpha-beta T cell	FOXP3;IL2RA;CTLA4;IKZF2	CD8A;MS4A1	FOXP3 mRNA is sparse (dropout); activated conventional CD4 T cells transiently express IL2RA/CTLA4 and low FOXP3, so use the combination; tumour Tregs additionally express TNFRSF4/TNFRSF18/LAYN	CL:0000792	CD4-positive, CD25-positive, alpha-beta regulatory T cell	Azimuth(PBMC:Treg +3)=4/4; PanglaoDB(T regulatory cells)=4/4; HPA(t-cells;top10)=3/4; lit=PMID:34062119|PMID:28622514	high
+human	any	naive CD4 T cell	CD4-positive, alpha-beta T cell	CCR7;SELL;TCF7;LEF1	CD8B;GZMK;FOXP3	CCR7/SELL/TCF7/LEF1 are shared with naive CD8 T and central memory T cells; distinguish from CD4 TCM by lower expression of memory genes (e.g. AQP3, CD69-independent) - naive vs TCM is a continuum in scRNA-seq	CL:0000895	naive thymus-derived CD4-positive, alpha-beta T cell	Azimuth(PBMC:CD4 Naive +2)=3/4; PanglaoDB(T cells naive)=2/4; HPA(t-cells;top10)=4/4; lit=PMID:34062119	medium
+human	any	memory CD4 T cell	CD4-positive, alpha-beta T cell	IL7R;S100A4;ANXA1;KLRB1	CD8B;FOXP3	covers central (CCR7+) and effector (CCR7-) memory; CCR7 negativity applies to effector memory only; KLRB1 is also high in MAIT cells (exclude with SLC4A10/TRAV1-2)	CL:0000897	CD4-positive, alpha-beta memory T cell	Azimuth(PBMC:CD4 TCM +8)=3/4; PanglaoDB(T memory cells)=1/4; HPA(t-cells;top10)=2/4; lit=PMID:34062119	medium
+human	any	naive CD8 T cell	CD8-positive, alpha-beta T cell	CCR7;SELL;LEF1;TCF7	CD4;GZMK;GZMB	naive CD4 and CD8 T cells share most naive genes; rely on CD8A/CD8B from the parent	CL:0000900	naive thymus-derived CD8-positive, alpha-beta T cell	Azimuth(PBMC:CD8 Naive +3)=3/4; PanglaoDB(T cells naive)=2/4; HPA(t-cells;top10)=4/4; lit=PMID:34062119	medium
+human	any	effector memory CD8 T cell	CD8-positive, alpha-beta T cell	GZMK;CCL5;GZMA;CST7	CCR7;SELL;CD4	GZMK+ effector memory; GZMK is also expressed by MAIT, CD56bright NK and some CD4 TEM; resident memory CD8 T (ITGAE/CXCR6/ZNF683) are a separate tissue state	CL:0000913	effector memory CD8-positive, alpha-beta T cell	Azimuth(PBMC:CD8 TEM +9)=3/4; PanglaoDB(T cytotoxic cells)=0/4; HPA(t-cells;top10)=4/4; lit=PMID:34062119|PMID:31474513	medium
+human	any	CD8 TEMRA cell	CD8-positive, alpha-beta T cell	GZMB;GNLY;FGFBP2;CX3CR1;ZNF683	CCR7;GZMK;CD4	terminally differentiated effector memory (CD45RA+); transcriptionally close to CD56dim NK cells (GNLY/FGFBP2/CX3CR1 shared), separate using CD8B/CD3D/TRBC; ZNF683 (Hobit) is variable	CL:0001062	effector memory CD8-positive, alpha-beta T cell, terminally differentiated	Azimuth(PBMC:CD8 TEM_1 +5)=4/5; PanglaoDB(T cytotoxic cells)=1/5; HPA(t-cells;top10)=5/5; lit=PMID:34062119	medium
+human	any	exhausted CD8 T cell	CD8-positive, alpha-beta T cell	PDCD1;HAVCR2;LAG3;TOX;CXCL13	CCR7;SELL;CD4	mainly tumour/chronic infection; PDCD1/LAG3 are also induced on recent activation; progenitor-exhausted (TCF7+PDCD1+TOX+) cells lack HAVCR2; CXCL13 is also high in human Tfh	CL:0020031	CD8-positive exhausted alpha-beta T cell	lit=PMID:28622514|PMID:30388456|PMID:34914499	medium
+human	any	gamma-delta T cell	T cell	TRDC;TRGC1;TRGC2;TRDV2;TRGV9	CD8B;CD4;TRAC	TRDC transcripts are also found in NK cells and ILCs (germline transcription), so require TRGC1/TRGC2 and lack of TRAC/CD8B; Vd2Vg9 (TRDV2/TRGV9) dominate blood, Vd1 (TRDV1) dominate tissues; TRDV2/TRGV9 are positive only for the blood Vd2 subset	CL:0000798	gamma-delta T cell	Azimuth(PBMC:gdT +4)=5/5; PanglaoDB(Gamma delta T cells)=5/5; HPA(t-cells;top10)=4/5; lit=PMID:34062119	medium
+human	any	MAIT cell	T cell	SLC4A10;TRAV1-2;KLRB1;ZBTB16;RORC	CD4;TRDC;FOXP3	human mucosal-associated invariant T cells (TRAV1-2 with TRAJ33/12/20); KLRB1/RORC/ZBTB16 are shared with Th17, ILC3 and some gamma-delta T; mouse MAIT cells are rare in lab strains, so no mouse row	CL:0000940	mucosal-associated invariant T cell	Azimuth(PBMC:MAIT +2)=2/5; HPA(t-cells;top10)=1/5; lit=PMID:34062119	high
+human	lymphoid	T follicular helper cell	CD4-positive, alpha-beta T cell	CXCR5;PDCD1;CXCL13;BCL6;ICOS	CD8A;FOXP3;MS4A1	tonsil/lymph node/tertiary lymphoid structures; CXCL13 is a strong human Tfh marker but is NOT typically expressed by mouse Tfh; T follicular regulatory cells co-express FOXP3; circulating Tfh express CXCR5 with low BCL6	CL:0002038	T follicular helper cell	Azimuth(Tonsil v2:CD4 TFH +5)=4/5; PanglaoDB(T follicular helper cells)=4/5; HPA(t-cells;top10)=3/5; lit=PMID:38301653	high
+human	any	CD56bright NK cell	NK cell	NCAM1;GZMK;XCL1;SELL;KLRC1	FCGR3A;CD3D;FGFBP2	CD56bright/CD16- NK, enriched in lymph nodes, tonsil and tissues; GZMK/XCL1 are shared with ILC1 and MAIT/CD8 TEM	CL:0000938	CD16-negative, CD56-bright natural killer cell, human	Azimuth(PBMC:NK_CD56bright +3)=5/5; PanglaoDB(NK cells)=3/5; HPA(nk-cells;top10)=3/5; lit=PMID:34062119|PMID:30413361	medium
+human	any	CD56dim NK cell	NK cell	FCGR3A;FGFBP2;GZMB;PRF1;SPON2	CD3D;GZMK;CD14	majority blood NK; FCGR3A also in CD16+ monocytes (CD14 negative), FGFBP2/GZMB/PRF1 shared with CD8 TEMRA (CD3D negative)	CL:0000939	CD16-positive, CD56-dim natural killer cell, human	Azimuth(PBMC:NK_1 +3)=4/5; PanglaoDB(NK cells)=5/5; HPA(nk-cells;top10)=5/5; lit=PMID:34062119|PMID:30413361	medium
+human	any	innate lymphoid cell		IL7R;KIT;TNFRSF25;KLRB1	CD3D;CD3E;MS4A1;CD14	lineage-negative; IL7R/KLRB1 are shared with memory T and MAIT cells, so CD3D/CD3E/TRAC absence is essential; blood ILCs are mostly ILCP/ILC2	CL:0001065	innate lymphoid cell	Azimuth(PBMC:ILC +2)=2/4; PanglaoDB(Nuocytes)=1/4; HPA(innate lymphoid cells;top10)=4/4; lit=PMID:34062119	medium
+human	any	ILC2	innate lymphoid cell	GATA3;PTGDR2;HPGDS	CD3D;TPSAB1;NCR2	canonical CRTH2+ human ILC2 panel; CRTH2-negative ILC2 exist and can be missed; PTGDR2/HPGDS/GATA3 are shared with Th2 cells and some granulocytes or mast cells, so require CD3D/TPSAB1 absence and ILC parent context	CL:0001069	group 2 innate lymphoid cell	lit=PMID:33420427|PMID:30578872	medium
+human	any	ILC3	innate lymphoid cell	RORC;KIT;IL23R;NCR2;IL22	CD3D;GATA3;PTGDR2	mucosal/tonsil ILC3; NCR2 (NKp44) marks NCR+ ILC3; LTi-like ILC3 lack NCR2; RORC/IL23R are shared with Th17 and MAIT cells - require CD3 negativity	CL:0001071	group 3 innate lymphoid cell	Azimuth(Tonsil v2:ILC +3)=3/5; HPA(innate lymphoid cells;top10)=5/5; lit=PMID:38301653	medium
+human	any	naive B cell	B cell	IGHD;TCL1A;FCER2;IL4R	CD27;IGHG1;MZB1	IGHD/IGHM are also expressed by unswitched memory B cells; TCL1A is lost on activation; transitional B cells are similar (higher CD24/CD38/MME)	CL:0000788	naive B cell	Azimuth(PBMC:B naive +8)=4/4; PanglaoDB(B cells naive)=4/4; HPA(b-cells;top10)=4/4; lit=PMID:34062119	high
+human	any	memory B cell	B cell	CD27;AIM2;TNFRSF13B;SSPN	TCL1A;IGHD;MZB1	class-switched memory B cells express IGHG/IGHA constant genes, unswitched memory keep IGHM (and some IGHD); atypical/age-associated B cells are FCRL5+ITGAX+TBX21+	CL:0000787	memory B cell	Azimuth(PBMC:B memory +8)=4/4; PanglaoDB(B cells memory)=3/4; HPA(b-cells;top10)=4/4; lit=PMID:34062119	medium
+human	lymphoid	germinal center B cell	B cell	BCL6;RGS13;MEF2B;AICDA;LMO2	CCR7;MZB1;CD3E	secondary lymphoid organs/TLS; dark-zone GC B cells are highly proliferative (MKI67/TOP2A) and should not be confused with plasmablasts (MZB1/XBP1 high); MEF2B/BCL6 also in some lymphomas	CL:0000844	germinal center B cell	Azimuth(Tonsil v2:DZ GCB +9)=4/5; HPA(b-cells;top10)=1/5; lit=PMID:38301653	high
+human	any	cDC1		CLEC9A;XCR1;CADM1;IDO1;BATF3	CD1C;FCER1A;CD14	CLEC9A is also expressed on pDC precursors at low level; IDO1 is induced in mregDCs; cDC1 are rare in blood (<0.1% PBMC)	CL:0002394	CD141-positive myeloid dendritic cell	Azimuth(PBMC:cDC1 +4)=5/5; HPA(cdc;top10)=4/5; lit=PMID:28428369|PMID:34062119	high
+human	any	cDC2		CD1C;FCER1A;CLEC10A;HLA-DQA1	CLEC9A;CD14;LILRA4	CD1C/FCER1A are also on B cells and basophils/mast (FCER1A); DC3 (CD14+CD163+ cDC2-like) overlap with monocytes, so CD14 negativity is relative	CL:0002399	CD1c-positive myeloid dendritic cell	Azimuth(PBMC:cDC2 +5)=4/4; HPA(cdc;top10)=4/4; lit=PMID:28428369|PMID:31474513|PMID:34062119	high
+human	any	plasmacytoid dendritic cell		LILRA4;CLEC4C;IL3RA;TCF4;IRF7	CD1C;MS4A1;MZB1	pDCs express JCHAIN/MZB1/ITM2C/GZMB and can be mis-labelled as plasma cells (and vice versa), hence MZB1 negative as relative only; AXL+SIGLEC6+ DC (ASDC) share IL3RA/TCF4	CL:0000784	plasmacytoid dendritic cell	Azimuth(PBMC:pDC +4)=5/5; PanglaoDB(Plasmacytoid dendritic cells)=5/5; HPA(pdcs;top10)=5/5; lit=PMID:28428369|PMID:34062119	high
+human	any	mature regulatory dendritic cell		LAMP3;CCR7;FSCN1;CCL19;IDO1	CD14;CD3E;MS4A1	"activation state (mregDC / ""LAMP3+ DC""), mainly in tumours and lymph nodes; derived from both cDC1 and cDC2; CCR7 is shared with naive/central memory T and B cells; mapped to CL ""migratory dendritic cell"""	CL:4047054	migratory dendritic cell	Azimuth(Lung v2 (HLCA):Migratory DCs +1)=0/5; lit=PMID:32269339|PMID:30979687	medium
+human	any	neutrophil		FCGR3B;CSF3R;CXCR2;CMTM2;S100A8	CD3E;MS4A1	neutrophils have very low RNA content and are depleted by many 10x workflows and default QC (min genes) and lost in PBMC/Ficoll preparations; S100A8/S100A9 are shared with classical monocytes; immature neutrophils (bone marrow) express LTF/CAMP/LCN2/MPO instead	CL:0000775	neutrophil	Azimuth(Kidney:Neutrophil +2)=3/5; PanglaoDB(Neutrophils)=3/5; HPA(neutrophils;top10)=5/5; lit=PMID:30979687	high
+human	any	basophil		ENPP3;HDC;CCR3;IL3RA	CD3E;KIT;TPSAB1	ENPP3/HDC/CCR3/IL3RA are expressed in human basophil single-cell data; ENPP3 and CCR3 can also occur in eosinophils, IL3RA in pDCs, and HDC in mast cells; require KIT/TPSAB1 absence to separate mast cells	CL:0000767	basophil	lit=PMID:41498390	medium
+human	any	mast cell		TPSAB1;TPSB2;CPA3;KIT;MS4A2	CD3E;CD14;CLC	tryptase genes TPSAB1/TPSB2 are highly specific; CPA3/MS4A2/HDC are shared with basophils; mucosal mast cells have low CMA1 (chymase) compared with connective-tissue mast cells	CL:0000097	mast cell	Azimuth(Lung v1:Basophil/Mast +14)=5/5; PanglaoDB(Mast cells)=5/5; HPA(mast cells;top10)=5/5; lit=PMID:35549404	high
+human	any	LYVE1+ resident macrophage		LYVE1;FOLR2;TIMD4;MRC1;SELENOP	S100A8;CD3E;CCR2	perivascular/interstitial tissue-resident macrophages (TLF+: TIMD4/LYVE1/FOLR2) conserved across organs; MRC1/LYVE1 are also expressed by lymphatic EC (LYVE1) and border-associated macrophages	CL:0000864	tissue-resident macrophage	Azimuth(Lung v2 (HLCA):Interstitial macrophages +2)=1/5; HPA(macrophages;top10)=5/5; lit=PMID:34331874|PMID:34995099	medium
+human	lung	interstitial macrophage		F13A1;LYVE1;FOLR2;SELENOP;CD163	MARCO;FABP4;INHBA	lung interstitial (perivascular) macrophages; separated from alveolar macrophages by low MARCO/FABP4/PPARG	CL:4033043	lung interstitial macrophage	Azimuth(Lung v2 (HLCA):Interstitial macrophages +2)=1/5; HPA(macrophages;top10)=5/5; lit=PMID:37291214|PMID:33208946|PMID:36103853	medium
+human	lymphoid	red pulp macrophage		SPIC;VCAM1	CD3E;MS4A1;S100A8	splenic red pulp macrophages; SPIC and VCAM1 are observed in human spleen single-cell data; iron-recycling genes HMOX1/SLC40A1 are not specific to this cell type	CL:0000874	splenic red pulp macrophage	lit=PMID:41384851	medium
+human	brain	border-associated macrophage		LYVE1;CD163	P2RY12;TMEM119;CD3E	LYVE1+ CD163+ parenchymal border macrophage subset near brain arteries; this pair does not cover every meningeal or choroid-plexus macrophage; P2RY12/TMEM119 distinguish from homeostatic microglia	CL:4042003	border associated macrophage	lit=PMID:36352225	medium
+human	skin	Langerhans cell		CD207;CD1A;FCGBP;S100B;EPCAM	CD14;CD3E;CD1C	epidermal Langerhans cells; CD1A is also on some cDC2/DC3 and CD207 on a minor dermal cDC subset; LCs express EPCAM (epithelial negative not applicable)	CL:0000453	Langerhans cell	PanglaoDB(Langerhans cells)=3/5; lit=PMID:33479125	medium
+human	any	megakaryocyte		ITGA2B;GP9;PF4;PPBP;VWF	PTPRC	nucleated megakaryocytes and their progenitors; platelets share all these genes - distinguish by higher gene counts/nucleated profile; megakaryocyte-erythroid progenitors express ITGA2B at low level	CL:0000556	megakaryocyte	Azimuth(Bone Marrow:Progenitor Megakaryocyte)=1/5; PanglaoDB(Megakaryocytes)=4/5; HPA(megakaryocytes;top10)=5/5; lit=PMID:31160568	medium
+human	any	hematopoietic stem and progenitor cell		CD34;SPINK2;PRSS57;CRHBP;HLF	MPO;GATA1	CD34 is also expressed by endothelial cells (exclude with PECAM1/VWF in tissue) and by fibroblasts in some tissues; HLF/CRHBP/AVP enrich for HSC/MPP; PTPRC is expressed by HSPCs at lower level than mature leukocytes, use as relative negative only	CL:0008001	hematopoietic precursor cell	Azimuth(PBMC:HSPC +3)=4/5; PanglaoDB(Hematopoietic stem cells)=2/5; HPA(hematopoietic stem cells;top10)=5/5; lit=PMID:34062119|PMID:31160568	medium
+human	any	granulocyte-monocyte progenitor	hematopoietic stem and progenitor cell	MPO;ELANE;AZU1;PRTN3;CTSG	GATA1;HBB;CD3E	also cover promyelocytes; MPO/ELANE/AZU1 transcripts persist into early neutrophil differentiation	CL:0000557	granulocyte monocyte progenitor cell	Azimuth(Bone Marrow:Granulocyte Monocyte Progenitor)=4/5; HPA(neutrophil progenitors;top10)=5/5; lit=PMID:31160568	medium
+human	any	megakaryocyte-erythroid progenitor	hematopoietic stem and progenitor cell	GATA1;TFRC;KLF1;CNRIP1;PKLR	MPO;ELANE;CD3E	early erythroid/megakaryocyte-primed progenitors; boundaries with early erythroblasts are continuous	CL:0000050	megakaryocyte-erythroid progenitor cell	Azimuth(Bone Marrow:Erythroid Megakaryocyte Progenitor)=0/5; HPA(megakaryocyte-erythroid progenitors;top10)=4/5; lit=PMID:31160568	medium
+human	any	erythroblast		GYPA;ALAS2;HBB;CA1;KLF1	PTPRC;MPO	nucleated erythroid precursors (bone marrow, fetal liver, spleen); hemoglobin genes are ambient-prone - use GYPA/CA1/KLF1 and a nucleated (higher gene count) profile	CL:0000765	erythroblast	Azimuth(Bone Marrow:Early Erythroid +1)=1/5; PanglaoDB(Erythroblasts)=2/5; HPA(erythrocyte progenitors;top10)=5/5; lit=PMID:31160568	medium
+human	any	fibroblast		DCN;LUM;COL1A1;COL1A2;PDGFRA	PECAM1;PTPRC	COL1A1/COL1A2 are also expressed by smooth muscle cells, pericytes, myofibroblasts and osteoblasts; ACTA2 is high in myofibroblasts (relative negative); fibroblast subtypes are organ-specific (e.g. PI16+ universal, COL15A1+ etc.)	CL:0000057	fibroblast	Azimuth(Lung v1:Fibroblast +11)=4/5; PanglaoDB(Fibroblasts)=5/5; HPA(fibroblasts;top10)=5/5; lit=PMID:33981032|PMID:35549404	high
+human	any	pericyte		RGS5;PDGFRB;KCNJ8;ABCC9;NOTCH3	PECAM1;PTPRC;DCN	RGS5/PDGFRB/NOTCH3 are shared with vascular smooth muscle cells (which have higher MYH11/DES); pericyte-endothelial doublets are common	CL:0000669	pericyte	Azimuth(Lung v1:Pericyte +11)=3/5; PanglaoDB(Pericytes)=5/5; HPA(pericytes;top10)=5/5; lit=PMID:35549404	high
+human	any	smooth muscle cell		ACTA2;MYH11;CNN1;DES;TAGLN	PECAM1;PTPRC	covers vascular and visceral SMC; ACTA2/TAGLN are also high in myofibroblasts and pericytes, MYH11/CNN1 are more specific; DES is higher in visceral (gut, airway) than vascular SMC	CL:0000192	smooth muscle cell	Azimuth(Lung v1:Smooth Muscle +7)=5/5; PanglaoDB(Smooth muscle cells)=5/5; HPA(smooth muscle cells;top10)=5/5; lit=PMID:35549404	high
+human	any	lymphatic endothelial cell	endothelial cell	PROX1;LYVE1;CCL21;PDPN;TFF3	PTPRC;ACKR1	LYVE1 is also on macrophages and liver sinusoidal EC; PDPN on AT1, FRCs and mesothelium; CCL21 is also produced by T-zone FRCs	CL:0002138	endothelial cell of lymphatic vessel	Azimuth(Lung v1:Lymphatic +13)=3/5; PanglaoDB(Endothelial cells)=3/5; HPA(lymphatic endothelial cells;top10)=5/5; lit=PMID:35549404	high
+human	any	arterial endothelial cell	endothelial cell	GJA5;HEY1;SEMA3G;EFNB2;DLL4	ACKR1;PROX1;PTPRC	GJA5 is prominent in larger arteries; capillary-arterial transitions are continuous	CL:1000413	endothelial cell of artery	Azimuth(Lung v2 (HLCA):EC arterial +2)=4/5; HPA(vascular endothelial cells;top10)=5/5; lit=PMID:34030460	medium
+human	any	venous endothelial cell	endothelial cell	ACKR1;SELP;NR2F2;VWF	GJA5;PROX1;PTPRC	ACKR1 marks post-capillary venules and veins (also expressed on erythrocytes as Duffy antigen at protein level); SELP is inducible	CL:0002543	vein endothelial cell	Azimuth(Lung v2 (HLCA):EC venous +5)=2/4; HPA(vascular endothelial cells;top10)=3/4; lit=PMID:34030460	medium
+human	any	mesothelial cell		MSLN;UPK3B;WT1;KRT19;CALB2	PTPRC;PECAM1	lines pleura, pericardium, peritoneum; WT1/UPK3B are also expressed by some fibroblast populations; MSLN by some airway/tumour epithelia	CL:0000077	mesothelial cell	Azimuth(Lung v1:Mesothelial +6)=3/5; PanglaoDB(Mesothelial cells)=3/5; HPA(mesothelial cells;top10)=4/5; lit=PMID:33208946|PMID:35549404	high
+human	lung	club cell		SCGB1A1;SCGB3A1;BPIFB1;MSMB;CYP2F1	FOXJ1;KRT5;SFTPC	SCGB1A1/SCGB3A2 are strong airway ambient RNAs; human club and goblet cells form a continuum (secretory cells); transitional club-AT2 / AT0 cells co-express SCGB3A2 and SFTPC	CL:0000158	club cell	Azimuth(Lung v1:Club +6)=5/5; PanglaoDB(Clara cells)=2/5; HPA(respiratory secretory cells;top10)=5/5; lit=PMID:33208946|PMID:37291214	high
+human	lung	ciliated cell		FOXJ1;CAPS;TPPP3;RSPH1;DNAH5	SCGB1A1;KRT5;SFTPC	multiciliated airway cells; FOXJ1/CAPS also mark ependymal and fallopian/endometrial ciliated cells; deuterosomal precursors express DEUP1/FOXN4	CL:1000271	lung multiciliated epithelial cell	Azimuth(Lung v1:Ciliated +7)=2/5; PanglaoDB(Ciliated cells)=1/5; HPA(respiratory ciliated cells;top10)=5/5; lit=PMID:33208946|PMID:37291214	high
+human	lung	basal cell		KRT5;TP63;KRT15;S100A2	FOXJ1;SCGB1A1;SFTPC	airway basal stem cells; KRT5/TP63/KRT15 are also basal markers in skin, prostate, esophagus and breast - interpret within lung	CL:0002633	respiratory basal cell	Azimuth(Lung v1:Basal +4)=3/4; PanglaoDB(Basal cells)=3/4; HPA(respiratory basal cells;top10)=4/4; lit=PMID:33208946|PMID:37291214	high
+human	lung	lung goblet cell		MUC5AC;SPDEF;AGR2	FOXJ1;KRT5;MUC2	airway MUC5AC+ goblet cells; SPDEF/AGR2 are enriched in mucus-producing airway epithelium; MUC5B also occurs in submucosal gland mucous cells, and SCGB1A1 marks club/secretory cells	CL:1000143	lung goblet cell	lit=PMID:33208946|PMID:19759516	medium
+human	lung	ionocyte		FOXI1;CFTR;ASCL3;BSND	FOXJ1;SCGB1A1	rare (<1% airway epithelium); negatives are relative because airway ambient RNA (SCGB1A1, SFTPC) contaminates rare cells; FOXI1/ATP6V1B1 are shared with kidney intercalated cells and salivary ionocytes	CL:0017000	pulmonary ionocyte	Azimuth(Lung v1:Ionocyte +3)=3/4; PanglaoDB(Ionocytes)=3/4; HPA(respiratory ionocytes;top10)=4/4; lit=PMID:30069044|PMID:30069046	high
+human	lung	pulmonary neuroendocrine cell		ASCL1;CALCA;GRP;CHGA	FOXJ1;SFTPC;PTPRC	rare; CHGA/GRP are also expressed by other neuroendocrine/enteroendocrine cells and small-cell lung cancer	CL:1000223	pulmonary neuroendocrine cell	Azimuth(Lung v1:Neuroendocrine +3)=1/4; PanglaoDB(Neuroendocrine cells)=0/4; HPA(neuroendocrine cells;top10)=2/4; lit=PMID:33208946	medium
+human	lung	aerocyte capillary endothelial cell	endothelial cell	EDNRB;HPGD;APLN;SOSTDC1;CA4	APLNR;PTPRB;PTPRC	"aCap / ""aerocyte"" (Gillich 2020); CA4 is not fully restricted (also some gCap); counterpart of mouse Car4-high aCap"	CL:4028003	alveolar capillary type 2 endothelial cell	Azimuth(Lung v1:Capillary Aerocyte +3)=4/5; lit=PMID:33057196|PMID:33208946|PMID:34030460	medium
+human	lung	general capillary endothelial cell	endothelial cell	APLNR;GPIHBP1;FCN3;IL7R;PTPRB	HPGD;APLN;EDNRB	gCap; IL7R is unexpectedly expressed by human gCap (and lymphocytes; exclude with PTPRC)	CL:4028002	alveolar capillary type 1 endothelial cell	Azimuth(Lung v1:Capillary +3)=2/5; lit=PMID:33057196|PMID:33208946|PMID:34030460	medium
+human	lung	alveolar fibroblast	fibroblast	NPNT;FGFR4;GPC3;ITGA8;LIMCH1	PI16;SCARA5;PECAM1	alveolar (lipo)fibroblasts; adventitial fibroblasts (PI16/SCARA5) are the closest neighbours	CL:4028004	alveolar type 1 fibroblast cell	Azimuth(Lung v1:Alveolar Fibroblast +2)=1/5; HPA(fibroblasts;top10)=2/5; lit=PMID:33208946	medium
+human	lung	adventitial fibroblast	fibroblast	PI16;SCARA5;SFRP2;MFAP5;SERPINF1	NPNT;ITGA8;PECAM1	"perivascular/peribronchial adventitial fibroblasts; PI16/SCARA5 mark ""universal"" fibroblasts across tissues"	CL:4028006	alveolar adventitial fibroblast	Azimuth(Lung v1:Adventitial Fibroblast +2)=2/5; HPA(fibroblasts;top10)=5/5; lit=PMID:33208946|PMID:33981032	medium
+human	liver	cholangiocyte		KRT19;KRT7;SOX9;EPCAM;CFTR	ALB;PTPRC	biliary epithelial cells; hepatocyte-cholangiocyte doublets and hepatic progenitors co-express ALB with KRT19/KRT7	CL:1000488	cholangiocyte	Azimuth(Liver:Cholangiocyte +1)=2/5; PanglaoDB(Cholangiocytes)=5/5; HPA(cholangiocytes;top10)=1/5; lit=PMID:30348985|PMID:31292543	high
+human	liver	hepatic stellate cell		DCN;RGS5;LRAT;RELN;COLEC11	PECAM1;PTPRC;ALB	quiescent HSC (LRAT/RELN/COLEC11/HGF); activated HSC/myofibroblasts gain COL1A1/ACTA2 and lose LRAT; RGS5 is shared with pericytes	CL:0000632	hepatic stellate cell	Azimuth(Liver:HSC/mFB +1)=3/5; PanglaoDB(Hepatic stellate cells)=4/5; HPA(hepatic stellate cells;top10)=3/5; lit=PMID:30348985|PMID:31597160	medium
+human	liver	liver sinusoidal endothelial cell	endothelial cell	STAB2;CLEC4G;CLEC4M;FCN2;CRHBP	PTPRC;VWF;ALB	LSEC lack a basement membrane and express low CLDN5/VWF (zone 2/3); periportal LSECs and portal vein EC express more VWF; FCN2/STAB2 are also expressed at low level in some Kupffer cells	CL:1000398	endothelial cell of hepatic sinusoid	Azimuth(Liver:Sinusoidal Endothelial)=4/5; lit=PMID:30348985|PMID:31292543	high
+human	brain	oligodendrocyte precursor cell		PDGFRA;CSPG4;OLIG2;VCAN;PCDH15	MOG;AQP4;SLC17A7	OLIG2 is shared with mature oligodendrocytes; CSPG4 (NG2) and PDGFRA are also expressed by pericytes/fibroblasts and VLMCs, so interpret within neural cells	CL:0002453	oligodendrocyte precursor cell	Azimuth(Motor Cortex:OPC +2)=3/5; PanglaoDB(Oligodendrocyte progenitor cells)=5/5; HPA(oligodendrocyte progenitor cells;top10)=5/5; lit=PMID:34616062	high
+human	brain	ependymal cell		FOXJ1;DRC12;RARRES2;DYNLRB2;CIMAP3	TTR;PLP1;SLC17A7	ventricle-lining multiciliated glia; ependymal cells express AQP4 (HPA), so AQP4 is not used as a negative; TTR excludes choroid plexus epithelium; DRC12 and CIMAP3 are the current HGNC symbols for former CCDC153 and PIFO (older references may use the old names); FOXJ1/DYNLRB2 shared with choroid plexus (TTR high) and airway ciliated cells	CL:0000065	ependymal cell	PanglaoDB(Ependymal cells)=5/5; HPA(ependymal cells;top10)=4/5; lit=PMID:34234280	medium
+human	brain	brain endothelial cell	endothelial cell	CLDN5;FLT1;SLC2A1;ABCB1;MFSD2A	PDGFRB;AQP4;PTPRC	BBB endothelium; often contaminated by pericyte transcripts (and vice versa) due to tight association	CL:2000044	brain microvascular endothelial cell	Azimuth(Motor Cortex:Endo +2)=1/5; PanglaoDB(Endothelial cells (blood brain barrier))=0/5; HPA(vascular endothelial cells;top10)=3/5; lit=PMID:34616062	medium
+human	brain	brain pericyte	pericyte	PDGFRB;RGS5;KCNJ8;ABCC9	CLDN5;AQP4;PTPRC	brain pericyte-associated mural genes; PDGFRB/RGS5 overlap with vascular smooth muscle, while KCNJ8/ABCC9 help distinguish pericytes; exclude ACTA2/MYH11-high smooth muscle and CLDN5-high endothelium	CL:2000043	brain pericyte	lit=PMID:34027687|PMID:35084939	medium
+human	brain	vascular leptomeningeal cell	fibroblast	DCN;COL1A2;SLC6A13;PDGFRA;LUM	AQP4;CLDN5;PLP1	meningeal/perivascular fibroblast-like cells; PDGFRA is shared with OPCs (which lack COL1A2/DCN)	CL:4023051	vascular leptomeningeal cell	Azimuth(Motor Cortex:VLMC +2)=2/5; PanglaoDB(Meningeal cells)=3/5; HPA(fibroblasts;top10)=5/5; lit=PMID:34616062	medium
+human	brain	PVALB interneuron	inhibitory neuron	PVALB;GAD1;ERBB4;KCNS3;LHX6	SST;VIP;SLC17A7	fast-spiking basket and chandelier cells; chandelier cells have low PVALB; PVALB is also in cerebellar Purkinje cells and some thalamic neurons	CL:4023018	pvalb GABAergic interneuron	Azimuth(Motor Cortex:Pvalb +17)=2/5; PanglaoDB(Interneurons)=3/5; HPA(brain inhibitory neurons;top10)=4/5; lit=PMID:34616062	high
+human	brain	SST interneuron	inhibitory neuron	SST;GAD1;LHX6;NPY;GRIN3A	PVALB;VIP;SLC17A7	SST is also expressed by some PVALB+ cells (Sst Pvalb) and hypothalamic neurons; NPY marks the Sst Chodl long-range subset among others	CL:4023017	sst GABAergic interneuron	Azimuth(Motor Cortex:Sst +32)=3/5; PanglaoDB(Interneurons)=4/5; HPA(brain inhibitory neurons;top10)=5/5; lit=PMID:34616062	high
+human	brain	VIP interneuron	inhibitory neuron	VIP;GAD1;CALB2;CNR1;ADARB2	PVALB;SST;SLC17A7	caudal ganglionic eminence-derived; CALB2/ADARB2 shared with LAMP5/SNCG interneurons	CL:4023016	VIP GABAergic interneuron	Azimuth(Motor Cortex:Vip +28)=4/5; PanglaoDB(Interneurons)=3/5; HPA(brain inhibitory neurons;top10)=5/5; lit=PMID:34616062	high
+human	brain	LAMP5 interneuron	inhibitory neuron	LAMP5;GAD1;ADARB2;NDNF	PVALB;SST;VIP	neurogliaform and related CGE interneurons; LAMP5 is also expressed by some excitatory neurons (L2/3 IT, L6b), so interpret only within GABAergic neurons	CL:4023011	lamp5 GABAergic interneuron	Azimuth(Motor Cortex:Lamp5 +13)=2/4; PanglaoDB(Interneurons)=2/4; HPA(brain inhibitory neurons;top10)=3/4; lit=PMID:34616062	medium
+human	intestine	enterocyte		FABP2;APOA4;RBP2;ALPI;SI	MUC2;LGR5;PTPRC	small intestine absorptive cells; APOA4/APOB/FABP2 are proximal-biased, FABP6/SLC10A2 mark ileum; colon uses colonocyte row	CL:0000584	enterocyte	PanglaoDB(Enterocytes)=5/5; HPA(enterocytes;top10)=5/5; lit=PMID:34497389	high
+human	intestine	colonocyte		CA1;CA2;SLC26A3;CEACAM7;AQP8	MUC2;LGR5;PTPRC	colon absorptive cells; BEST4+ cells (BEST4/OTOP2/CA7) are a distinct absorptive subtype; CA1 is also high in erythroid cells	CL:1000347	colonocyte	HPA(colonocytes;top10)=5/5; lit=PMID:31348891|PMID:34497389	medium
+human	intestine	intestine goblet cell		MUC2;TFF3;CLCA1;FCGBP;ZG16	FABP2;LGR5;PTPRC	intestinal goblet cells; TFF3 is also expressed by enteroendocrine cells, lymphatic EC and others; immature goblet cells overlap with transit-amplifying cells	CL:0019031	intestine goblet cell	PanglaoDB(Goblet cells)=5/5; HPA(goblet cells;top10)=5/5; lit=PMID:31348891|PMID:34497389	high
+human	intestine	Paneth cell		DEFA5;DEFA6;REG3A;ITLN2;PLA2G2A	MUC2;FABP2;PTPRC	small-intestinal crypt base; DEFA5/DEFA6 can be ectopically expressed in Crohn disease colon (Paneth cell metaplasia); mouse equivalent uses Defa/Lyz1	CL:0000510	paneth cell	PanglaoDB(Paneth cells)=3/5; HPA(paneth cells;top10)=5/5; lit=PMID:34497389	high
+human	intestine	enteroendocrine cell		CHGA;CHGB;PCSK1N;NEUROD1;SCGN	MUC2;FABP2;PTPRC	subtypes defined by hormones (TPH1/TAC1 enterochromaffin, GCG/PYY L cells, GIP K cells, SST D cells, CCK I cells)	CL:0000164	enteroendocrine cell	PanglaoDB(Enteroendocrine cells)=4/5; lit=PMID:34497389	high
+human	intestine	tuft cell		POU2F3;TRPM5;SH2D6;IRAG2;AVIL	MUC2;CHGA;PTPRC	rare chemosensory cells; IRAG2 is the current HGNC symbol for former LRMP; POU2F3/TRPM5 also mark airway tuft/brush cells; mouse markers Dclk1/Trpm5/Il25	CL:0002204	tuft cell	PanglaoDB(Tuft cells)=4/5; HPA(tuft cells;top10)=5/5; lit=PMID:34497389	high
+human	intestine	intestinal stem cell		LGR5;OLFM4;SMOC2;ASCL2	MUC2;FABP2;PTPRC	OLFM4 is also expressed by a neutrophil subset and is induced in inflamed epithelium; LGR5 mRNA is low and dropout-prone; transit-amplifying cells share OLFM4 and are MKI67 high	CL:0002250	intestinal crypt stem cell	PanglaoDB(Crypt cells)=4/4; HPA(enteric stem cells;top10)=4/4; lit=PMID:34497389	medium
+human	kidney	podocyte		NPHS1;NPHS2;PODXL;PTPRO;CLIC5	LRP2;PECAM1;PTPRC	PODXL/CLIC5 are also expressed by glomerular endothelial cells; parietal epithelial cells (CLDN1/CFH) are the closest epithelial neighbour	CL:0000653	podocyte	Azimuth(Kidney:Podocyte +2)=3/5; PanglaoDB(Podocytes)=5/5; HPA(podocytes;top10)=5/5; lit=PMID:37468583|PMID:31896769	high
+human	kidney	proximal tubule cell		LRP2;CUBN;SLC34A1;HNF4A;SLC5A12	UMOD;SLC12A3;AQP2	"largest kidney population; injured/""failed-repair"" PT (VCAM1/HAVCR1) lose SLC34A1/LRP2; PT transcripts dominate kidney ambient RNA in snRNA-seq"	CL:0002306	epithelial cell of proximal tubule	Azimuth(Kidney:Proximal Tubule Epithelial Segment 1 +6)=3/5; PanglaoDB(Proximal tubule cells)=4/5; HPA(proximal tubule cells;top10)=5/5; lit=PMID:37468583|PMID:31896769	high
+human	kidney	thick ascending limb cell		UMOD;SLC12A1;CASR;CLDN16	LRP2;SLC12A3;AQP2	UMOD is also abundant in kidney ambient RNA; macula densa (NOS1) is a TAL-adjacent subtype	CL:1001106	kidney loop of Henle thick ascending limb epithelial cell	Azimuth(Kidney:Cortical Thick Ascending Limb +4)=3/4; PanglaoDB(Loop of Henle cells)=3/4; HPA(loop of henle epithelial cells;top10)=4/4; lit=PMID:37468583	high
+human	kidney	distal convoluted tubule cell		SLC12A3;CALB1;TRPM6;PVALB	UMOD;AQP2;LRP2	CALB1 extends into the connecting tubule; PVALB marks early DCT (DCT1) and is weaker in human than mouse	CL:1000849	kidney distal convoluted tubule epithelial cell	Azimuth(Kidney:Distal Convoluted Tubule Type 1 +3)=2/4; PanglaoDB(Distal tubule cells)=4/4; HPA(distal convoluted tubule cells;top10)=3/4; lit=PMID:37468583	high
+human	kidney	collecting duct principal cell		AQP2;AQP3;SCNN1G;FXYD4;GATA3	FOXI1;ATP6V1B1;UMOD	connecting tubule cells co-express AQP2 with CALB1/SLC8A1; GATA3 is shared with intercalated cells and urothelium	CL:1001431	kidney collecting duct principal cell	Azimuth(Kidney:Cortical Collecting Duct Principal +2)=2/5; PanglaoDB(Principal cells)=5/5; HPA(renal collecting duct principal cells;top10)=4/5; lit=PMID:37468583|PMID:31896769	high
+human	kidney	collecting duct intercalated cell		FOXI1;ATP6V1B1;ATP6V0D2;SLC4A1;SLC26A4	AQP2;UMOD;LRP2	type A (SLC4A1+) and type B (SLC26A4+) intercalated cells; FOXI1/ATP6V1B1 are shared with airway ionocytes	CL:0005010	renal intercalated cell	Azimuth(Kidney:Cortical Collecting Duct Intercalated Type A +4)=2/5; PanglaoDB(Intercalated cells)=5/5; HPA(renal collecting duct intercalated cells;top10)=5/5; lit=PMID:37468583|PMID:31896769	high
+human	heart	cardiomyocyte		TNNT2;MYH7;MYL2;ACTC1;RYR2	PTPRC;PECAM1;DCN	human ventricular cardiomyocytes express predominantly MYH7 (beta-MHC) and MYL2, atrial cardiomyocytes MYH6/NPPA/MYL7 (opposite to mouse ventricle, which is Myh6-dominant); cardiomyocytes are too large for droplet scRNA-seq - use snRNA-seq; MYL2/MYH7/TTN are major heart ambient RNAs	CL:0000746	cardiac muscle cell	Azimuth(Heart:Cardiomyocyte +2)=3/5; PanglaoDB(Cardiomyocytes)=5/5; HPA(cardiomyocytes;top10)=5/5; lit=PMID:32971526|PMID:32403949	high
+human	skin	basal keratinocyte		KRT5;KRT14;KRT15;COL17A1;TP63	KRT1;KRT10;PTPRC	basal layer; KRT5/KRT14/TP63 shared with myoepithelial and other basal epithelia	CL:0002187	basal cell of epidermis	PanglaoDB(Basal cells)=4/5; HPA(basal keratinocytes;top10)=5/5; lit=PMID:33479125|PMID:29080679	high
+human	skin	suprabasal keratinocyte		KRT1;KRT10;DMKN;KRTDAP	KRT15;COL17A1;PTPRC	spinous/granular layers; granular cells additionally express LOR/FLG/IVL	CL:4033013	suprabasal keratinocyte	HPA(suprabasal keratinocytes;top10)=4/4; lit=PMID:33479125	high
+human	skin	melanocyte		PMEL;MLANA;TYRP1;DCT;TYR	KRT14;PTPRC	PMEL/MLANA are also expressed by retinal pigment epithelium and melanoma; nevus cells share these markers	CL:0000148	melanocyte	PanglaoDB(Melanocytes)=5/5; HPA(melanocytes;top10)=5/5; lit=PMID:33479125|PMID:29080679	high
+human	pancreas	pancreatic alpha cell		GCG;IRX2;ARX;TTR;LOXL4	INS;SST;PPY	ARX/IRX2 are alpha-lineage transcription factors; TTR is also high in hepatocytes and choroid plexus	CL:0000171	pancreatic A cell	Azimuth(Pancreas:alpha)=2/5; PanglaoDB(Alpha cells)=5/5; HPA(pancreatic islet cells;top10)=5/5; lit=PMID:27667365|PMID:27667667|PMID:27693023	high
+human	pancreas	pancreatic beta cell		INS;IAPP;MAFA;NPTX2;PDX1	GCG;SST;PPY	INS ambient RNA is ubiquitous in islet data, so INS alone is insufficient; PDX1 is also in delta cells; human beta cells have low MAFB vs mouse	CL:0000169	type B pancreatic cell	Azimuth(Pancreas:beta)=3/5; PanglaoDB(Beta cells)=5/5; HPA(pancreatic islet cells;top10)=5/5; lit=PMID:27667365|PMID:27667667|PMID:27693023	high
+human	pancreas	pancreatic delta cell		SST;HHEX;LEPR;RBP4	INS;GCG;PPY	SST is also expressed in gut D cells and neurons; HHEX is a delta-cell TF	CL:0000173	pancreatic D cell	Azimuth(Pancreas:delta)=4/4; PanglaoDB(Delta cells)=4/4; HPA(pancreatic islet cells;top10)=2/4; lit=PMID:27667365|PMID:27667667	high
+human	pancreas	pancreatic PP cell		PPY;SPP1;MEIS2;ETV1	INS;GCG;SST	PP/gamma cells are concentrated in the head (ventral) of the pancreas; SPP1 is also in ductal cells and macrophages	CL:0002275	pancreatic PP cell	Azimuth(Pancreas:gamma)=3/4; PanglaoDB(Gamma (PP) cells)=2/4; HPA(pancreatic islet cells;top10)=1/4; lit=PMID:27667365|PMID:27667667	medium
+human	pancreas	pancreatic acinar cell		PRSS1;CPA1;CELA3A;CTRB2;PNLIP	KRT19;INS;PTPRC	digestive enzyme transcripts are among the most abundant ambient RNAs in pancreas preparations and can make other cell types appear acinar-positive	CL:0002064	pancreatic acinar cell	Azimuth(Pancreas:acinar)=4/5; PanglaoDB(Acinar cells)=5/5; HPA(pancreatic acinar cells;top10)=5/5; lit=PMID:27667365|PMID:27667667|PMID:27693023	high
+human	pancreas	pancreatic ductal cell		KRT19;CFTR;SOX9;SPP1;MMP7	PRSS1;INS;PTPRC	centroacinar cells and acinar-to-ductal metaplasia blur the acinar/ductal boundary	CL:0002079	pancreatic ductal cell	Azimuth(Pancreas:ductal)=4/5; PanglaoDB(Ductal cells)=4/5; HPA(pancreatic duct cells;top10)=3/5; lit=PMID:27667365|PMID:27667667|PMID:27693023	high
+human	lymphoid	follicular dendritic cell		FDCSP;CR2;CLU;CXCL13;FCAMR	PTPRC;PECAM1	stromal (not haematopoietic) cells of B-cell follicles; CR2 is also expressed on B cells (PTPRC negative needed); CXCL13 is also produced by human Tfh	CL:0000442	follicular dendritic cell	Azimuth(Tonsil v2:FDC +2)=4/5; lit=PMID:38301653	medium
+human	lymphoid	T-zone reticular cell	fibroblast	CCL19;CCL21;PDPN;LUM;COL1A1	PTPRC;PECAM1;CR2	fibroblastic reticular cells of the T zone; CCL21 is shared with lymphatic EC (PECAM1/PROX1 negative)	CL:0009105	T cell zone reticular cell	Azimuth(Tonsil v2:FRC)=0/5; lit=PMID:38301653	medium
+human	lymphoid	marginal zone B cell	B cell	MS4A1;CR2;CD1C;IGHM;CD27	FCER2;TCL1A;CD3E	splenic MZ B are IgM-hi IgD-lo CD21-hi CD23-lo CD1c-hi; in adults mostly CD27+ (overlap with IgM memory B), in children a CD27-negative MZ subset exists, so CD27 is not reliable there	CL:0000845	marginal zone B cell of spleen	lit=PMID:24733829|PMID:16180256	medium
+human	any	naive T cell	T cell	CCR7;SELL;LEF1;TCF7;CD3E	GZMK;S100A4;MS4A1	covers naive CD4 and CD8; prefer the naive CD4/CD8 rows when CD4/CD8 is resolved	CL:0000898	naive T cell	lit=PMID:34062119	high
+mouse	any	T cell		Cd3d;Cd3e;Cd3g;Trac	Ms4a1;Cd79a;Lyz2	lineage; mouse NKT and gamma-delta T cells are included; Trac may be poorly annotated in some references (Tcra locus), Cd3 genes are the most robust	CL:0000084	T cell	PanglaoDB(T cells)=4/4; lit=PMID:30283141	high
+mouse	any	CD4-positive, alpha-beta T cell	T cell	Cd3e;Il7r	Cd8a;Cd8b1;Ms4a1	Cd4 is also expressed by splenic cDC2 (CD4+ DC subset), some macrophages and LTi-like ILC3, so it adds to the score only when enriched and is not required; Il7r is shared with ILCs and memory CD8 T	CL:0000624	CD4-positive, alpha-beta T cell	PanglaoDB(T helper cells)=1/3; lit=PMID:30283141	high	Cd4
+mouse	any	CD8-positive, alpha-beta T cell	T cell	Cd3e;Cd8a;Cd8b1	Cd4;Ms4a1	Cd8b1 is the mouse symbol (CD8beta); Cd8a is also expressed by splenic/lymph-node cDC1 (CD8alpha+ DC) and CD8aa intraepithelial T cells, so Cd8b1 is the more specific gene	CL:0000625	CD8-positive, alpha-beta T cell	PanglaoDB(T cytotoxic cells)=1/3; lit=PMID:30283141	high
+mouse	any	B cell		Ms4a1;Cd79a;Cd79b;Cd19;Pax5	Cd3e;Cd3d	Cd79a/Cd79b are retained in plasma cells while Ms4a1/Cd19/Pax5 are lost	CL:0000236	B cell	PanglaoDB(B cells)=5/5; lit=PMID:30283141	high
+mouse	any	plasma cell		Jchain;Mzb1;Xbp1;Sdc1;Tnfrsf17	Ms4a1;Cd3e	"Ms4a1 is lost; Sdc1 = CD138; immunoglobulin transcripts (Igkc/Ighg/Igha) are strong ambient RNAs; in Cell Ontology plasma cell is not a subclass of ""B cell"""	CL:0000786	plasma cell	PanglaoDB(Plasma cells)=4/5; lit=PMID:30283141	high
+mouse	any	NK cell		Nkg7;Klrd1;Klrb1c;Ncr1;Gzma	Cd3e;Ms4a1;Cd3g;Cd5	Klrb1c is NK1.1 and is strain-dependent (NK1.1 epitope present in C57BL/6, absent in BALB/c; transcript detection also varies), Ncr1 (NKp46) is strain-independent; mouse has no Gnly ortholog; NKT cells (abundant in mouse liver) co-express Klrb1c/Nkg7 and must be excluded by Cd3 genes; liver ILC1 share Ncr1/Klrb1c (Itga1+, Eomes-)	CL:0000623	natural killer cell	PanglaoDB(NK cells)=4/5; lit=PMID:30283141|PMID:30413361	high
+mouse	any	monocyte		Lyz2;Cd14;Csf1r	Cd3e;Ms4a1;Ly6g	mouse lysozyme M is Lyz2 (Lyz1 is Paneth-cell lysozyme); Lyz2 is also high in neutrophils, macrophages, DCs and alveolar type 2 cells (LysM-Cre is active in AT2), so Lyz2 alone is not monocyte-specific	CL:0000576	monocyte	PanglaoDB(Monocytes)=2/3; lit=PMID:30283141	high
+mouse	any	classical monocyte	monocyte	Ly6c2;Ccr2;Cd14;Plac8;Sell	Cd3e;Treml4;Ly6g	Ly6Chi monocytes (Cx3cr1-int Ccr2+ Sell+); Treml4 is a relative negative because a Treml4+ Ly6Chi intermediate exists; Cx3cr1 was removed from negatives because Ly6Chi monocytes are Cx3cr1-intermediate (not negative) at mRNA level; Ly6c2 is also expressed by some T cells, endothelial cells and neutrophils at lower levels; Ly6g distinguishes neutrophils	CL:0000860	classical monocyte	PanglaoDB(Monocytes)=3/5; lit=PMID:30283141|PMID:28514690|PMID:27264183	high
+mouse	any	non-classical monocyte	monocyte	Cx3cr1;Fcgr4;Nr4a1;Treml4	Ly6c2;Cd3e;Ccr2	Ly6Clo patrolling monocytes; Nr4a1 is an immediate-early gene induced by tissue dissociation, so use it together with Treml4/Fcgr4; Cx3cr1 is also high in NK cells, microglia and some macrophages	CL:0000875	non-classical monocyte	PanglaoDB(Monocytes)=1/4; lit=PMID:30283141|PMID:28514690|PMID:27264183	high
+mouse	any	platelet		Ppbp;Pf4;Gp9;Itga2b;Tubb1	Ptprc;Lyz2	shares all markers with megakaryocytes; mouse Pf4 is also expressed by several macrophage populations (lung interstitial, border-associated, Lyve1+ resident), so Pf4 alone is not platelet-specific; platelet-leukocyte aggregates co-express Ppbp/Pf4 with Ptprc and Lyz2, so both are relative negatives	CL:0000233	platelet	PanglaoDB(Platelets)=5/5; lit=PMID:30283141	high
+mouse	any	erythrocyte		Hbb-bt;Hba-a1;Hbb-bs;Hba-a2;Alas2	Ptprc	hemoglobin transcripts are the most common ambient RNAs (Hbb-bs/Hbb-bt/Hba-a1/Hba-a2); require a very high hemoglobin UMI fraction and low gene count, and consider SoupX/CellBender; Hbb-b1/Hbb-b2 (single haplotype) symbols may appear in older annotations	CL:0000232	erythrocyte	PanglaoDB(Erythroid-like and erythroid precursor cells)=1/5; lit=PMID:30283141|PMID:33367645|PMID:37550580	high
+mouse	any	endothelial cell		Pecam1;Cdh5;Kdr;Cldn5;Flt1	Ptprc;Epcam	pan-endothelial; Pecam1 is also on leukocytes/platelets; Cldn5 is low in liver sinusoidal EC; Kdr is low in lymphatic and some large-vessel EC	CL:0000115	endothelial cell	Azimuth(mMotor Cortex:Endo +2)=1/5; PanglaoDB(Endothelial cells)=5/5; lit=PMID:30283141|PMID:32059779	high
+mouse	lung	pulmonary alveolar type 2 cell		Sftpc;Sftpb;Abca3;Lamp3;Slc34a2	Ager;Ptprc	Sftpc/Sftpb are dominant lung ambient RNAs (also seen in macrophages); mouse AT2 also express Lyz1/Lyz2 (LysM-Cre labels AT2); transitional Krt8+ ADI/DATP cells co-express AT2 and AT1 genes	CL:0002063	pulmonary alveolar type 2 cell	PanglaoDB(Pulmonary alveolar type II cells)=5/5; lit=PMID:30283141|PMID:30069044	high
+mouse	lung	pulmonary alveolar type 1 cell		Ager;Aqp5;Pdpn;Rtkn2;Akap5	Sftpc;Pecam1	Pdpn is also expressed by lymphatic EC, mesothelium and FRCs; Aqp5 also in airway submucosal glands; Hopx also marks AT1 but is expressed in AT2 subsets; AT1-endothelial doublets are frequent	CL:0002062	pulmonary alveolar type 1 cell	PanglaoDB(Pulmonary alveolar type I cells)=5/5; lit=PMID:30283141|PMID:30069044	high
+mouse	lung	alveolar macrophage		Marco;Fabp4;Ear1;Siglecf;Chil3	S100a8;Cd3e	mouse AMs are Siglecf-high (unlike human); Siglecf, Ear1/Ear2 and Chil3 are also expressed by eosinophils and Chil3 by neutrophils, so use the combination with Marco/Fabp4 and absence of S100a8; Ca4 (former Car4) and Krt79 are additional AM genes (Ca4 is also high in aCap EC); Mrc1 is expressed by AMs and interstitial macrophages	CL:0000583	alveolar macrophage	PanglaoDB(Alveolar macrophages)=1/5; lit=PMID:30283141|PMID:36103853	high
+mouse	liver	hepatocyte		Alb;Apoa1;Ttr;Apoc3;Fgb	Ptprc;Krt19	liver ambient RNA is dominated by hepatocyte transcripts (Alb, Apoa1, Mup genes, Serpina1a-e); zonation: Glul/Cyp2e1/Oat pericentral, Cyp2f2/Hal/Sds periportal	CL:0000182	hepatocyte	PanglaoDB(Hepatocytes)=5/5; lit=PMID:30283141|PMID:28166538	high
+mouse	liver	Kupffer cell		Clec4f;Vsig4;Timd4;Cd5l;Marco	Ly6c2;Cd3e	Clec4f is mouse Kupffer-specific (low in human); Timd4 is absent on recently monocyte-derived KCs, so Timd4-negative KCs may still be bona fide KCs; Vsig4/Cd5l are shared with other iron-recycling macrophages	CL:0000091	Kupffer cell	PanglaoDB(Kupffer cells)=4/5; lit=PMID:30283141|PMID:26813785|PMID:35021063	high
+mouse	brain	microglial cell		P2ry12;Tmem119;Cx3cr1;Sall1;Hexb	S100a8;Cd3e;Mrc1;Lyve1	Mrc1/Lyve1 added to exclude border-associated macrophages; Sall1 and Hexb are relatively stable microglial identity genes while P2ry12/Tmem119 drop in disease-associated microglia; Siglech is also microglia-expressed (not only pDCs); enzymatic dissociation at 37C induces artefactual activation genes (Fos, Jun, Hspa1a)	CL:0000129	microglial cell	Azimuth(mMotor Cortex:Micro-PVM +2)=2/5; PanglaoDB(Microglia)=4/5; lit=PMID:26884166|PMID:28836308|PMID:35260865	high
+mouse	brain	oligodendrocyte		Plp1;Mbp;Mog;Mobp	Aqp4;Slc17a7;Pdgfra	Mbp (Golli-Mbp) transcripts are expressed by immune cells outside the CNS; Plp1/Mbp/Mobp are major brain ambient RNAs (especially in snRNA-seq) and appear in neuronal and microglial clusters; Pdgfra excludes OPCs	CL:0000128	oligodendrocyte	Azimuth(mMotor Cortex:Oligo +10)=4/4; PanglaoDB(Oligodendrocytes)=3/4; lit=PMID:27284195|PMID:30096314	high
+mouse	brain	astrocyte		Aqp4;Gfap;Slc1a3;Slc1a2;Aldh1l1	Plp1;Slc17a7	Gfap is low in many grey-matter protoplasmic astrocytes and high in white matter/reactive astrocytes, Bergmann glia and neural stem cells; Aldh1l1/Slc1a3 are more uniform	CL:0000127	astrocyte	Azimuth(mMotor Cortex:Astro +5)=4/5; PanglaoDB(Astrocytes)=5/5; lit=PMID:30096314	high
+mouse	brain	excitatory neuron		Slc17a7;Satb2	Gad1;Gad2	CL term: glutamatergic neuron; Slc17a7 cortical/hippocampal, Slc17a6 thalamic/subcortical; Satb2 mainly cortical IT neurons	CL:0000679	glutamatergic neuron	Azimuth(mMotor Cortex:Glutamatergic)=1/3; PanglaoDB(Glutaminergic neurons)=2/3; lit=PMID:30382198|PMID:30096314	high
+mouse	brain	inhibitory neuron		Gad1;Gad2;Slc32a1	Slc17a7;Slc17a6	CL term: GABAergic neuron; includes cortical interneurons, striatal medium spiny neurons and cerebellar Purkinje cells	CL:0000617	GABAergic neuron	Azimuth(mMotor Cortex:GABAergic)=2/3; PanglaoDB(GABAergic neurons)=3/3; lit=PMID:30382198|PMID:30096314	high
+mouse	any	regulatory T cell	CD4-positive, alpha-beta T cell	Foxp3;Il2ra;Ctla4;Ikzf2	Cd8b1;Ms4a1	Foxp3 mRNA is sparse; activated conventional CD4 T cells transiently express Il2ra/Ctla4; Ikzf2 (Helios) marks thymus-derived Tregs but is not absolute	CL:0000792	CD4-positive, CD25-positive, alpha-beta regulatory T cell	PanglaoDB(T regulatory cells)=4/4; lit=PMID:30283141	high
+mouse	any	naive T cell	T cell	Ccr7;Sell;Lef1;Tcf7	Cd44;Gzmk;Ms4a1	covers naive CD4 and CD8 T cells; central memory cells share Ccr7/Sell/Tcf7; Dapl1 marks only a subset of naive CD8 T cells and is excluded from the pan-naive panel (Dapl1 subset: PMID 40845112)	CL:0000898	naive T cell	lit=PMID:30283141|PMID:40163732	medium
+mouse	any	gamma-delta T cell	T cell	Trdc;Trgc1;Trgc2;Trgc4;Sox13	Cd8b1;Cd4;Trac	mouse TRG constant genes are Trgc1/Trgc2/Trgc4 in current MGI nomenclature (named Tcrg-C1/C2/C4 in older references such as 10x mm10); Trdc germline transcripts occur in NK cells/ILCs; IL-17-producing gamma-delta T (Rorc/Il17a/Blk) and dendritic epidermal T cells (Trgv5 in older nomenclature) are major tissue subsets	CL:0000798	gamma-delta T cell	PanglaoDB(Gamma delta T cells)=1/5; lit=PMID:30283141	medium
+mouse	lymphoid	T follicular helper cell	CD4-positive, alpha-beta T cell	Cxcr5;Pdcd1;Bcl6;Icos;Sh2d1a	Cd8b1;Foxp3;Ms4a1	unlike human Tfh, mouse Tfh do not typically express Cxcl13, so Cxcl13 is not used; T follicular regulatory cells co-express Foxp3	CL:0002038	T follicular helper cell	PanglaoDB(T follicular helper cells)=4/5; lit=PMID:38001088	medium
+mouse	any	ILC2		Gata3;Il1rl1;Klrg1;Arg1;Areg	Cd3e;Rorc;Ncr1	lung, gut, adipose and skin ILC2; Il1rl1 is shared with Tregs and mast cells, Gata3 with Th2 cells, Arg1 with some macrophages - require Cd3 negativity	CL:0001069	group 2 innate lymphoid cell	PanglaoDB(Nuocytes)=3/5; lit=PMID:30201992	medium
+mouse	any	ILC3		Rorc;Il22;Il23r;Ncr1;Il7r	Cd3e;Gata3;Klrg1	mainly intestinal; NCR+ ILC3 express Ncr1, LTi-like ILC3 are Ncr1-negative and can be Cd4+; Rorc/Il23r are shared with Th17 and gamma-delta T17 cells	CL:0001071	group 3 innate lymphoid cell	lit=PMID:27545347	medium
+mouse	any	naive B cell	B cell	Ighd;Fcer2a;Cr2;Sell	Aicda;Jchain;Cd3e	follicular B cells (Fcer2a/CD23 high, Ighd+Ighm+); marginal zone B cells are Cr2-high but Fcer2a-low; transitional B cells are similar	CL:0000788	naive B cell	PanglaoDB(B cells naive)=3/4; lit=PMID:30283141|PMID:42297974	medium
+mouse	lymphoid	marginal zone B cell	B cell	Cr2;Cd1d1;Cd9	Fcer2a;Ighd;Cd3e	splenic marginal zone (IgM-high IgD-low); Cr2 is also high on FDCs (stromal, Ptprc-negative); B1 B cells share Cd9; Dtx1 (Notch2 target) was not used because it is also GC-B-enriched	CL:0000845	marginal zone B cell of spleen	lit=PMID:42297974	medium
+mouse	lymphoid	germinal center B cell	B cell	Aicda;S1pr2;Mef2b;Rgs13;Bcl6	Ccr6;Jchain;Cd3e	dark-zone GC B cells are highly proliferative (Mki67/Top2a); Ccr6 marks pre-memory/memory B cells; Dtx1 is GC-enriched as well	CL:0000844	germinal center B cell	lit=PMID:36205653|PMID:42297974	high
+mouse	any	cDC1		Xcr1;Clec9a;Cadm1;Wdfy4;Naaa	Sirpa;Cd209a;Siglech	lymphoid-tissue cDC1 express Cd8a, migratory/tissue cDC1 express Itgae (CD103); Clec9a is also expressed by pDCs at low level; CL mapping uses the lymphoid-tissue cDC1 term (CD8-alpha-positive CD11b-negative DC), tissue CD103+ cDC1 map to CL:0002461	CL:0001000	CD8-alpha-positive CD11b-negative dendritic cell	lit=PMID:31668803	high
+mouse	any	cDC2		Sirpa;Cd209a;Clec4a4;Mgl2	Xcr1;Clec9a;Siglech	cDC2 are heterogeneous: Cd209a/Mgl2/Clec10a mark the T-bet-negative (cDC2B) subset while Esam/Dtx1 mark the Notch2-dependent T-bet-positive (cDC2A) subset (Brown 2019), so not every cDC2 expresses all positives; Sirpa is shared with monocytes/macrophages; splenic cDC2 are partly Cd4+ (Esam-high subset); monocyte-derived DCs overlap transcriptionally; CL mapping uses CD11b-positive dendritic cell	CL:0002465	CD11b-positive dendritic cell	lit=PMID:31668803	medium
+mouse	any	plasmacytoid dendritic cell		Siglech;Ccr9;Ly6d;Cox6a2;Bst2	Xcr1;Ms4a1;Cd209a	Siglech is also expressed by microglia and some macrophages; Bst2 (PDCA-1) is interferon-inducible on many cells; Ly6d is also on B cells; pDC-like cells and transitional DCs express Siglech/Ly6d/Ccr9 at intermediate levels	CL:0000784	plasmacytoid dendritic cell	PanglaoDB(Plasmacytoid dendritic cells)=2/5; lit=PMID:36928414	high
+mouse	any	mature regulatory dendritic cell		Ccr7;Fscn1;Il4i1;Ccl22;Cacnb3	Cd14;Cd3e;Ms4a1	"activation state (mregDC / ""CCR7+ DC"") of cDC1 and cDC2 in tumours and lymph nodes; Ccr7 is shared with naive/central memory lymphocytes; mapped to CL ""migratory dendritic cell"""	CL:4047054	migratory dendritic cell	lit=PMID:32269339	medium
+mouse	any	neutrophil		S100a8;S100a9;Retnlg;Csf3r;Ly6g	Csf1r;Cd3e;Ms4a1	low RNA content and lost with stringent QC; Ly6g transcript is relatively low (better detected at protein level); immature bone-marrow neutrophils express Ngp/Camp/Ltf/Lcn2 instead of Retnlg; S100a8/S100a9 are strong ambient RNAs	CL:0000775	neutrophil	PanglaoDB(Neutrophils)=3/5; lit=PMID:30283141|PMID:32719519	high
+mouse	any	basophil		Mcpt8;Prss34	Kit;Cma1;Cd3e	Mcpt8 and Prss34 (Mcpt11) are basophil-specific proteases in mouse; KIT/CMA1 absence helps separate mast cells	CL:0000767	basophil	lit=PMID:39660487	medium
+mouse	any	mast cell		Cpa3;Kit;Tpsb2;Cma1;Fcer1a	Mcpt8;Prss34;Cd3e	connective-tissue mast cells express Cma1/Mcpt4/Tpsb2/Cpa3; mucosal mast cells express Mcpt1/Mcpt2 and little Cma1, so Cma1 is subset-dependent	CL:0000097	mast cell	PanglaoDB(Mast cells)=5/5; lit=PMID:30283141	high
+mouse	any	Lyve1+ resident macrophage		Lyve1;Folr2;Timd4;Mrc1;Cd163	Ccr2;S100a8;Cd3e	perivascular/interstitial TLF+ macrophages (Timd4/Lyve1/Folr2) found across organs; Lyve1 is also on lymphatic EC and liver sinusoidal EC; Pf4 is frequently co-expressed	CL:0000864	tissue-resident macrophage	lit=PMID:34995099|PMID:30872492	medium
+mouse	lung	interstitial macrophage		C1qa;Mrc1;Lyve1;Pf4;Folr2	Siglecf;Marco;Ear1	lung interstitial macrophages (Lyve1hi MHC-II-lo and Lyve1lo MHC-II-hi subsets); Pf4 is expressed (not platelet-specific in this context); low Siglecf/Marco/Ear1 separates them from alveolar macrophages	CL:4033043	lung interstitial macrophage	lit=PMID:30872492|PMID:28257233|PMID:36103853	medium
+mouse	lymphoid	red pulp macrophage		Spic;Vcam1	Cd3e;Ms4a1;S100a8	splenic red pulp macrophages; Spic controls this lineage and Vcam1 is regulated by Spic; Hmox1/Slc40a1 are shared iron-handling genes	CL:0000874	splenic red pulp macrophage	lit=PMID:19037245	medium
+mouse	brain	border-associated macrophage		Mrc1;Pf4;Lyve1;Cd163;F13a1	P2ry12;Tmem119;Sall1	perivascular, meningeal and choroid-plexus macrophages; P2ry12/Tmem119/Sall1 absence distinguishes them from homeostatic microglia; choroid-plexus and dural BAMs have lower Lyve1/Mrc1 and higher MHC-II	CL:4042003	border associated macrophage	Azimuth(mMotor Cortex:PVM_1 +2)=1/5; lit=PMID:31061494|PMID:29426702	high
+mouse	any	megakaryocyte		Itga2b;Gp9;Pf4;Ppbp;Vwf	Ptprc	nucleated megakaryocytes share all genes with platelets; Pf4 is also expressed by macrophages in mouse; Vwf also by endothelium	CL:0000556	megakaryocyte	PanglaoDB(Megakaryocytes)=4/5; lit=PMID:30283141	medium
+mouse	any	hematopoietic stem and progenitor cell		Kit;Procr;Hlf;Mecom;Ly6a	Mpo;Gata1;Cd3e	mouse long-term HSCs are Cd34-low/negative (unlike human), so Cd34 is not used; Ly6a (Sca-1) expression depends on the Ly6 haplotype (Ly6.2 strains such as C57BL/6 express it on HSPCs, Ly6.1 strains such as BALB/c show low expression) and Ly6a is also on endothelium; Kit is also on mast cells	CL:0008001	hematopoietic precursor cell	PanglaoDB(Hematopoietic stem cells)=4/5; lit=PMID:27365425|PMID:8662508	medium
+mouse	any	granulocyte-monocyte progenitor	hematopoietic stem and progenitor cell	Mpo;Elane;Ctsg;Prtn3;Ms4a3	Gata1;Ca1;Cd3e	granulocyte-monocyte progenitors and promyelocytes; Mpo/Elane persist in early neutrophil precursors	CL:0000557	granulocyte monocyte progenitor cell	lit=PMID:27365425	medium
+mouse	any	megakaryocyte-erythroid progenitor	hematopoietic stem and progenitor cell	Gata1;Klf1;Ca1;Tfrc	Mpo;Elane;Cd3e	Ca1 (former Car1) is a mouse erythroid-primed progenitor gene; continuous with early erythroblasts	CL:0000050	megakaryocyte-erythroid progenitor cell	lit=PMID:27365425	medium
+mouse	any	erythroblast		Gypa;Klf1;Alas2;Ca2;Hbb-bt	Ptprc;Mpo	nucleated erythroid precursors in bone marrow, spleen and fetal liver; Ca2 = former Car2; hemoglobin transcripts are ambient-prone, prefer Gypa/Klf1/Alas2 with a nucleated (higher gene count) profile	CL:0000765	erythroblast	PanglaoDB(Erythroblasts)=2/5; lit=PMID:30283141	medium
+mouse	any	fibroblast		Dcn;Lum;Col1a1;Col1a2;Pdgfra	Pecam1;Ptprc	Col1a1/Col1a2 are shared with smooth muscle, pericytes and osteoblasts; Pi16+ and Col15a1+ universal fibroblasts exist across organs	CL:0000057	fibroblast	PanglaoDB(Fibroblasts)=5/5; lit=PMID:30283141|PMID:33981032	high
+mouse	any	pericyte		Rgs5;Pdgfrb;Kcnj8;Abcc9;Higd1b	Pecam1;Ptprc;Dcn	Rgs5/Pdgfrb/Notch3 are shared with vascular smooth muscle (higher Acta2/Myh11); pericyte-endothelial doublets are common	CL:0000669	pericyte	Azimuth(mMotor Cortex:Peri +1)=2/5; PanglaoDB(Pericytes)=5/5; lit=PMID:29443965	high
+mouse	any	smooth muscle cell		Acta2;Myh11;Cnn1;Des;Tagln	Pecam1;Ptprc	covers vascular and visceral SMC; Acta2/Tagln are also in myofibroblasts and pericytes	CL:0000192	smooth muscle cell	Azimuth(mMotor Cortex:SMC +1)=3/5; PanglaoDB(Smooth muscle cells)=5/5; lit=PMID:30283141	high
+mouse	any	lymphatic endothelial cell	endothelial cell	Prox1;Lyve1;Ccl21a;Pdpn;Mmrn1	Ptprc;Ackr1	the mouse genome contains several Ccl21 copies (Ccl21a, Ccl21b, Ccl21c...) and reads may be split or multimapped; Lyve1 is also on macrophages and LSEC	CL:0002138	endothelial cell of lymphatic vessel	PanglaoDB(Endothelial cells)=4/5; lit=PMID:32059779	high
+mouse	any	arterial endothelial cell	endothelial cell	Gja5;Hey1;Sema3g;Efnb2;Bmx	Ackr1;Prox1;Ptprc	Gja5/Bmx mark larger arteries; arteriole-capillary transition is continuous	CL:1000413	endothelial cell of artery	PanglaoDB(Endothelial cells (aorta))=3/5; lit=PMID:32059779	medium
+mouse	any	venous endothelial cell	endothelial cell	Nr2f2;Ackr1;Vwf;Selp;Vcam1	Gja5;Prox1;Ptprc	Ackr1 marks post-capillary venules; Selp/Vcam1 are inflammation-inducible	CL:0002543	vein endothelial cell	lit=PMID:32059779	medium
+mouse	any	mesothelial cell		Msln;Upk3b;Wt1;Lrrn4	Ptprc;Pecam1	Wt1/Upk3b are also expressed by some fibroblast populations (e.g. in lung and gonads)	CL:0000077	mesothelial cell	PanglaoDB(Mesothelial cells)=3/4; lit=PMID:30283141	medium
+mouse	lung	club cell		Scgb1a1;Scgb3a2;Cyp2f2;Cbr2	Foxj1;Sftpc;Krt5	Scgb1a1/Scgb3a2 are strong airway ambient RNAs; bronchioalveolar stem cells co-express Scgb1a1 and Sftpc; mouse airways have few goblet cells at baseline	CL:0000158	club cell	PanglaoDB(Clara cells)=2/4; lit=PMID:30283141|PMID:30069044	high
+mouse	lung	ciliated cell		Foxj1;Drc12;Tppp3;Rsph1;Dynlrb2	Scgb1a1;Sftpc;Krt5	multiciliated airway cells; Drc12 is the current MGI symbol for former Ccdc153; Foxj1/Drc12 are shared with brain ependymal cells	CL:1000271	lung multiciliated epithelial cell	PanglaoDB(Ciliated cells)=2/5; lit=PMID:30283141|PMID:30069044	high
+mouse	lung	basal cell		Krt5;Trp63;Krt15;Krt14	Foxj1;Scgb1a1;Sftpc	in mouse, basal cells are largely restricted to the trachea and main bronchi (rare in intrapulmonary airways, unlike human); mouse p63 symbol is Trp63	CL:0002633	respiratory basal cell	PanglaoDB(Basal cells)=3/4; lit=PMID:30069044	high
+mouse	lung	ionocyte		Foxi1;Cftr;Ascl3;Atp6v1b1	Foxj1;Scgb1a1	rare tracheal/airway cells; Foxi1/Atp6v1b1 shared with kidney intercalated cells	CL:0017000	pulmonary ionocyte	PanglaoDB(Ionocytes)=3/4; lit=PMID:30069044|PMID:30069046	high
+mouse	lung	pulmonary neuroendocrine cell		Ascl1;Calca;Chga;Scg5	Foxj1;Sftpc;Ptprc	rare; Calca/Chga shared with other neuroendocrine cells	CL:1000223	pulmonary neuroendocrine cell	PanglaoDB(Neuroendocrine cells)=0/4; lit=PMID:30069044	medium
+mouse	lung	aerocyte capillary endothelial cell	endothelial cell	Ca4;Ednrb;Apln;Tbx2	Aplnr;Gpihbp1;Ptprc	aCap / aerocytes (Gillich 2020); Ca4 is the current MGI symbol for former Car4 and is also expressed by alveolar macrophages (Ptprc negative)	CL:4028003	alveolar capillary type 2 endothelial cell	lit=PMID:33057196|PMID:34030460	high
+mouse	lung	general capillary endothelial cell	endothelial cell	Gpihbp1;Plvap;Aplnr;Kit	Ca4;Apln;Ednrb	gCap; Kit (c-Kit) marks the gCap progenitor-like population in mouse; Kit is also on mast cells and HSPCs (Ptprc+)	CL:4028002	alveolar capillary type 1 endothelial cell	lit=PMID:33057196|PMID:34030460	high
+mouse	lung	alveolar fibroblast	fibroblast	Npnt;Ces1d;Itga8;Fgfr4	Pi16;Dpt;Pecam1	alveolar (lipo)fibroblasts; Tsukui 2020 defines Npnt/Ces1d/Itga8 alveolar fibroblasts	CL:4028004	alveolar type 1 fibroblast cell	lit=PMID:32317643	medium
+mouse	lung	adventitial fibroblast	fibroblast	Pi16;Dpt;Scara5;Sfrp2	Npnt;Ces1d;Pecam1	adventitial/perivascular fibroblasts; Pi16/Dpt mark universal fibroblasts across organs	CL:4028006	alveolar adventitial fibroblast	lit=PMID:32317643|PMID:33981032	medium
+mouse	liver	cholangiocyte		Krt19;Krt7;Sox9;Epcam;Spp1	Alb;Ptprc	biliary epithelium; hepatocyte-cholangiocyte doublets co-express Alb	CL:1000488	cholangiocyte	PanglaoDB(Cholangiocytes)=5/5; lit=PMID:30283141	high
+mouse	liver	hepatic stellate cell		Lrat;Reln;Dcn;Rgs5;Colec11	Pecam1;Ptprc;Alb	quiescent HSC; activated HSC/myofibroblasts gain Col1a1/Acta2/Timp1; Lrat-Cre labels HSCs	CL:0000632	hepatic stellate cell	PanglaoDB(Hepatic stellate cells)=4/5; lit=PMID:31722201	high
+mouse	liver	liver sinusoidal endothelial cell	endothelial cell	Stab2;Clec4g;Fcgr2b;Dnase1l3;Kdr	Ptprc;Vwf;Alb	LSEC are low in Cldn5/Vwf (except periportal); Fcgr2b is also on B cells and Kupffer cells, Dnase1l3 on some DCs	CL:1000398	endothelial cell of hepatic sinusoid	lit=PMID:28166538|PMID:32059779	high
+mouse	brain	oligodendrocyte precursor cell		Pdgfra;Cspg4;Olig2;Vcan	Mog;Aqp4;Slc17a7	Olig2 is shared with oligodendrocytes; Pdgfra/Cspg4 are also on pericytes/fibroblasts/VLMC; committed OPCs express Gpr17/Bmp4	CL:0002453	oligodendrocyte precursor cell	Azimuth(mMotor Cortex:OPC +2)=2/4; PanglaoDB(Oligodendrocyte progenitor cells)=4/4; lit=PMID:27284195|PMID:30096314	high
+mouse	brain	ependymal cell		Foxj1;Drc12;Rarres2;Dynlrb2;Tmem212	Ttr;Plp1;Slc17a7	ventricle-lining multiciliated glia; ependymal cells express Aqp4, so Aqp4 is not used as a negative; Ttr excludes choroid plexus epithelium; Drc12 = former Ccdc153; distinguish from choroid plexus epithelium (Ttr very high)	CL:0000065	ependymal cell	PanglaoDB(Ependymal cells)=5/5; lit=PMID:30096314	medium
+mouse	brain	brain endothelial cell	endothelial cell	Cldn5;Flt1;Slc2a1;Ly6c1;Mfsd2a	Pdgfrb;Aqp4;Ptprc	BBB endothelium; often contaminated by pericyte/astrocyte endfoot transcripts	CL:2000044	brain microvascular endothelial cell	Azimuth(mMotor Cortex:Endo +2)=3/5; PanglaoDB(Endothelial cells (blood brain barrier))=0/5; lit=PMID:29443965	high
+mouse	brain	brain pericyte	pericyte	Pdgfrb;Rgs5;Kcnj8;Abcc9;Vtn	Cldn5;Aqp4;Ptprc	frequently carries endothelial doublet/ambient signal; vascular SMC share Pdgfrb/Rgs5 but have higher Acta2/Myh11	CL:2000043	brain pericyte	Azimuth(mMotor Cortex:Peri +1)=3/5; PanglaoDB(Pericytes)=5/5; lit=PMID:29443965	high
+mouse	brain	vascular leptomeningeal cell	fibroblast	Dcn;Col1a2;Slc6a13;Pdgfra	Aqp4;Cldn5;Plp1	meningeal/perivascular fibroblast-like cells; Pdgfra shared with OPCs	CL:4023051	vascular leptomeningeal cell	Azimuth(mMotor Cortex:VLMC +8)=0/4; PanglaoDB(Meningeal cells)=2/4; lit=PMID:29443965|PMID:30096314	medium
+mouse	brain	PVALB interneuron	inhibitory neuron	Pvalb;Gad1;Erbb4;Lhx6	Sst;Vip;Slc17a7	fast-spiking basket and chandelier cells; Pvalb is also in cerebellar Purkinje cells and kidney DCT	CL:4023018	pvalb GABAergic interneuron	Azimuth(mMotor Cortex:Pvalb +12)=2/4; PanglaoDB(Interneurons)=3/4; lit=PMID:30382198	high
+mouse	brain	SST interneuron	inhibitory neuron	Sst;Gad1;Lhx6;Npy	Pvalb;Vip;Slc17a7	Sst Chodl long-range projecting cells co-express Npy/Nos1; some Sst cells co-express Pvalb	CL:4023017	sst GABAergic interneuron	Azimuth(mMotor Cortex:Sst +29)=2/4; PanglaoDB(Interneurons)=4/4; lit=PMID:30382198	high
+mouse	brain	VIP interneuron	inhibitory neuron	Vip;Gad1;Calb2;Cnr1	Pvalb;Sst;Slc17a7	caudal ganglionic eminence-derived; Calb2 shared with other CGE interneurons	CL:4023016	VIP GABAergic interneuron	Azimuth(mMotor Cortex:Vip +18)=2/4; PanglaoDB(Interneurons)=3/4; lit=PMID:30382198	high
+mouse	brain	LAMP5 interneuron	inhibitory neuron	Lamp5;Gad1;Ndnf	Pvalb;Sst;Vip	neurogliaform and related CGE interneurons; Lamp5 is also in some excitatory neurons (interpret within GABAergic cells)	CL:4023011	lamp5 GABAergic interneuron	Azimuth(mMotor Cortex:Lamp5 +13)=2/3; PanglaoDB(Interneurons)=2/3; lit=PMID:30382198	medium
+mouse	intestine	enterocyte		Fabp2;Apoa4;Rbp2;Alpi;Fabp1	Muc2;Lgr5;Ptprc	small-intestinal absorptive cells; proximal-distal and villus-tip zonation (e.g. Fabp6 ileum, Ada/Nt5e villus tip)	CL:0000584	enterocyte	PanglaoDB(Enterocytes)=5/5; lit=PMID:29144463	high
+mouse	intestine	colonocyte		Ca1;Slc26a3;Aqp8	Muc2;Lgr5;Ptprc	colon absorptive cells; Ca1 (former Car1) is also high in erythroid progenitors (Ptprc-low) - check context	CL:1000347	colonocyte	lit=PMID:30283141	medium
+mouse	intestine	intestine goblet cell		Muc2;Tff3;Clca1;Fcgbp;Zg16	Fabp2;Lgr5;Ptprc	Tff3 is shared with enteroendocrine and other secretory cells; immature goblet cells overlap with secretory progenitors	CL:0019031	intestine goblet cell	PanglaoDB(Goblet cells)=5/5; lit=PMID:29144463	high
+mouse	intestine	Paneth cell		Lyz1;Defa24;Ang4;Mptx2;Itln1	Muc2;Fabp2;Ptprc	mouse Paneth cells express Lyz1 (not Lyz2) and many alpha-defensin paralogs (Defa genes; read mapping can be ambiguous); C57BL/6 mice carry a Pla2g2a null mutation, so Pla2g2a is not used	CL:0000510	paneth cell	PanglaoDB(Paneth cells)=1/5; lit=PMID:29144463	high
+mouse	intestine	enteroendocrine cell		Chga;Chgb;Neurod1;Scg5	Muc2;Fabp2;Ptprc	subtypes defined by hormones (Tph1/Tac1 EC cells, Gcg/Pyy L cells, Gip K cells, Sst D cells, Cck I cells)	CL:0000164	enteroendocrine cell	PanglaoDB(Enteroendocrine cells)=3/4; lit=PMID:29144463	high
+mouse	intestine	tuft cell		Dclk1;Trpm5;Pou2f3;Il25;Avil	Muc2;Chga;Ptprc	rare chemosensory cells; Dclk1 is also expressed by enteric neurons	CL:0002204	tuft cell	PanglaoDB(Tuft cells)=5/5; lit=PMID:29144463	high
+mouse	intestine	intestinal stem cell		Lgr5;Olfm4;Smoc2;Ascl2	Muc2;Fabp2;Ptprc	Lgr5 mRNA is low and dropout-prone; transit-amplifying cells share Olfm4 and are Mki67-high	CL:0002250	intestinal crypt stem cell	PanglaoDB(Crypt cells)=4/4; lit=PMID:29144463	high
+mouse	kidney	podocyte		Nphs1;Nphs2;Podxl;Ptpro	Lrp2;Pecam1;Ptprc	Podxl is also on glomerular endothelium	CL:0000653	podocyte	PanglaoDB(Podocytes)=4/4; lit=PMID:29622724|PMID:31689386	high
+mouse	kidney	proximal tubule cell		Lrp2;Slc34a1;Cubn;Slc5a2;Hnf4a	Umod;Slc12a3;Aqp2	Slc5a2 (SGLT2) marks S1/S2; PT transcripts (e.g. Kap, Gpx3) dominate kidney ambient RNA; male mouse PT has strong sex-dimorphic gene expression (e.g. Cyp2e1, Slco1a1)	CL:0002306	epithelial cell of proximal tubule	PanglaoDB(Proximal tubule cells)=4/5; lit=PMID:29622724|PMID:31689386	high
+mouse	kidney	thick ascending limb cell		Umod;Slc12a1;Cldn16;Ptger3	Lrp2;Slc12a3;Aqp2	Umod is a strong kidney ambient RNA; macula densa (Nos1) is a TAL-adjacent subtype	CL:1001106	kidney loop of Henle thick ascending limb epithelial cell	PanglaoDB(Loop of Henle cells)=3/4; lit=PMID:29622724|PMID:31689386	high
+mouse	kidney	distal convoluted tubule cell		Slc12a3;Pvalb;Calb1;Trpm6	Umod;Aqp2;Lrp2	Pvalb is a strong early-DCT marker in mouse (weaker in human)	CL:1000849	kidney distal convoluted tubule epithelial cell	PanglaoDB(Distal tubule cells)=4/4; lit=PMID:29622724|PMID:31689386	high
+mouse	kidney	collecting duct principal cell		Aqp2;Aqp3;Scnn1g;Fxyd4;Hsd11b2	Atp6v1b1;Foxi1;Umod	connecting tubule cells co-express Aqp2 with Calb1	CL:1001431	kidney collecting duct principal cell	PanglaoDB(Principal cells)=5/5; lit=PMID:29622724|PMID:31689386	high
+mouse	kidney	collecting duct intercalated cell		Foxi1;Atp6v1b1;Atp6v0d2;Slc4a1;Slc26a4	Aqp2;Umod;Lrp2	type A (Slc4a1+) and type B (Slc26a4+) intercalated cells; Foxi1/Atp6v1b1 shared with airway ionocytes	CL:0005010	renal intercalated cell	PanglaoDB(Intercalated cells)=5/5; lit=PMID:29622724|PMID:31689386	high
+mouse	heart	cardiomyocyte		Tnnt2;Myh6;Myl2;Actc1;Ryr2	Ptprc;Pecam1;Dcn	adult mouse ventricular cardiomyocytes express predominantly Myh6 (alpha-MHC), whereas adult human ventricles express mainly MYH7 (beta-MHC); Myl2 marks ventricle, Myl7/Nppa atria; use snRNA-seq for adult cardiomyocytes	CL:0000746	cardiac muscle cell	PanglaoDB(Cardiomyocytes)=5/5; lit=PMID:30283141	high
+mouse	skin	basal keratinocyte		Krt5;Krt14;Krt15;Col17a1;Trp63	Krt1;Krt10;Ptprc	basal layer; mouse p63 symbol is Trp63	CL:0002187	basal cell of epidermis	PanglaoDB(Basal cells)=3/5; lit=PMID:27641957	high
+mouse	skin	suprabasal keratinocyte		Krt1;Krt10;Dmkn;Krtdap	Krt15;Col17a1;Ptprc	spinous/granular layers; granular cells express Lor/Flg/Ivl	CL:4033013	suprabasal keratinocyte	lit=PMID:27641957	high
+mouse	skin	melanocyte		Pmel;Mlana;Tyrp1;Dct;Tyr	Krt14;Ptprc	in adult mouse back skin melanocytes are mostly in hair follicles (few interfollicular); albino strains carry Tyr mutations but still transcribe Tyr	CL:0000148	melanocyte	PanglaoDB(Melanocytes)=5/5; lit=PMID:30283141	medium
+mouse	pancreas	pancreatic alpha cell		Gcg;Arx;Irx2;Ttr;Mafb	Ins1;Ins2;Sst	Mafb is also expressed by mouse delta cells and by macrophages	CL:0000171	pancreatic A cell	PanglaoDB(Alpha cells)=5/5; lit=PMID:27667365	high
+mouse	pancreas	pancreatic beta cell		Ins1;Ins2;Iapp;Mafa;Pdx1	Gcg;Sst;Ppy	mouse has two insulin genes (Ins1, Ins2) whereas human has one (INS); insulin ambient RNA is ubiquitous in islet data	CL:0000169	type B pancreatic cell	PanglaoDB(Beta cells)=3/5; lit=PMID:27667365	high
+mouse	pancreas	pancreatic delta cell		Sst;Hhex;Rbp4;Ghsr	Ins1;Gcg;Ppy	Sst is also expressed in gut D cells and neurons	CL:0000173	pancreatic D cell	PanglaoDB(Delta cells)=4/4; lit=PMID:27667365	high
+mouse	pancreas	pancreatic acinar cell		Cpa1;Cela3b;Ctrb1;Pnlip;Cel	Krt19;Ins1;Ptprc	digestive enzyme transcripts are among the most abundant ambient RNAs in pancreas preparations	CL:0002064	pancreatic acinar cell	PanglaoDB(Acinar cells)=5/5; lit=PMID:27667365	high
+mouse	pancreas	pancreatic ductal cell		Krt19;Krt7;Sox9;Spp1;Cftr	Cpa1;Ins1;Ptprc	centroacinar cells and acinar-to-ductal metaplasia blur the acinar/ductal boundary	CL:0002079	pancreatic ductal cell	PanglaoDB(Ductal cells)=4/5; lit=PMID:27667365	high
+mouse	lymphoid	follicular dendritic cell		Cr2;Cxcl13;Mfge8;Fcgr2b	Ptprc;Pecam1	stromal follicular cells; Cr2/Fcgr2b are also on B cells (Ptprc negative needed)	CL:0000442	follicular dendritic cell	lit=PMID:29752062	medium
+mouse	lymphoid	T-zone reticular cell	fibroblast	Ccl19;Ccl21a;Pdpn;Il7;Grem1	Ptprc;Pecam1;Cr2	T-zone fibroblastic reticular cells; Ccl21a is shared with lymphatic EC (Pecam1/Prox1 negative)	CL:0009105	T cell zone reticular cell	lit=PMID:29752062	medium
+mouse	any	MAIT cell	T cell	Trav1;Zbtb16;Rorc;Il18r1;Icos	Trdc;Foxp3;Cd4	rare in lab mice; mouse MAIT17/MAIT1 are transcriptionally near-identical to NKT17/NKT1, so marker genes alone cannot separate MAIT from iNKT: require Trav1-Traj33 TCR (VDJ) or MR1-tetramer data	CL:0000940	mucosal-associated invariant T cell	lit=PMID:30518599|PMID:38117256	medium
+mouse	any	effector memory CD8 T cell	CD8-positive, alpha-beta T cell	Cd8b1;Gzmk;Ccl5;Cxcr3	Ccr7;Sell;Cd4	Gzmk+ effector-memory-like CD8 subset; Gzmk/Ccl5/Cxcr3 are also seen in some cytotoxic or effector-memory CD4 T cells, so CD8 identity is required; Gzmk-negative memory CD8 cells can be missed	CL:0000913	effector memory CD8-positive, alpha-beta T cell	lit=PMID:40163732	medium
+mouse	any	exhausted CD8 T cell	CD8-positive, alpha-beta T cell	Pdcd1;Havcr2;Tox;Lag3;Entpd1	Sell;Ccr7;Cd4	Havcr2/Entpd1 mark terminally exhausted cells; progenitor-exhausted cells are Tcf7+ Slamf6+ Havcr2-low, so do not use Tcf7 as negative	CL:0020031	CD8-positive exhausted alpha-beta T cell	lit=PMID:30778252	high
+mouse	lung	lung goblet cell		Muc5ac;Spdef;Agr2	Foxj1;Krt5;Muc2	Muc5ac+ airway goblet cells are scarce at baseline and expand after allergen or cytokine exposure; Spdef and Agr2 rise during goblet differentiation; club cells can be transitional precursors	CL:1000143	lung goblet cell	lit=PMID:19759516|PMID:21791528	medium
+mouse	any	memory B cell	B cell	Cd19;Cd80;Pdcd1lg2;Nt5e	Fcer2a;Ighd;Jchain	mouse memory B lack a CD27-like pan-marker; Cd80/Pdcd1lg2/Nt5e mark the mature subsets, the double-negative memory subset is naive-like and will be missed	CL:0000787	memory B cell	lit=PMID:21078902|PMID:24880458	medium
+mouse	any	memory CD4 T cell	CD4-positive, alpha-beta T cell	Cd4;S100a4;Cd44	Cd8b1;Foxp3	CD4 identity comes from the parent; S100a4 is enriched in mouse memory T cells, especially effector memory, and Cd44-high marks antigen-experienced cells; central memory may have lower S100a4	CL:0000897	CD4-positive, alpha-beta memory T cell	lit=PMID:26734465	medium
+mouse	any	naive CD4 T cell	CD4-positive, alpha-beta T cell	Cd4;Ccr7;Sell;Lef1	Cd8b1;Cd44;Foxp3	CD4 identity comes from the parent; Ccr7/Sell/Lef1 indicate a naive-like state but overlap with central memory; Dapl1 is a subset marker of naive CD8, not a pan-naive CD4 marker (Dapl1 subset: PMID 40845112)	CL:0000895	naive thymus-derived CD4-positive, alpha-beta T cell	lit=PMID:40163732	medium
+mouse	any	naive CD8 T cell	CD8-positive, alpha-beta T cell	Cd8b1;Ccr7;Sell;Lef1	Cd4;Cd44;Gzmk	CD8 identity comes from the parent; Ccr7/Sell/Lef1 indicate a naive-like state but overlap with central memory; Dapl1 is restricted to a subset of naive CD8 cells (Dapl1 subset: PMID 40845112)	CL:0000900	naive thymus-derived CD8-positive, alpha-beta T cell	lit=PMID:40163732	medium
+mouse	skin	Langerhans cell		Cd207;Epcam;H2-Ab1	Xcr1;Itgae;Cd3e	Cd207 is shared with Xcr1+ CD103+ dermal cDC1, which lack Epcam; an Epcam+ Cd207+ cDC2-like population has also been described, so validate	CL:0000453	Langerhans cell	lit=PMID:18086865|PMID:19218433	medium
+mouse	pancreas	pancreatic PP cell		Ppy;Pyy;Chga	Ins1;Ins2;Cpa1	mouse gamma cells are heterogeneous and partly bihormonal (Ppy with Gcg or Sst), so Gcg/Sst are not used as negatives; Pyy also occurs in some alpha cells	CL:0002275	pancreatic PP cell	lit=PMID:34294685	medium
+human	adipose	adipocyte		ADIPOQ;PLIN1;FABP4	PTPRC;PECAM1	mature white adipocyte; FABP4 also occurs in macrophages; large lipid-filled adipocytes are often depleted in whole-cell scRNA-seq, so snRNA-seq is preferable	CL:0000136	adipocyte	lit=PMID:35296864|PMID:37380767	high
+mouse	adipose	adipocyte		Adipoq;Plin1;Fabp4	Ptprc;Pecam1	mature white adipocyte; Fabp4 is shared with macrophages; whole-cell dissociation under-recovers mature adipocytes	CL:0000136	adipocyte	lit=PMID:35296864	high
+human	muscle	skeletal muscle satellite cell		PAX7;NCAM1	ACTA1;PECAM1;PTPRC	PAX7+ muscle stem cells; NCAM1 is also expressed by NK cells, so muscle context and PTPRC absence matter; activated satellite cells may downregulate PAX7	CL:0000594	skeletal muscle satellite cell	lit=PMID:32624006|PMID:26352798	medium
+mouse	muscle	skeletal muscle satellite cell		Pax7;Myf5	Acta1;Pecam1;Ptprc	Pax7+ muscle stem cells; Myf5 varies with activation and lineage state; myonuclei have high Acta1	CL:0000594	skeletal muscle satellite cell	lit=PMID:37292698	medium
+human	muscle	skeletal muscle fiber		ACTA1;CKM	TNNT2;ACTA2;PTPRC	mature skeletal myofiber/myonuclei; multinucleated fibers are poorly recovered by whole-cell scRNA-seq; ACTA1 may also appear as ambient RNA in muscle preparations	CL:0008002	skeletal muscle fiber	lit=PMID:36123393|PMID:42673766	medium
+mouse	muscle	skeletal muscle fiber		Acta1;Ckm	Tnnt2;Acta2;Ptprc	mature skeletal myofiber/myonuclei; whole-cell scRNA-seq under-recovers intact fibers; Acta1 can contaminate nearby droplets	CL:0008002	skeletal muscle fiber	lit=PMID:37292698	medium
+human	bone	osteoblast		IBSP;BGLAP;IFITM5	ACP5;CTSK;PTPRC	mature bone-forming osteoblasts; BGLAP is maturation-dependent and can also be expressed by osteocytes; COL1A1 alone is shared with fibroblasts	CL:0000062	osteoblast	lit=PMID:34428745	medium
+mouse	bone	osteoblast		Ibsp;Bglap	Acp5;Ctsk;Ptprc	active bone-forming osteoblasts; Bglap varies with maturation and is absent from some osteoblasts; pair with Ibsp and bone context	CL:0000062	osteoblast	lit=PMID:38477760	medium
+human	bone	osteoclast		CTSK;ACP5;MMP9	IBSP;BGLAP;PECAM1	bone-resorbing osteoclasts; ACP5 and MMP9 may occur in other myeloid cells, so require a coherent CTSK+ bone-resorption program	CL:0000092	osteoclast	lit=PMID:38263167	medium
+mouse	bone	osteoclast		Ctsk;Acp5	Ibsp;Bglap;Pecam1	bone-resorbing osteoclasts; Acp5 can occur in other myeloid cells, and Ctsk can occur outside bone; use their combination in bone tissue	CL:0000092	osteoclast	lit=PMID:38477760	medium
+human	heart	cardiac fibroblast	fibroblast	DCN;PDGFRA;COL1A1	TNNT2;PECAM1;PTPRC	heart-resident fibroblasts; DCN/COL1A1 are shared with fibroblasts of other organs; POSTN marks activated subsets, not all cardiac fibroblasts	CL:0002548	fibroblast of cardiac tissue	lit=PMID:38905342	medium
+mouse	heart	cardiac fibroblast	fibroblast	Dcn;Pdgfra;Col1a1	Tnnt2;Pecam1;Ptprc	heart-resident fibroblasts; Dcn/Col1a1 are shared with other fibroblasts; Postn is activation-dependent	CL:0002548	fibroblast of cardiac tissue	lit=PMID:30912746	medium
+human	tendon	tenocyte	fibroblast	SCX;MKX;TNMD	PTPRC;PECAM1;COL2A1	differentiated tendon-lineage cells; SCX/MKX/TNMD are not uniformly detected across all tendon fibroblasts, so this panel identifies a tenogenic subset rather than every stromal cell in tendon	CL:0000388	tendon cell	lit=PMID:41863796|PMID:32883960	medium
+mouse	tendon	tenocyte	fibroblast	Scx;Tnmd;Fmod	Ptprc;Pecam1;Col2a1	tenogenic tendon cells; single-cell data show Scx/Tnmd in only subsets of adult Achilles fibroblasts; Fmod supports tendon matrix identity but is not tissue-specific	CL:0000388	tendon cell	lit=PMID:32877217|PMID:39420021	medium
+human	stomach	foveolar cell		MUC5AC;GKN1;TFF1	MUC6;ATP4A;PTPRC	surface/pit mucous cells; GKN1 and TFF1 support the stomach pit lineage; MUC5AC alone is also present in respiratory goblet cells	CL:0002179	foveolar cell of stomach	lit=PMID:37402315	high
+mouse	stomach	foveolar cell		Muc5ac;Gkn1;Tff1	Muc6;Atp4a;Ptprc	surface/pit mucous cells; Muc5ac is not exclusive to the stomach and transitional cells may coexpress neck markers	CL:0002179	foveolar cell of stomach	lit=PMID:36717627	high
+human	stomach	mucous neck cell		MUC6;TFF2	MUC5AC;ATP4A;PTPRC	corpus mucous neck/antral gland base cells; TFF2 can rise in injury-associated metaplasia and MUC6 may persist in chief-cell precursors	CL:0002181	mucous neck cell of gastric gland	lit=PMID:37402315	medium
+mouse	stomach	mucous neck cell		Muc6;Tff2	Muc5ac;Atp4a;Ptprc	corpus mucous neck/antral gland base cells; Muc6 and Tff2 can occur in transitional or metaplastic cells	CL:0002181	mucous neck cell of gastric gland	lit=PMID:36717627|PMID:29642375	medium
+human	stomach	parietal cell		ATP4A;ATP4B	MUC5AC;PGC;PTPRC	acid-secreting corpus cells; ATP4A and ATP4B encode the gastric proton pump; chiefly absent from the antrum	CL:0000162	parietal cell	lit=PMID:37402315	high
+mouse	stomach	parietal cell		Atp4a;Atp4b	Muc5ac;Pgc;Ptprc	acid-secreting corpus cells; Atp4a and Atp4b encode the gastric proton pump; absent from normal mouse antrum	CL:0000162	parietal cell	lit=PMID:29642375|PMID:36717627	high
+human	stomach	gastric chief cell		PGA5;PGC;LIPF	ATP4A;MUC5AC;PTPRC	mature zymogenic corpus cells; PGA5 and LIPF are human chief-cell enriched; PGC also appears in neck/chief transitions; human GIF is parietal-enriched	CL:0000155	peptic cell	lit=PMID:37402315	high
+mouse	stomach	gastric chief cell		Pgc;Cblif	Atp4a;Muc5ac;Ptprc	mature zymogenic corpus cells; mouse Cblif (formerly Gif) marks chief cells, unlike human GIF; Muc6/Cblif transitional cells can occur	CL:0000155	peptic cell	lit=PMID:29642375|PMID:36717627|PMID:42094467	high
+human	cartilage	chondrocyte		COL2A1;ACAN;SOX9	PTPRC;PECAM1;COL1A1	cartilage matrix-producing cells; SOX9 is not specific by itself; COL2A1 and ACAN provide the stronger cartilage signal; dedifferentiation may lower these genes	CL:0000138	chondrocyte	lit=PMID:30026257|PMID:38433390	high
+mouse	cartilage	chondrocyte		Col2a1;Acan;Sox9	Ptprc;Pecam1;Col1a1	cartilage matrix-producing cells; Sox9 also occurs in progenitors; Col2a1/Acan support identity and may drop with dedifferentiation	CL:0000138	chondrocyte	lit=PMID:34200880	high
+human	cartilage	superficial zone articular chondrocyte	chondrocyte	PRG4;COL2A1	PTPRC;PECAM1;COL10A1	articular cartilage surface cells; PRG4 also marks synovial lining fibroblasts, so require cartilage context and COL2A1; not every superficial cell coexpresses both transcripts	CL:0020037	superficial zone articular chondrocyte	lit=PMID:38433390	medium
+mouse	cartilage	superficial zone articular chondrocyte	chondrocyte	Prg4;Col2a1	Ptprc;Pecam1;Col10a1	articular cartilage surface cells; Prg4 also occurs in synovial lining fibroblasts, so require cartilage context and Col2a1	CL:0020037	superficial zone articular chondrocyte	lit=PMID:37681409	medium
+human	cartilage	hypertrophic chondrocyte	chondrocyte	COL10A1;MMP13	PRG4;PTPRC;PECAM1	hypertrophic cartilage program, especially in growth plate or osteoarthritic cartilage; MMP13 is also induced by inflammation; validate location and COL10A1	CL:0000743	hypertrophic chondrocyte	lit=PMID:30026257	medium
+mouse	cartilage	hypertrophic chondrocyte	chondrocyte	Col10a1;Ihh	Prg4;Ptprc;Pecam1	growth plate or hypertrophic cartilage program; Ihh begins in prehypertrophic cells, so the pair can include the transition zone	CL:0000743	hypertrophic chondrocyte	lit=PMID:34200880	medium
+human	drg	satellite glial cell		FABP7;KCNJ10	MPZ;AVIL;PTPRC	perineuronal satellite glia of dorsal root ganglia; FABP7 is also an astrocyte marker, so this row is DRG-scoped; GFAP rises after injury and is not required	CL:0000516	perineuronal satellite cell	lit=PMID:32810432|PMID:25420068	high
+mouse	drg	satellite glial cell		Fabp7;Kcnj10	Mpz;Avil;Ptprc	perineuronal satellite glia of dorsal root ganglia; Fabp7 is also an astrocyte marker, so this row is DRG-scoped; Gfap rises after injury and is not required	CL:0000516	perineuronal satellite cell	lit=PMID:32810432|PMID:25420068	high
+human	drg	myelinating Schwann cell		MPZ;PMP22	NGFR;FABP7;AVIL	myelinating Schwann cells; MPZ and PMP22 are the myelin program; MBP transcripts also occur outside Schwann cells	CL:0000218	myelinating Schwann cell	lit=PMID:32810432|PMID:25420068	high
+mouse	drg	myelinating Schwann cell		Mpz;Pmp22	Ngfr;Fabp7;Avil	myelinating Schwann cells; Mpz and Pmp22 are the myelin program; Mbp transcripts also occur outside Schwann cells	CL:0000218	myelinating Schwann cell	lit=PMID:32810432|PMID:25420068	high
+human	drg	non-myelinating Schwann cell		NGFR;SCN7A	MPZ;FABP7;AVIL	Remak Schwann cells; NGFR and SCN7A stay high where the myelin program is low	CL:0002376	non-myelinating Schwann cell	lit=PMID:32810432|PMID:25420068	high
+mouse	drg	non-myelinating Schwann cell		Ngfr;Scn7a	Mpz;Fabp7;Avil	Remak Schwann cells; Ngfr and Scn7a stay high where the myelin program is low	CL:0002376	non-myelinating Schwann cell	lit=PMID:32810432|PMID:25420068	high
+human	drg	sensory neuron		AVIL;PRPH	MPZ;FABP7;PTPRC	dorsal root ganglion sensory neurons; AVIL is shared across subtypes and PRPH is higher in small-diameter neurons	CL:1001451	sensory neuron of dorsal root ganglion	lit=PMID:25420068|PMID:31915380|PMID:32810432	high
+mouse	drg	sensory neuron		Avil;Prph	Mpz;Fabp7;Ptprc	dorsal root ganglion sensory neurons; Avil is shared across subtypes and Prph is higher in small-diameter neurons	CL:1001451	sensory neuron of dorsal root ganglion	lit=PMID:25420068|PMID:31915380|PMID:32810432	high
+human	drg	peptidergic nociceptor	sensory neuron	CALCA;TAC1	MRGPRD;NEFH;PVALB	CGRP peptidergic nociceptors; CALCA is also in some large neurons at low level	CL:4033176	dorsal root ganglion CGRP neuron	lit=PMID:25420068|PMID:31915380	high
+mouse	drg	peptidergic nociceptor	sensory neuron	Calca;Tac1	Mrgprd;Nefh;Pvalb	CGRP peptidergic nociceptors; Calca is also in some large neurons at low level	CL:4033176	dorsal root ganglion CGRP neuron	lit=PMID:25420068|PMID:31915380	high
+human	drg	non-peptidergic nociceptor	sensory neuron	MRGPRD;P2RX3	CALCA;NEFH;PVALB	non-peptidergic nociceptors; MRGPRD marks the NP1 group and P2RX3 is broader	CL:4033182	dorsal root ganglion RET neuron	lit=PMID:25420068|PMID:31915380	high
+mouse	drg	non-peptidergic nociceptor	sensory neuron	Mrgprd;P2rx3	Calca;Nefh;Pvalb	non-peptidergic nociceptors; Mrgprd marks the NP1 group and P2rx3 is broader	CL:4033182	dorsal root ganglion RET neuron	lit=PMID:25420068|PMID:31915380	high
+human	drg	large diameter sensory neuron	sensory neuron	NEFH;NTRK3	CALCA;MRGPRD;PVALB	neurofilament-high mechanoreceptors; NTRK3 is shared with proprioceptors, which are separated by PVALB	CL:1001451	sensory neuron of dorsal root ganglion	lit=PMID:25420068|PMID:31915380	medium
+mouse	drg	large diameter sensory neuron	sensory neuron	Nefh;Ntrk3	Calca;Mrgprd;Pvalb	neurofilament-high mechanoreceptors; Ntrk3 is shared with proprioceptors, which are separated by Pvalb	CL:1001451	sensory neuron of dorsal root ganglion	lit=PMID:25420068|PMID:31915380	medium
+human	drg	proprioceptive neuron	sensory neuron	PVALB;RUNX3	CALCA;MRGPRD;TH	large proprioceptors; PVALB here is not the cortical PVALB interneuron marker	CL:1001451	sensory neuron of dorsal root ganglion	lit=PMID:25420068|PMID:31915380	high
+mouse	drg	proprioceptive neuron	sensory neuron	Pvalb;Runx3	Calca;Mrgprd;Th	large proprioceptors; Pvalb here is not the cortical Pvalb interneuron marker	CL:1001451	sensory neuron of dorsal root ganglion	lit=PMID:25420068|PMID:31915380	high
+human	drg	C-LTMR	sensory neuron	TH;TAFA4	CALCA;NEFH;PVALB	C-fiber low-threshold mechanoreceptors; TAFA4 is the current symbol for FAM19A4	CL:1001451	sensory neuron of dorsal root ganglion	lit=PMID:25420068|PMID:31915380	high
+mouse	drg	C-LTMR	sensory neuron	Th;Tafa4	Calca;Nefh;Pvalb	C-fiber low-threshold mechanoreceptors; Tafa4 is the current symbol for Fam19a4	CL:1001451	sensory neuron of dorsal root ganglion	lit=PMID:25420068|PMID:31915380	high
+human	bone	osteocyte		DMP1;SOST	IBSP;CTSK;PTPRC	mature osteocytes; SOST is more restricted than DMP1, which is also in late osteoblasts	CL:0000137	osteocyte	lit=PMID:34428745	medium
+mouse	bone	osteocyte		Dmp1;Sost	Ibsp;Ctsk;Ptprc	mature osteocytes; Sost is more restricted than Dmp1, which is also in late osteoblasts	CL:0000137	osteocyte	lit=PMID:38477760	medium
+human	adipose	brown adipocyte	adipocyte	UCP1;CIDEA	PTPRC;PECAM1	thermogenic adipocytes; UCP1 defines the type and CIDEA is also detected in some white adipocytes	CL:0000449	brown adipocyte	lit=PMID:35296864	medium
+mouse	adipose	brown adipocyte	adipocyte	Ucp1;Cidea	Ptprc;Pecam1	thermogenic adipocytes; Ucp1 defines the type and Cidea is also detected in some white adipocytes	CL:0000449	brown adipocyte	lit=PMID:35296864	medium
+human	adipose	preadipocyte	fibroblast	PDGFRA;DLK1	ADIPOQ;PTPRC	adipocyte precursors; PDGFRA is shared with other fibroblasts and DLK1 marks the precursor before lipid filling	CL:0002334	preadipocyte	lit=PMID:35296864	medium
+mouse	adipose	preadipocyte	fibroblast	Pdgfra;Dlk1	Adipoq;Ptprc	adipocyte precursors; Pdgfra is shared with other fibroblasts and Dlk1 marks the precursor before lipid filling	CL:0002334	preadipocyte	lit=PMID:35296864	medium
+human	heart	endocardial cell	endothelial cell	NPR3;NFATC1	TNNT2;GJA5	chamber endocardium; NPR3 separates it from coronary endothelium	CL:0002350	endocardial cell	lit=PMID:32971526	medium
+mouse	heart	endocardial cell	endothelial cell	Npr3;Nfatc1	Tnnt2;Gja5	chamber endocardium; Npr3 separates it from coronary endothelium	CL:0002350	endocardial cell	lit=PMID:32971526	medium
+human	skin	sebocyte		FASN;SCD	KRT14;PTPRC	sebaceous gland cells; FASN and SCD are also in adipocytes, so this row is skin-scoped	CL:0002140	skin sebocyte	lit=PMID:33479125	medium
+mouse	skin	sebocyte		Fasn;Scd1	Krt14;Ptprc	sebaceous gland cells; the mouse stearoyl-CoA desaturase symbol is Scd1; Fasn is also in adipocytes	CL:0002140	skin sebocyte	lit=PMID:33479125	medium
+human	stomach	enterochromaffin-like cell		HDC;CHGA	ATP4A;MUC5AC;PTPRC	corpus enterochromaffin-like cells; CHGA is shared with other enteroendocrine cells and HDC is the histamine enzyme	CL:0000504	enterochromaffin-like cell	lit=PMID:37402315	medium
+mouse	stomach	enterochromaffin-like cell		Hdc;Chga	Atp4a;Muc5ac;Ptprc	corpus enterochromaffin-like cells; Chga is shared with other enteroendocrine cells and Hdc is the histamine enzyme	CL:0000504	enterochromaffin-like cell	lit=PMID:37402315	medium
+human	pancreas	pancreatic stellate cell	fibroblast	RGS5;PDGFRB	CPA1;INS;PTPRC	quiescent pancreatic stellate cells; RGS5 and PDGFRB are shared with pericytes, and activated cells gain ACTA2	CL:0002410	pancreatic stellate cell	lit=PMID:27693023	medium
+mouse	pancreas	pancreatic stellate cell	fibroblast	Rgs5;Pdgfrb	Cpa1;Ins2;Ptprc	quiescent pancreatic stellate cells; Rgs5 and Pdgfrb are shared with pericytes, and activated cells gain Acta2	CL:0002410	pancreatic stellate cell	lit=PMID:27667365	medium
+human	stomach	type G cell of stomach		GAST	SST;HDC;PTPRC	antral gastrin-producing endocrine cells; GAST is the defining transcript; CHGA is not required because some gastric G cells lack it	CL:4047025	type G cell of stomach	lit=PMID:24488499|PMID:37698169	high
+mouse	stomach	type G cell of stomach		Gast	Sst;Hdc;Ptprc	antral gastrin-producing endocrine cells; Gast is the defining transcript; Chga is not required in G cells	CL:4047025	type G cell of stomach	lit=PMID:37698169|PMID:26352512	high
+human	stomach	type D cell of stomach		SST	GAST;HDC;PTPRC	gastric somatostatin-producing endocrine cells; SST also identifies D cells elsewhere so retain stomach scope	CL:0002267	type D cell of stomach	lit=PMID:24488499|PMID:25363776	high
+mouse	stomach	type D cell of stomach		Sst	Gast;Hdc;Ptprc	gastric somatostatin-producing endocrine cells in antrum and corpus; Sst alone is not organ-specific	CL:0002267	type D cell of stomach	lit=PMID:26241122	high
+human	stomach	tuft cell of stomach		POU2F3;TRPM5	CHGA;GAST;PTPRC	rare gastric chemosensory tuft cells; POU2F3 and TRPM5 are shared with tuft cells in other organs so stomach scope is required	CL:4052040	tuft cell of stomach	lit=PMID:38117182|PMID:21688022	medium	DCLK1
+mouse	stomach	tuft cell of stomach		Pou2f3;Trpm5	Chga;Gast;Ptprc	rare gastric tuft cells; Dclk1 supports identity but can label other epithelial states	CL:4052040	tuft cell of stomach	lit=PMID:38117182|PMID:21688022	medium	Dclk1
+human	intestine	M cell of gut		GP2;SPIB	MUC2;LGR5;PTPRC	follicle-associated antigen-sampling epithelial cells; GP2 identifies mature M cells and SPIB their differentiation program; GP2 is also expressed in pancreas so retain intestine scope	CL:0000682	M cell of gut	lit=PMID:26820624	high
+mouse	intestine	M cell of gut		Gp2;Spib	Muc2;Lgr5;Ptprc	Peyer's patch follicle-associated epithelial M cells; Gp2 marks mature cells and Spib is needed for differentiation	CL:0000682	M cell of gut	lit=PMID:22706340	high
+human	heart	regular atrial cardiac myocyte	cardiomyocyte	NPPA;MYL7	MYL2;IRX4;PTPRC	atrial chamber cardiomyocytes; NPPA can rise in stressed ventricles so require the atrial MYL7 program and heart context	CL:0002129	regular atrial cardiac myocyte	lit=PMID:32971526|PMID:41056371	high	MYL4
+mouse	heart	regular atrial cardiac myocyte	cardiomyocyte	Nppa;Myl7	Myl2;Irx4;Ptprc	atrial cardiomyocytes; Nppa may be induced by ventricular stress but Myl7 provides a second chamber marker	CL:0002129	regular atrial cardiac myocyte	lit=PMID:32597844|PMID:35254919	high	Myl4
+human	heart	regular ventricular cardiac myocyte	cardiomyocyte	MYL3;HEY2	MYL7;PTPRC;PECAM1	ventricular chamber cardiomyocytes; MYL3 and HEY2 support ventricular identity; MYL2 and MYH7 are enriched but can also be detected in atria or ambient RNA	CL:0002131	regular ventricular cardiac myocyte	lit=PMID:32971526|PMID:30464173|PMID:37327991	high	MYL2;MYH7
+mouse	heart	regular ventricular cardiac myocyte	cardiomyocyte	Myl2;Hey2	Myl7;Ptprc;Pecam1	ventricular cardiomyocytes; adult mouse Myh6 is broadly cardiac and is not used as a ventricular discriminator	CL:0002131	regular ventricular cardiac myocyte	lit=PMID:32597844|PMID:37669370	high	Myh6
+human	kidney	mesangial cell		ITGA8;GATA3	PECAM1;NPHS1;LRP2	intraglomerular mesangial cells; ITGA8 and GATA3 together distinguish them from podocytes and endothelium; PDGFRB alone also labels pericytes	CL:0000650	mesangial cell	lit=PMID:33837218|PMID:31405951	medium	PDGFRB
+mouse	kidney	mesangial cell		Itga8;Gata3	Pecam1;Nphs1;Lrp2	intraglomerular mesangial cells; Itga8 and Gata3 provide the core pair while Pdgfrb is shared with other mural cells	CL:0000650	mesangial cell	lit=PMID:33837218|PMID:31405951	medium	Pdgfrb
+human	kidney	glomerular capillary endothelial cell	endothelial cell	EHD3;PECAM1	NPHS1;ITGA8;PTPRC	glomerular capillary endothelium; EHD3 distinguishes it from most other renal endothelial beds while PECAM1 confirms endothelial identity	CL:1001005	glomerular capillary endothelial cell	lit=PMID:33837218|PMID:32651223	high	KDR
+mouse	kidney	glomerular capillary endothelial cell	endothelial cell	Ehd3;Pecam1	Nphs1;Itga8;Ptprc	glomerular capillary endothelium; Ehd3 is enriched over other kidney endothelial populations and Pecam1 confirms lineage	CL:1001005	glomerular capillary endothelial cell	lit=PMID:17251388|PMID:32651223	high	Kdr
+human	kidney	macula densa epithelial cell		NOS1;NT5C1A	LRP2;SLC12A3;AQP2	rare juxtaglomerular tubular cells; NOS1 with NT5C1A is supported by human tissue staining and separates this population from neighboring tubule classes	CL:1000850	macula densa epithelial cell	lit=PMID:33837218	medium	SLC29A1
+mouse	kidney	macula densa epithelial cell		Nos1;Nt5c1a	Lrp2;Slc12a3;Aqp2	rare juxtaglomerular tubular cells; Nos1 and Nt5c1a identify macula densa in mouse single-cell data and tissue sections	CL:1000850	macula densa epithelial cell	lit=PMID:33837218	medium	Slc29a1
+human	pancreas	pancreatic epsilon cell		GHRL	INS;GCG;SST;PPY	rare ghrelin-producing pancreatic endocrine cells; GHRL also marks gastric endocrine cells so this row is pancreas-scoped	CL:0005019	pancreatic epsilon cell	lit=PMID:30380031|PMID:27864352	high	CHGA
+mouse	pancreas	pancreatic epsilon cell		Ghrl	Ins1;Gcg;Sst;Ppy	rare ghrelin-producing pancreatic endocrine cells; Ghrl is not pancreas-specific and epsilon cells are uncommon in adult islets	CL:0005019	pancreatic epsilon cell	lit=PMID:14970313|PMID:23251675	medium	Chga
+human	thyroid	thyroid follicular cell		TG;TPO	CALCA	Thyroid hormone-producing follicular lineage	CL:0002258	thyroid follicular cell	lit=PMID:36396935|PMID:41727685	high
+mouse	thyroid	thyroid follicular cell		Tg;Tpo	Calca	Thyroid hormone-producing follicular lineage	CL:0002258	thyroid follicular cell	lit=PMID:34916298	high
+human	thyroid	parafollicular cell		CALCA;CHGA	TG	Rare parafollicular C cells; CALCA distinguishes from follicular cells	CL:0000570	parafollicular cell	lit=PMID:41727685	high
+mouse	thyroid	parafollicular cell		Calca	Tg	Rare parafollicular C cells; Calca is supported directly in mouse thyroid, with Chga as a neuroendocrine support marker	CL:0000570	parafollicular cell	lit=PMID:34916298	high	Chga
+human	bladder	bladder urothelial cell		UPK1B;UPK2	PTPRC	Uroplakin-positive differentiated urothelium; basal urothelial cells may score lower	CL:1001428	bladder urothelial cell	lit=PMID:26694548|PMID:31462402	medium
+mouse	bladder	bladder urothelial cell		Upk1b;Upk2	Ptprc	Uroplakin-positive differentiated urothelium; basal urothelial cells may score lower	CL:1001428	bladder urothelial cell	lit=PMID:26694548|PMID:31462402	medium
+human	salivary	serous acinar cell of salivary gland		AMY1A;STATH	MUC5B	Serous secretory acinar cells; symbols and secretory products differ by species	CL:4052065	serous acinar cell of salivary gland	lit=PMID:33207190|PMID:38715201	high
+mouse	salivary	serous acinar cell of salivary gland		Amy1;Bpifa2	Muc19	Serous secretory acinar cells; symbols and secretory products differ by species	CL:4052065	serous acinar cell of salivary gland	lit=PMID:33207190|PMID:38715201	high
+human	salivary	mucous acinar cell of salivary gland		MUC5B;TFF3	AMY1A	Mucous secretory acinar cells; human MUC5B/TFF3 and mouse Muc19/A2ml1 are supported by species-specific atlases	CL:4052066	mucous acinar cell of salivary gland	lit=PMID:36726292|PMID:36544475	high
+mouse	salivary	mucous acinar cell of salivary gland		Muc19;A2ml1	Amy1	Mucous secretory acinar cells; human MUC5B/TFF3 and mouse Muc19/A2ml1 are supported by species-specific atlases	CL:4052066	mucous acinar cell of salivary gland	lit=PMID:36726292|PMID:36544475	high
+human	salivary	basal duct cell of salivary gland		KRT5;TP63	AQP5;ACTA2	Basal salivary duct lineage; ACTA2 helps separate myoepithelial cells; KRT5 and TP63 are also found in other basal epithelia	CL:0020060	basal duct cell of salivary gland	lit=PMID:41707649|PMID:30232460	medium
+mouse	salivary	basal duct cell of salivary gland		Krt5;Trp63	Aqp5;Acta2	Basal salivary duct lineage; ACTA2 helps separate myoepithelial cells; KRT5 and TP63 are also found in other basal epithelia	CL:0020060	basal duct cell of salivary gland	lit=PMID:41707649|PMID:30232460	medium
+human	salivary	myoepithelial cell of salivary gland		ACTA2;KRT14	AQP5	Myoepithelial contractile epithelial cells; co-expression helps distinguish smooth muscle	CL:0020066	myoepithelial cell of salivary gland	lit=PMID:35672412|PMID:30232460	high
+mouse	salivary	myoepithelial cell of salivary gland		Acta2;Krt14	Aqp5	Myoepithelial contractile epithelial cells; co-expression helps distinguish smooth muscle	CL:0020066	myoepithelial cell of salivary gland	lit=PMID:35672412|PMID:30232460	high
+human	retina	retinal rod cell		RHO;NRL	ARR3	Rod photoreceptors	CL:0000604	retinal rod cell	lit=PMID:31436334|PMID:38812536	high
+mouse	retina	retinal rod cell		Rho;Nrl	Arr3	Rod photoreceptors	CL:0000604	retinal rod cell	lit=PMID:31436334|PMID:38812536	high
+human	retina	retinal cone cell		ARR3;GNAT2	RHO	Cone photoreceptors	CL:0000573	retinal cone cell	lit=PMID:31436334|PMID:38812536	high
+mouse	retina	retinal cone cell		Arr3;Gnat2	Rho	Cone photoreceptors	CL:0000573	retinal cone cell	lit=PMID:31436334|PMID:38812536	high
+human	retina	retinal bipolar neuron		VSX2;OTX2	RHO	Retinal bipolar neurons; OTX2 is shared with photoreceptors	CL:0000748	retinal bipolar neuron	lit=PMID:31436334|PMID:38812536	high
+mouse	retina	retinal bipolar neuron		Vsx2;Otx2	Rho	Retinal bipolar neurons; OTX2 is shared with photoreceptors	CL:0000748	retinal bipolar neuron	lit=PMID:31436334|PMID:38812536	high
+human	retina	retinal ganglion cell		RBPMS;SNCG	RHO	Retinal ganglion neurons	CL:0000740	retinal ganglion cell	lit=PMID:31436334|PMID:38812536	high
+mouse	retina	retinal ganglion cell		Rbpms;Sncg	Rho	Retinal ganglion neurons	CL:0000740	retinal ganglion cell	lit=PMID:31436334|PMID:38812536	high
+human	retina	retinal pigment epithelial cell		RPE65;BEST1	RHO	Mature retinal pigment epithelium; RPE65 can be lower in some RPE states and cells may be absent from neural-retina preparations	CL:0002586	retinal pigment epithelial cell	lit=PMID:36775060|PMID:34977041	high
+mouse	retina	retinal pigment epithelial cell		Rpe65;Lrat	Rho	Mature retinal pigment epithelium; mouse Best1 is not a reliable RPE marker, so use visual-cycle genes Rpe65 and Lrat	CL:0002586	retinal pigment epithelial cell	lit=PMID:36142331	high
+human	testis	Sertoli cell		SOX9;CLDN11	DDX4	Sertoli support cells; AMH omitted because adult expression varies	CL:0000216	Sertoli cell	lit=PMID:30146481|PMID:38577799	high
+mouse	testis	Sertoli cell		Sox9;Cldn11	Ddx4	Sertoli support cells; AMH omitted because adult expression varies	CL:0000216	Sertoli cell	lit=PMID:30146481|PMID:38577799	high
+human	testis	Leydig cell		INSL3;CYP17A1	DDX4	Steroidogenic Leydig cells	CL:0000178	Leydig cell	lit=PMID:34626582|PMID:30146481	high
+mouse	testis	Leydig cell		Insl3;Cyp17a1	Ddx4	Steroidogenic Leydig cells	CL:0000178	Leydig cell	lit=PMID:34626582|PMID:30146481	high
+human	testis	male germ cell		DDX4;DAZL	SOX9	Broad male germ-cell lineage; no spermatogenesis-stage split	CL:0000015	male germ cell	lit=PMID:38577799|PMID:30146481	high
+mouse	testis	male germ cell		Ddx4;Dazl	Sox9	Broad male germ-cell lineage; no spermatogenesis-stage split	CL:0000015	male germ cell	lit=PMID:38577799|PMID:30146481	high
+human	ovary	granulosa cell		FOXL2;INHA	GDF9	Granulosa support cells; expression may vary by follicular stage	CL:0000501	granulosa cell	lit=PMID:34769386|PMID:39834231	high
+mouse	ovary	granulosa cell		Foxl2;Inha	Gdf9	Granulosa support cells; expression may vary by follicular stage	CL:0000501	granulosa cell	lit=PMID:34769386|PMID:39834231	high
+human	ovary	theca cell		CYP17A1;STAR	GDF9	Steroidogenic theca cells; excludes non-steroidogenic theca states	CL:0000503	theca cell	lit=PMID:36575161|PMID:34769386	high
+mouse	ovary	theca cell		Cyp17a1;Star	Gdf9	Steroidogenic theca cells; excludes non-steroidogenic theca states	CL:0000503	theca cell	lit=PMID:36575161|PMID:34769386	high
+human	ovary	oocyte		GDF9;ZP3	FOXL2	Oocytes; low recovery in standard dissociation	CL:0000023	oocyte	lit=PMID:38578993|PMID:34769386	high
+mouse	ovary	oocyte		Gdf9;Zp3	Foxl2	Oocytes; low recovery in standard dissociation	CL:0000023	oocyte	lit=PMID:38578993|PMID:34769386	high
+human	mammary	basal-myoepithelial cell of mammary gland		ACTA2;KRT14	KRT18	Basal myoepithelial lineage; ACTA2 also occurs in smooth muscle	CL:0002324	basal-myoepithelial cell of mammary gland	lit=PMID:25173976|PMID:29795293	high
+mouse	mammary	basal-myoepithelial cell of mammary gland		Acta2;Krt14	Krt18	Basal myoepithelial lineage; ACTA2 also occurs in smooth muscle	CL:0002324	basal-myoepithelial cell of mammary gland	lit=PMID:25173976|PMID:29795293	high
+human	mammary	luminal epithelial cell of mammary gland		KRT8;KRT18	ACTA2	Broad luminal mammary epithelium	CL:0002326	luminal epithelial cell of mammary gland	lit=PMID:29795293|PMID:34187545	high
+mouse	mammary	luminal epithelial cell of mammary gland		Krt8;Krt18	Acta2	Broad luminal mammary epithelium	CL:0002326	luminal epithelial cell of mammary gland	lit=PMID:29795293|PMID:34187545	high
+human	prostate	luminal cell of prostate epithelium		KLK3;ACPP	KRT5	Differentiated androgen-responsive secretory luminal prostate epithelium; KLK3/ACPP and mouse Pbsn can decrease after androgen deprivation	CL:0002340	luminal cell of prostate epithelium	lit=PMID:39825401|PMID:32355025	high
+mouse	prostate	luminal cell of prostate epithelium		Nkx3-1;Pbsn	Krt5	Differentiated androgen-responsive secretory luminal prostate epithelium; KLK3/ACPP and mouse Pbsn can decrease after androgen deprivation	CL:0002340	luminal cell of prostate epithelium	lit=PMID:39825401|PMID:32355025	high
+human	prostate	basal cell of prostate epithelium		KRT5;TP63	KLK3	Basal prostate epithelium; keratin and p63 co-expression	CL:0002341	basal cell of prostate epithelium	lit=PMID:39825401|PMID:32355025	high
+mouse	prostate	basal cell of prostate epithelium		Krt5;Trp63	Pbsn	Basal prostate epithelium; keratin and p63 co-expression	CL:0002341	basal cell of prostate epithelium	lit=PMID:39825401|PMID:32355025	high
+human	endometrium	glandular epithelial cell of endometrium		FOXA2;EPCAM	HAND2	Glandular endometrial epithelium; FOXA2 varies with developmental or hormonal state	CL:0009084	glandular epithelial cell of endometrium	lit=PMID:32929266|PMID:40074766	high
+mouse	endometrium	glandular epithelial cell of endometrium		Foxa2;Epcam	Hand2	Glandular endometrial epithelium; FOXA2 varies with developmental or hormonal state	CL:0009084	glandular epithelial cell of endometrium	lit=PMID:32929266|PMID:40074766	high
+human	endometrium	stromal cell of endometrium		HAND2;WT1	EPCAM	Endometrial stromal cells; hormonal state changes expression	CL:0002255	stromal cell of endometrium	lit=PMID:35169075|PMID:40627402	high
+mouse	endometrium	stromal cell of endometrium		Hand2;Wt1	Epcam	Endometrial stromal cells; hormonal state changes expression	CL:0002255	stromal cell of endometrium	lit=PMID:35169075|PMID:40627402	high
+human	retina	Mueller cell		RLBP1;GLUL	RPE65	Mueller glia; GLUL is shared with retinal astrocytes but RLBP1 enriches Mueller cells	CL:0000636	Mueller cell	lit=PMID:31436334|PMID:38812536	high
+mouse	retina	Mueller cell		Rlbp1;Glul	Rpe65	Mueller glia; GLUL is shared with retinal astrocytes but RLBP1 enriches Mueller cells	CL:0000636	Mueller cell	lit=PMID:31436334|PMID:38812536	high
+human	cornea	corneal epithelial cell		KRT3;KRT12	KRT13	Differentiated corneal epithelium; limbal basal progenitors can have lower KRT12	CL:0000575	corneal epithelial cell	lit=PMID:38514716|PMID:37792336	high
+mouse	cornea	corneal epithelial cell		Krt3;Krt12	Krt13	Differentiated corneal epithelium; limbal basal progenitors can have lower KRT12	CL:0000575	corneal epithelial cell	lit=PMID:38514716|PMID:37792336	high
+human	cornea	corneal endothelial cell		SLC4A11;COL8A2	PECAM1	Corneal endothelium is not vascular endothelium; the collagen-VIII marker differs in available human and mouse atlases	CL:0000132	corneal endothelial cell	lit=PMID:23844023|PMID:37792336|PMID:41060151	high
+mouse	cornea	corneal endothelial cell		Slc4a11;Col8a1	Pecam1	Corneal endothelium is not vascular endothelium; the collagen-VIII marker differs in available human and mouse atlases	CL:0000132	corneal endothelial cell	lit=PMID:23844023|PMID:37792336|PMID:41060151	high
+human	cornea	keratocyte		KERA;LUM	KRT12	Corneal stromal keratocytes; LUM is shared with other fibroblasts	CL:0002363	keratocyte	lit=PMID:34741068|PMID:41060151	high
+mouse	cornea	keratocyte		Kera;Lum	Krt12	Corneal stromal keratocytes; LUM is shared with other fibroblasts	CL:0002363	keratocyte	lit=PMID:34741068|PMID:41060151	high
+human	adrenal	cortical cell of adrenal gland		STAR;CYP11A1	TH	Steroidogenic adrenal cortex; these enzymes also occur in gonadal steroidogenic cells so tissue scope is essential	CL:0002097	cortical cell of adrenal gland	lit=PMID:39167619|PMID:42711427	high
+mouse	adrenal	cortical cell of adrenal gland		Star;Cyp11a1	Th	Steroidogenic adrenal cortex; these enzymes also occur in gonadal steroidogenic cells so tissue scope is essential	CL:0002097	cortical cell of adrenal gland	lit=PMID:39167619|PMID:42711427	high
+human	adrenal	adrenal medulla chromaffin cell		TH;DBH	STAR	Catecholamine-producing adrenal medulla chromaffin cells; TH and DBH are shared with sympathetic neurons	CL:0000336	adrenal medulla chromaffin cell	lit=PMID:39167619|PMID:33500353	high
+mouse	adrenal	adrenal medulla chromaffin cell		Th;Dbh	Star	Catecholamine-producing adrenal medulla chromaffin cells; TH and DBH are shared with sympathetic neurons	CL:0000336	adrenal medulla chromaffin cell	lit=PMID:39167619|PMID:33500353	high
+human	placenta	mononuclear cytotrophoblast cell		EGFR;TP63	HLA-G;CGA	Villous cytotrophoblast; markers and human placental lineage are not transferred to mouse	CL:0000523	mononuclear cytotrophoblast cell	lit=PMID:38880601|PMID:30042384	high
+human	placenta	syncytiotrophoblast cell		CYP19A1;CSH1	TP63;HLA-G	Syncytiotrophoblast; large fused cells may be under-recovered by whole-cell dissociation	CL:0000525	syncytiotrophoblast cell	lit=PMID:40424181|PMID:30042384	high
+human	placenta	extravillous trophoblast		HLA-G;MMP2	CGA;TP63	Extravillous trophoblast; invasive maternal-interface lineage	CL:0008036	extravillous trophoblast	lit=PMID:30042384|PMID:35796428	high
+human	any	eosinophil		CLC;SIGLEC8	FCGR3B;TPSAB1	Human eosinophil granule and surface transcripts; SIGLEC8 can also occur in mast cells and CLC in basophils; low-RNA granulocytes can be lost during dissociation or QC	CL:0000771	eosinophil	lit=PMID:38934897|PMID:10625619	medium	EPX;IL5RA
+mouse	any	eosinophil		Epx;Prg2	Ly6g;Cpa3	Mouse eosinophil granule transcripts; Siglecf is shared with alveolar macrophages; granule expression changes with tissue state and low-RNA cells can be missed	CL:0000771	eosinophil	lit=PMID:36509106|PMID:39331714	medium	Il5ra
+human	thymus	epithelial cell of thymus		FOXN1;EPCAM	PTPRC	Thymic epithelial lineage; FOXN1 may be sparse in aged or cultured cells, so absence does not exclude every TEC state	CL:0002293	epithelial cell of thymus	lit=PMID:33597545|PMID:24936476	medium
+mouse	thymus	epithelial cell of thymus		Foxn1;Epcam	Ptprc	Thymic epithelial lineage; Foxn1 may be sparse in aged cells, so absence does not exclude every TEC state	CL:0002293	epithelial cell of thymus	lit=PMID:40500437|PMID:31243087	medium
+human	intestine	enteric neuron		ELAVL4;PHOX2B	EPCAM;ACTG2	Enteric neurons are rare in whole-intestine scRNA-seq and often require enrichment or nuclei profiling; ELAVL4 marks neurons while PHOX2B also occurs in some enteric glia	CL:0007011	enteric neuron	lit=PMID:33444816|PMID:32888429	medium	SNAP25
+mouse	intestine	enteric neuron		Elavl4;Phox2b	Epcam;Actg2	Enteric neurons are rare in whole-intestine scRNA-seq and often require enrichment or nuclei profiling; Elavl4 marks neurons while Phox2b also occurs in some enteric glia	CL:0007011	enteric neuron	lit=PMID:33444816|PMID:32888429	medium	Snap25
+human	heart	mesothelial cell of epicardium	mesothelial cell	UPK3B;MSLN	TNNT2;PECAM1	Heart-restricted epicardial mesothelium; both positive genes are shared with other serosal mesothelia, so location and parent-level annotation matter	CL:0011019	mesothelial cell of epicardium	lit=PMID:36938497|PMID:37390825	medium	ITLN1
+mouse	heart	mesothelial cell of epicardium	mesothelial cell	Upk3b;Msln	Tnnt2;Pecam1	Heart-restricted epicardial mesothelium; both positive genes are shared with other serosal mesothelia, so location and parent-level annotation matter	CL:0011019	mesothelial cell of epicardium	lit=PMID:37719196	medium	Efemp1
+human	intestine	interstitial cell of Cajal		KIT;ANO1	PTPRC;TPSAB1	GI muscularis propria ICC; KIT is shared with mast cells, while ANO1 alone also occurs in epithelium; use their co-expression and exclude mast cells; rare cells may be missed in mucosal-only preparations	CL:0002088	interstitial cell of Cajal	lit=PMID:19372102|PMID:37206377	high
+mouse	intestine	interstitial cell of Cajal		Kit;Ano1	Ptprc;Cpa3	GI muscularis propria ICC; Kit is shared with mast cells and Ano1 alone is not exclusive across intestinal compartments; require their combination; rare in mucosal-only preparations	CL:0002088	interstitial cell of Cajal	lit=PMID:19372102|PMID:27979828	high
+human	kidney	parietal epithelial cell		CLDN1;CFH;ALDH1A2	NPHS1;EHD3	glomerular Bowman capsule; CFH and ALDH1A2 are shared with other cell types, and ALDH1A2 has scRNA dropout; distinguish podocytes and glomerular endothelium with relative negative markers	CL:1000452	parietal epithelial cell	CAP(adult human kidney PEC:CLDN1,CFH,ALDH1A2); lit=PMID:39360029|PMID:35675394	medium
+mouse	kidney	parietal epithelial cell		Cldn1;Pax8	Nphs1;Ehd3	glomerular Bowman capsule; Pax8 is also expressed by renal tubules and Cldn1 alone is not specific; use co-expression in glomerular context and exclude podocytes and endothelium	CL:1000452	parietal epithelial cell	lit=PMID:39177649	medium