Azimuth References

Human - PBMC

Overview

Modalities: RNA, ADT

Cells in Reference: 161,764

Species: Human

Reference Dataset(s): Hao and Hao et al, bioRvix 2020

Demo Dataset(s): 11,769 PBMCs from 10x Genomics

This PBMC reference dataset was generated as part of the Hao and Hao et al, bioRvix 2020 paper. It is comprised of data from eight volunteers enrolled in an HIV vaccine trial from which three time point samples were taken at day 0, 3, and 7 following vaccination. All 24 samples were processed with a CITE-seq panel of 228 TotalSeq A antibodies to generate single-cell RNA and ADT data. The data were then integrated using metholody described in the pre-print linked above to generate a weighted nearest neighbor (WNN) representation of the RNA and protein data jointly. This WNN representation is used in the Azimuth app to assign celltypes, embed in the reference UMAP, and impute protein levels for the query dataset.


Annotation Details

celltype.l1
LabelExpanded LabelOBO Ontology IDMarkers
MonoMonocytemonocyteCTSS, FCN1, NEAT1, LYZ, PSAP, S100A9, AIF1, MNDA, SERPINA1, TYROBP
CD4 TCD4+ T cellCD4-positive, alpha-beta T cellIL7R, MAL, LTB, CD4, LDHB, TPT1, TRAC, TMSB10, CD3D, CD3G
CD8 TCD8+ T cellCD8-positive, alpha-beta T cellCD8B, CD8A, CD3D, TMSB10, HCST, CD3G, LINC02446, CTSW, CD3E, TRAC
NKnatural killer cellnatural killer cellNKG7, KLRD1, TYROBP, GNLY, FCER1G, PRF1, CD247, KLRF1, CST7, GZMB
BB cellmature B cellCD79A, RALGPS2, CD79B, MS4A1, BANK1, CD74, TNFRSF13C, HLA-DQA1, IGHM, MEF2C
other Tother T cellmature T cellCD3D, TRDC, GZMK, KLRB1, NKG7, TRGC2, CST7, LYAR, KLRG1, GZMA
DCdendritic celldendritic cellCD74, HLA-DPA1, HLA-DPB1, HLA-DQA1, CCDC88A, HLA-DRA, HLA-DMA, CST3, HLA-DQB1, HLA-DRB1
celltype.l2 (default)
LabelExpanded LabelOBO Ontology IDMarkers
B intermediateIntermediate B cellmature B cellMS4A1, TNFRSF13B, IGHM, IGHD, AIM2, CD79A, LINC01857, RALGPS2, BANK1, CD79B
B memoryMemory B cellmemory B cellMS4A1, COCH, AIM2, BANK1, SSPN, CD79A, TEX9, RALGPS2, TNFRSF13C, LINC01781
B naiveNaive B cellnaive B cellIGHM, IGHD, CD79A, IL4R, MS4A1, CXCR4, BTG1, TCL1A, CD79B, YBX3
PlasmablastPlasmablastplasmablastIGHA2, MZB1, TNFRSF17, DERL3, TXNDC5, TNFRSF13B, POU2AF1, CPNE5, HRASLS2, NT5DC2
CD4 CTLCD4+ Cytotoxic TCD4-positive, alpha-beta cytotoxic T cellGZMH, CD4, FGFBP2, ITGB1, GZMA, CST7, GNLY, B2M, IL32, NKG7
CD4 NaiveCD4+ Naive Tnaive thymus-derived CD4-positive, alpha-beta T cellTCF7, CD4, CCR7, IL7R, FHIT, LEF1, MAL, NOSIP, LDHB, PIK3IP1
CD4 ProliferatingCD4+ Proliferating Tactivated CD4-positive, alpha-beta T cellMKI67, TOP2A, PCLAF, CENPF, TYMS, NUSAP1, ASPM, PTTG1, TPX2, RRM2
CD4 TCMCD4+ Central Memory TCD4-positive, alpha-beta memory T cellIL7R, TMSB10, CD4, ITGB1, LTB, TRAC, AQP3, LDHB, IL32, MAL
CD4 TEMCD4+ Effector Memory Teffector CD4-positive, alpha-beta T cellIL7R, CCL5, FYB1, GZMK, IL32, GZMA, KLRB1, TRAC, LTB, AQP3
TregRegulatory Tregulatory T cellRTKN2, FOXP3, AC133644.2, CD4, IL2RA, TIGIT, CTLA4, FCRL3, LAIR2, IKZF2
CD8 NaiveCD8+ Naive Tnaive thymus-derived CD8-positive, alpha-beta T cellCD8B, S100B, CCR7, RGS10, NOSIP, LINC02446, LEF1, CRTAM, CD8A, OXNAD1
CD8 ProliferatingCD8+ Proliferating Tactivated CD8-positive, alpha-beta T cellMKI67, CD8B, TYMS, TRAC, PCLAF, CD3D, CLSPN, CD3G, TK1, RRM2
CD8 TCMCD8+ Central Memory TCD8-positive, alpha-beta memory T cellCD8B, ANXA1, CD8A, KRT1, LINC02446, YBX3, IL7R, TRAC, NELL2, LDHB
CD8 TEMCD8+ Effector Memory Teffector CD8-positive, alpha-beta T cellCCL5, GZMH, CD8A, TRAC, KLRD1, NKG7, GZMK, CST7, CD8B, TRGC2
ASDCAXL+ Dendritic Celldendritic cellPPP1R14A, LILRA4, AXL, IL3RA, SCT, SCN9A, LGMN, DNASE1L3, CLEC4C, GAS6
cDC1Conventional Dendritic Cell 1CD141-positive myeloid dendritic cellCLEC9A, DNASE1L3, C1orf54, IDO1, CLNK, CADM1, FLT3, ENPP1, XCR1, NDRG2
cDC2Conventional Dendritic Cell 2CD1c-positive myeloid dendritic cellFCER1A, HLA-DQA1, CLEC10A, CD1C, ENHO, PLD4, GSN, SLC38A1, NDRG2, AFF3
pDCPlasmacytoid Dendritic Cellplasmacytoid dendritic cellITM2C, PLD4, SERPINF1, LILRA4, IL3RA, TPM2, MZB1, SPIB, IRF4, SMPD3
CD14 MonoCD14+ MonocyteCD14-positive, CD16-negative classical monocyteS100A9, CTSS, S100A8, LYZ, VCAN, S100A12, IL1B, CD14, G0S2, FCN1
CD16 MonoCD16+ MonocyteCD14-low, CD16-positive monocyteCDKN1C, FCGR3A, PTPRC, LST1, IER5, MS4A7, RHOC, IFITM3, AIF1, HES4
NKCD56-dim Natural KillerCD16-positive, CD56-dim natural killer cell, humanGNLY, TYROBP, NKG7, FCER1G, GZMB, TRDC, PRF1, FGFBP2, SPON2, KLRF1
NK ProliferatingProliferating Natural Killernatural killer cellMKI67, KLRF1, TYMS, TRDC, TOP2A, FCER1G, PCLAF, CD247, CLSPN, ASPM
NK_CD56brightCD56-bright Natural KillerCD16-negative, CD56-bright natural killer cell, humanXCL2, FCER1G, SPINK2, TRDC, KLRC1, XCL1, SPTSSB, PPP1R9A, NCAM1, TNFRSF11A
ErythErythroid cellerythroid lineage cellHBD, HBM, AHSP, ALAS2, CA1, SLC4A1, IFIT1B, TRIM58, SELENBP1, TMCC2
HSPCHematopoietic stem and progenitor cellhematopoietic precursor cellSPINK2, PRSS57, CYTL1, EGFL7, GATA2, CD34, SMIM24, AVP, MYB, LAPTM4B
ILCInnate Lymphoid Cellinnate lymphoid cellKIT, TRDC, TTLL10, LINC01229, SOX4, KLRB1, TNFRSF18, TNFRSF4, IL1R1, HPGDS
PlateletPlateletplateletPPBP, PF4, NRGN, GNG11, CAVIN2, TUBB1, CLU, HIST1H2AC, RGS18, GP9
dnTDouble-negative TCD4-negative, CD8-negative, alpha-beta intraepithelial T cellPTPN3, MIR4422HG, NUCB2, CAV1, DTHD1, GZMA, MYB, FXYD2, GZMK, AC004585.1
gdTgamma-delta Tgamma-delta T cellTRDC, TRGC1, TRGC2, KLRC1, NKG7, TRDV2, CD7, TRGV9, KLRD1, KLRG1
MAITMucosal associated invariant Tmucosal invariant T cellKLRB1, NKG7, GZMK, IL7R, SLC4A10, GZMA, CXCR6, PRSS35, RBM24, NCR3
celltype.l3
LabelExpanded LabelOBO Ontology IDMarkers
ASDC_mDCAXL+ myeloid dendritic cellmyeloid dendritic cellAXL, LILRA4, SCN9A, CLEC4C, LTK, PPP1R14A, LGMN, SCT, IL3RA, GAS6
ASDC_pDCAXL+ plasmacytoid dendritic cellplasmacytoid dendritic cellLILRA4, CLEC4C, SCT, EPHB1, AXL, PROC, LRRC26, SCN9A, LTK, DNASE1L3
B intermediate kappaIntermediate B cell, kappa light chainmature B cellMS4A1, IGKC, IGHM, LINC01857, MARCKS, IGHD, TNFRSF13B, CD24, FCRL2, BANK1
B intermediate lambdaIntermediate B cell, lambda light chainmature B cellMS4A1, IGLC2, IGHM, CD79A, IGLC3, IGHD, BANK1, TNFRSF13C, CD22, TNFRSF13B
B memory kappaMemory B cell, kappa light chainmemory B cellBANK1, IGKC, LINC01781, MS4A1, SSPN, CD79A, RALGPS2, TNFRSF13C, LINC00926
B memory lambdaMemory B cell, lambda light chainmemory B cellBANK1, IGLC2, MS4A1, IGLC3, COCH, TNFRSF13C, IGHA2, BLK, TNFRSF13B, LINC01781
B naive kappaNaive B cell, kappa light chainnaive B cellIGHM, TCL1A, IGHD, IGHG3, CD79A, IL4R, CD37, MS4A1, IGKC
B naive lambdaNaive B cell, lambda light chainnaive B cellIGHM, IGLC2, IGHD, IGLC3, CD79A, CXCR4, MS4A1, IL4R, TCL1A, CD79B
CD14 MonoCD14+ MonocyteCD14-positive, CD16-negative classical monocyteS100A9, CTSS, LYZ, CTSD, S100A8, VCAN, CD14, FCN1, S100A12, MS4A6A
CD16 MonoCD16+ MonocyteCD14-low, CD16-positive monocyteLST1, YBX1, AIF1, FCGR3A, NAP1L1, MS4A7, FCER1G, TCF7L2, COTL1, CDKN1C
CD4 CTLCD4+ Cytotoxic TCD4-positive, alpha-beta cytotoxic T cellGZMH, CD4, GNLY, FGFBP2, IL7R, S100A4, GZMA, CST7, IL32, CCL5
CD4 NaiveCD4+ Naive Tnaive thymus-derived CD4-positive, alpha-beta T cellTCF7, CD4, NUCB2, LDHB, TRAT1, SARAF, FHIT, LEF1, CCR7, IL7R
CD4 ProliferatingCD4+ Proliferating Tactivated CD4-positive, alpha-beta T cellMKI67, TYMS, PCLAF, TOP2A, CENPF, NUSAP1, CENPM, BIRC5, ZWINT, TPX2
CD4 TCM_1CD4+ Central Memory T_1CD4-positive, alpha-beta memory T cellLTB, CD4, FYB1, IL7R, LIMS1, MAL, TMSB4X, TSHZ2, AP3M2, TRAC
CD4 TCM_2CD4+ Central Memory T_2CD4-positive, alpha-beta memory T cellCTLA4, MIR4435-2HG, TMSB4X, CD28, CDCA7, TMSB10, MAF, ITM2A, TRAC, CD27
CD4 TCM_3CD4+ Central Memory T_3CD4-positive, alpha-beta memory T cellIL7R, ITGB1, LTB, S100A4, AQP3, TNFRSF4, IL32, TOB1, PDE4D, HOPX
CD4 TEM_1CD4+ Effector Memory T_1effector CD4-positive, alpha-beta T cellGZMK, IL7R, IL32, ITGB1, CCL5, GZMA, B2M, DUSP2, KLRB1, SYNE2
CD4 TEM_2CD4+ Effector Memory T_2effector CD4-positive, alpha-beta T cellGZMK, CD4, TIGIT, IFNG-AS1, CD40LG, MALAT1, CD3G, CD3D, TRAC, CD3E
CD4 TEM_3CD4+ Effector Memory T_3effector CD4-positive, alpha-beta T cellIL7R, CCL5, NOSIP, KLRB1, SERINC5, AQP3, ITGA4, IL32, TRAC, LTB
CD4 TEM_4CD4+ Effector Memory T_4effector CD4-positive, alpha-beta T cellCCR9, KDF1, DPP4, CD244, SLC4A4, KLRB1, TMIGD2, CD40LG, IL7R, ODF2L
CD8 NaiveCD8+ Naive Tnaive thymus-derived CD8-positive, alpha-beta T cellCD8B, LDHB, LEF1, LINC02446, CD8A, S100B, ID2, TCF7, VIM, CCR7
CD8 Naive_2CD8+ Naive T_2naive thymus-derived CD8-positive, alpha-beta T cellCD8B, CCR5, CHI3L2, SOX4, CD8A, TNFRSF9, CD38, SIRPG, LRRN3, LEF1
CD8 ProliferatingCD8+ Proliferating Tactivated CD8-positive, alpha-beta T cellPCLAF, CD8B, TYMS, CD3D, CLSPN, CD3G, MKI67, TRAC, CHEK1, TK1
CD8 TCM_1CD8+ Central Memory T_1CD8-positive, alpha-beta memory T cellCD8B, SELL, CD8A, LYAR, ITGB1, NELL2, DUSP2, IL7R, CCL5, LINC01871
CD8 TCM_2CD8+ Central Memory T_2CD8-positive, alpha-beta memory T cellCD8B, C1orf162, IL7R, GATA3, YBX3, KRT1, CD8A, CTSW, INPP4B, LTB
CD8 TCM_3CD8+ Central Memory T_3CD8-positive, alpha-beta memory T cellCD8B, KLRB1, CD8A, HOPX, IL7R, KLRD1, CCL5, SCML4, LINC02446, TRAC
CD8 TEM_1CD8+ Effector Memory T_1effector CD8-positive, alpha-beta T cellGZMK, CD8B, CD8A, CCL5, NKG7, DUSP2, CST7, IL32
CD8 TEM_2CD8+ Effector Memory T_2effector CD8-positive, alpha-beta T cellCD8A, CMC1, CD8B, CD160, GZMH, CST7, KLRD1, CCL5, TIGIT, KLRG1
CD8 TEM_3CD8+ Effector Memory T_3effector CD8-positive, alpha-beta T cellGZMK, CD8A, ITGB1, CD8B, HOPX, CCL5, KLRD1, NKG7, GNLY, YBX3
CD8 TEM_4CD8+ Effector Memory T_4effector CD8-positive, alpha-beta T cellGZMH, THEMIS, GNLY, CD8A, ITGB1, FGFBP2, CD2, GZMB, KLRD1, CD8B
CD8 TEM_5CD8+ Effector Memory T_5effector CD8-positive, alpha-beta T cellGZMH, GNLY, ZNF683, TRAC, KLRC2, TYROBP, CD8B, CD8A, TRGC2, GZMB
CD8 TEM_6CD8+ Effector Memory T_6effector CD8-positive, alpha-beta T cellTRGC2, CD8A, IFNG-AS1, CD8B, ZNF683, KLRC2, NCR3, IKZF2, DUSP2, RTKN2
cDC1Conventional Dendritic Cell 1CD141-positive myeloid dendritic cellWDFY4, C1orf54, CLEC9A, BATF3, CLNK, TSPAN33, FLT3, CADM1, IDO1, DNASE1L3
cDC2_1Conventional Dendritic Cell 2_1CD1c-positive myeloid dendritic cellFCER1A, CD14, CLEC10A, CTSS, ENHO, CD1C, MRC1, FCGR2B, PID1, IL13RA1
cDC2_2Conventional Dendritic Cell 2_2CD1c-positive myeloid dendritic cellFCER1A, BASP1, CD1C, CD74, CLEC10A, HLA-DPA1, ENHO, HLA-DPB1, PLD4, HLA-DQA1
dnT_1Double-negative T_1CD4-negative, CD8-negative, alpha-beta intraepithelial T cellGZMK, NUCB2, CD8B, GPR183, TCF7, LYAR, MALAT1, C12orf57, LEF1, LDHB
dnT_2Double-negative T_2CD4-negative, CD8-negative, alpha-beta intraepithelial T cellAC004585.1, GPR183, FXYD2, NUCB2, CAV1, CD27, MYB, TMSB4X, GZMK, FGFR1
ErythErythroid cellerythroid lineage cellHBM, ALAS2, HBD, AHSP, SLC4A1, TRIM58, SELENBP1, CA1, IFIT1B, SNCA
gdT_1gamma-delta T_1gamma-delta T cellTRDC, TRGC1, TRGV9, TRDV2, KLRD1, IL7R, KLRC1, DUSP2, GNLY, KLRG1
gdT_2gamma-delta T_2gamma-delta T cellKLRC2, CD3G, KIR3DL2, CD3D, TRDC, TRDV1, ZNF683, KLRC1, TRGC1, GZMH
gdT_3gamma-delta T_3gamma-delta T cellRTKN2, TRDC, TRGC2, LEF1, IKZF2, SOX4, ZNF331, ARID5B, NUCB2, CRTAM
gdT_4gamma-delta T_4gamma-delta T cellTRDC, TIGIT, KLRC2, TRGC2, IKZF2, GCSAM, FCRL6, TRDV1, CST7, CMC1
HSPCHematopoietic stem and progenitor cellhematopoietic precursor cellCDK6, SOX4, PRSS57, AC084033.3, ANKRD28, FAM30A, MYB, EGFL7, SPINK2, SMIM24
ILCInnate Lymphoid Cellinnate lymphoid cellKIT, TRDC, IL1R1, SOX4, TNFRSF18, TYROBP, TNFRSF4, FCER1G, IL2RA, GATA3
MAITMucosal associated invariant Tmucosal invariant T cellKLRB1, NKG7, GZMK, SLC4A10, NCR3, CTSW, IL7R, KLRG1, CEBPD, DUSP2
NK ProliferatingProliferating Natural Killernatural killer cellSTMN1, KLRF1, TYMS, FCER1G, PCNA, TYROBP, CLSPN, TRDC, PCLAF, SMC2
NK_1CD56-dim Natural Killer_1CD16-positive, CD56-dim natural killer cell, humanFGFBP2, KLRC2, GNLY, S100A4, CD3E, CST7, LGALS1, PRF1, NKG7, GZMB
NK_2CD56-dim Natural Killer_2CD16-positive, CD56-dim natural killer cell, humanNKG7, FCER1G, PRF1, KLRB1, SPON2, GZMB, FGFBP2, IGFBP7, CST7, B2M
NK_3CD56-dim Natural Killer_3CD16-positive, CD56-dim natural killer cell, humanKLRF1, CCL5, TRDC, SYNE2, KLRC1, CMC1, XCL2, KLRB1, KLRD1, IL2RB
NK_4CD56-dim Natural Killer_4CD16-positive, CD56-dim natural killer cell, humanXCL2, SELL, XCL1, GZMK, KLRC1, SPTSSB, KLRF1, IL2RB, TCF7, TRDC
NK_CD56brightCD56-bright Natural KillerCD16-negative, CD56-bright natural killer cell, humanXCL2, GPR183, SELL, IL2RB, CD44, GZMK, KLRF1, TPT1, KLRC1, XCL1
pDCPlasmacytoid Dendritic Cellplasmacytoid dendritic cellCCDC50, UGCG, TCF4, LILRA4, IRF8, IL3RA, PLD4, IRF7, SERPINF1, ITM2C
PlasmaPlasma cellplasma cellMZB1, JCHAIN, TNFRSF17, ITM2C, DERL3, TXNDC5, POU2AF1, IGHA1, TXNDC11, CD79A
PlasmablastPlasmablastplasmablastTYMS, TNFRSF17, SHCBP1, TK1, KNL1, ASPM, TXNDC5, TPX2, RRM2, BIRC5
PlateletPlateletplateletGNG11, PPBP, NRGN, PF4, CAVIN2, TUBB1, HIST1H2AC, PRKAR2B, CLU, F13A1
Treg MemoryMemory Regulatory Tregulatory T cellRTKN2, B2M, TIGIT, FCRL3, S100A4, AC133644.2, CTLA4, FOXP3, IKZF2, TRAC
Treg NaiveNaive Regulatory Tregulatory T cellRTKN2, LEF1, FOXP3, C12orf57, IL2RA, TOMM7, CCR7, TRAC, CD4, LDHB

Human - Motor Cortex

Overview

Modalities: RNA

Nuclei in Reference: 76,533

Species: Human

Reference Dataset(s): Bakken et al, bioRxiv 2020 (Portal)

Demo Dataset(s): Subset of M1C Data (Portal) [Seurat Object]

This reference of human motor cortex was generated from data and annotations available from the Allen Institute. Originally described in Bakken et al, bioRxiv 2020, this data was the integrated across the two individual donors to create the Azimuth reference used here. Annotations are provided at the level of class (e.g. GABAergic), subclass (e.g. L2/3 IT), cluster (e.g. Inh L1-2 VIP WNT4), and cross-species cluster (e.g. Sst_6).


Annotation Details

class
LabelExpanded LabelOBO Ontology IDMarkers
GlutamatergicGlutamatergic neuronglutamatergic neuronSV2B, SATB2, CELF2, PHACTR1, CHN1, KHDRBS3, RALYL, LDB2, NELL2, KALRN
GABAergicGABAergic neuronGABAergic neuronGAD1, GRIP1, KAZN, KCNC2, TCF4, GAD2, MAF, SLC6A1, RBMS3, NHS
Non-NeuronalNon-neuronal cellanimal cellQKI, ZBTB20, NCKAP5, PTGDS, PHLPP1, CDH20, PPP2R2B, PDE4B, DOCK1, MAP4K4
subclass
LabelExpanded LabelOBO Ontology IDMarkers
AstroAstrocyteastrocyteSLC1A2, ADGRV1, SLC1A3, GPC5, RNF219.AS1, ARHGAP24, CST3, HPSE2, AQP4, COL5A3
EndoEndothelial cellendothelial cellEBF1, ABCG2, CLDN5, FLI1, LEF1, EMCN, IFI27, HLA.E, ADGRL4, CLEC3B
L2/3 ITLayer 2-3 glutamatergic neuron, intratelencephalon-projectingglutamatergic neuronCBLN2, EPHA6, LAMA2, CNTN5, PDZD2, CUX2, RASGRF2, FAM19A1, LINC01378, CA10
L5 ETLayer 5 glutamatergic neuron, extratelencephalon-projectingglutamatergic neuronCOL5A2, FAM19A1, VAT1L, COL24A1, CBLN2, NRP1, PTCHD1.AS, NRG1, HOMER1, SLC35F3
L5 ITLayer 5 glutamatergic neuron, intratelencephalon-projectingglutamatergic neuronFSTL4, CNTN5, RORB, FSTL5, IL1RAPL2, CHN2, TOX, CPNE4, CADPS2, POU6F2
L5/6 NPLayer 5-6 glutamatergic neuron, near-projectingglutamatergic neuronTSHZ2, NPSR1.AS1, HTR2C, ITGA8, ZNF385D, ASIC2, CDH6, CRYM, NXPH2, CPNE4
L6 CTLayer 6 glutamatergic neuron, corticothalamic-projectingglutamatergic neuronADAMTSL1, KIAA1217, SORCS1, HS3ST4, TRPM3, TOX, SEMA3E, EGFEM1P, MEIS2, SEMA5A
L6 ITLayer 6 glutamatergic neuron, intratelencephalon-projectingglutamatergic neuronPTPRK, PDZRN4, CDH9, THEMIS, FSTL5, CDH13, CDH12, CBLN2, LY86.AS1, MLIP
L6 IT Car3Layer 6 Car3+ glutamatergic neuron, intratelencephalon-projectingglutamatergic neuronTHEMIS, RNF152, NTNG2, STK32B, KCNMB2, GAS2L3, OLFML2B, POSTN, B3GAT2, NR4A2
L6bLayer 6b glutamatergic neuronglutamatergic neuronHS3ST4, KCNMB2, MDFIC, C10orf11, NTM, CDH9, MARCH1, TLE4, FOXP2, KIAA1217
Lamp5Lamp5+ GABAergic neuronGABAergic neuronFGF13, PTPRT, PRELID2, GRIA4, RELN, PTCHD4, EYA4, MYO16, FBXL7, LAMP5
Micro-PVMmicroglia / perivascular macrophageperivascular macrophageDOCK8, P2RY12, APBB1IP, FYB, PTPRC, TBXAS1, CX3CR1, BLNK, SLCO2B1, CSF1R
OligooligodendrocyteoligodendrocytePLP1, ST18, CTNNA3, MBP, MOBP, RNF220, NCKAP5, ENPP2, QKI, SLC44A1
OPColigodendrocyte precursor celloligodendrocyte precursor cellVCAN, PDGFRA, OLIG1, SMOC1, COL9A1, STK32A, BCAS1, FERMT1, BCHE, ZCCHC24
PvalbPvalb+ GABAergic neuronGABAergic neuronADAMTS17, ERBB4, DPP10, ZNF804A, MYO16, BTBD11, GRIA4, SLIT2, SDK1, PVALB
SncgSncg+ GABAergic neuronGABAergic neuronCNR1, SLC8A1, ASIC2, CXCL14, MAML3, ADARB2, NPAS3, CNTN5, FSTL5, SNCG
SstSst+ GABAergic neuronGABAergic neuronGRIK1, RALYL, SST, TRHDE, GRID2, NXPH1, COL25A1, SLC8A1, SOX6, ST6GALNAC5
Sst ChodlSst+ Chodl+ GABAergic neuronGABAergic neuronNPY, FAM46A, STAC, OTOF, NPY2R, CRHBP, ANKRD34B, NOS1, SST, CHODL
VipVip+ GABAergic neuronGABAergic neuronGALNTL6, LRP1B, VIP, GRM7, KCNT2, THSD7A, ERBB4, SYNPR, ADARB2, SLC24A3
VLMCvascular lepotomeningeal cellbrain pericyteCOLEC12, ITIH5, COL1A2, TBX18, EBF1, C7, COL6A2, SRPX2, FLVCR2, FMO2
cluster
LabelExpanded LabelOBO Ontology IDMarkers
Astro L1 FGFR3 SERPINI2FGFR3+ SERPINI2+ Layer 1 astrocyteastrocyteGFAP, PDE4D, ID3, CTNNA2, FGFR3, GRM3, GJA1, TMEM132C, ETNPPL, SERPINI2
Astro L1-6 FGFR3 AQP1FGFR3+ AQP1+ Layer 1-6 astrocyteastrocyteGFAP, TNC, GJA1, ADAMTSL3, RASL12, LINC00609, ANGPTL4, FGFR3, AQP1
Astro L1-6 FGFR3 PLCG1FGFR3+ PLCG1+ Layer 1-6 astrocyteastrocyteFGFR3, HPSE2, GJA1, PLCB1, SLCO1C1, COL5A3, ETNPPL, NDRG2, PRODH, PLCG1
Endo L2-5 NOSTRIN SRGNNOSTRIN+ SRGN+ Layer 2-5 endothelial cellendothelial cellEBF1, CLDN5, ABCG2, FLI1, LEF1, IFI27, EMCN, HLA-E, NOSTRIN, SRGN
Exc L2 LAMP5 KCNG3LAMP5+ KCNG3+ Layer 2 glutamatergic neuronglutamatergic neuronSEMA3C, PARD3, GRM1, SPON1, TMEM196, PALMD, LINGO2, ADRA1A, LAMP5, KCNG3
Exc L2 LINC00507 ATP7BLINC00507+ ATP7B+ Layer 2 glutamatergic neuronglutamatergic neuronOR1J2, KCNK2, ACVR1C, SEMA5A, BDNF, ITGB8, CHRM2, RASAL1, LINC00507, ATP7B
Exc L2 LINC00507 GLRA3LINC00507+ GLRA3+ Layer 2 glutamatergic neuronglutamatergic neuronLRRTM4, MAN1A1, LINC01378, DMD, ENC1, KIAA1217, DGKB, SLIT3, LINC00507, GLRA3
Exc L2-3 LINC00507 DSG3LINC00507+ DSG3+ Layer 2-3 glutamatergic neuronglutamatergic neuronBDNF, BMPR1B, ADCYAP1, SV2C, NOX4, CBLN2, SERPINE2, DLGAP1, LINC00507, DSG3
Exc L2-3 RORB CCDC68RORB+ CCDC68+ Layer 2-3 glutamatergic neuronglutamatergic neuronCOL5A2, LRRC4C, RORB, PTPRZ1, NTNG1, LINGO2, VIPR2, CNTNAP5, COBLL1, CCDC68
Exc L2-3 RORB PTPN3RORB+ PTPN3+ Layer 2-3 glutamatergic neuronglutamatergic neuronRORB, GRIA1, COL5A2, PEX5L, RMST, GRM1, NTNG1, GULP1, POU6F2, PTPN3
Exc L2-3 RORB RTKN2RORB+ RTKN2+ Layer 2-3 glutamatergic neuronglutamatergic neuronRMST, GALNT13, COL5A2, ROBO1, ZBTB7C, STXBP6, SCHLAP1, EPHA6, RORB, RTKN2
Exc L3 LAMP5 CARM1P1LAMP5+ CARM1P1+ Layer 3 glutamatergic neuronglutamatergic neuronSV2C, RYR2, SYT2, SLC38A11, BMPR1B, FMN1, MOXD1, PLXDC2, LAMP5, CARM1P1
Exc L3 RORB OTOGLRORB+ OTOGL+ Layer 3 glutamatergic neuronglutamatergic neuronCOL22A1, LINCR-0002, PLCH1, RMST, DPP10, TSHZ2, NCAM2, RORB, CPNE4, OTOGL
Exc L3 THEMIS ENPEPTHEMIS+ ENPEP+ Layer 3 glutamatergic neuronglutamatergic neuronTHEMIS, ITPR2, LAMA2, ASIC2, FAP, KIAA1217, LDB2, PPARGC1A, GAP43, ENPEP
Exc L3-5 FEZF2 ASGR2FEZF2+ ASGR2+ Layer 3-5 glutamatergic neuronglutamatergic neuronOR51E2, SORCS1, LINC00922, LINGO2, ERG, SEMA6D, GFRA1, RASAL2, FEZF2, ASGR2
Exc L3-5 FEZF2 LINC01107FEZF2+ LINC01107+ Layer 3-5 glutamatergic neuronglutamatergic neuronOR51E2, BTNL9, SGCZ, EDNRB, VWC2L, ADGRG6, PCDH11X, LINC00922, FEZF2, LINC01107
Exc L3-5 RORB LAMA4RORB+ LAMA4+ Layer 3-5 glutamatergic neuronglutamatergic neuronTRPC3, DACH1, PLCH1, RORB, CUX2, ANTXR2, IL1RAP, LAMA4, RORA, RMST
Exc L3-5 RORB LINC01202RORB+ LINC01202+ Layer 3-5 glutamatergic neuronglutamatergic neuronLINCR-0002, PCDH7, TSHZ2, HS3ST4, RORB, IL1RAPL2, TPBG, HTR1F, EPHA3, LINC01202
Exc L3-5 RORB LNX2RORB+ LNX2+ Layer 3-5 glutamatergic neuronglutamatergic neuronCADPS2, FAM19A1, LRRK1, NTM, PCP4, RGS6, COL11A1, GRM7, CHN2, LNX2
Exc L3-5 RORB RPRMRORB+ RPRM+ Layer 3-5 glutamatergic neuronglutamatergic neuronMKX, RPRM, RXFP1, CCK, RORB, SLC9A9, FSTL4, SPARCL1, IPCEF1, SEMA3E
Exc L3-5 RORB TNNT2RORB+ TNNT2+ Layer 3-5 glutamatergic neuronglutamatergic neuronLINCR-0002, IL1RAPL2, THEMIS, CPNE4, FSHR, LAMA2, UTRN, RORB, TSHZ2, TNNT2
Exc L5 FEZF2 CSN1S1FEZF2+ CSN1S1+ Layer 5 glutamatergic neuronglutamatergic neuronANGPT1, KCNIP1, SULF2, KCNG2, ANKRD26P3, NETO1, PAPPA, GRM1, FEZF2, CSN1S1
Exc L5 FEZF2 NREP-AS1FEZF2+ NREP-AS1+ Layer 5 glutamatergic neuronglutamatergic neuronCD36, NWD2, ADAMTS12, GPC5, LINC01507, GRIK1, FER1L6-AS2, MAST4, FEZF2, NREP-AS1
Exc L5 FEZF2 PKD2L1FEZF2+ PKD2L1+ Layer 5 glutamatergic neuronglutamatergic neuronFER1L6-AS2, GPC5, NPSR1-AS1, PDE1A, ROBO3, TRPM3, NPSR1, RALYL, FEZF2, PKD2L1
Exc L5 FEZF2 RNF144A-AS1FEZF2+ RNF144A-AS1+ Layer 5 glutamatergic neuronglutamatergic neuronIFNG-AS1, GPC6, CD36, GRIK1, GDNF-AS1, PVT1, NPSR1, LRRC4C, FEZF2, RNF144A-AS1
Exc L5 RORB MED8RORB+ MED8+ Layer 5 glutamatergic neuronglutamatergic neuronNPFFR2, COL22A1, FAM19A2, IL1RAPL2, FNBP1L, RXFP1, LRRC7, RORB, KCNH5, MED8
Exc L5 THEMIS FGF10THEMIS+ FGF10+ Layer 5 glutamatergic neuronglutamatergic neuronNPFFR2, TESPA1, CRH, RCAN2, THEMIS, NELL1, BDNF, CA10, RXFP1, FGF10
Exc L5 THEMIS LINC01116THEMIS+ LINC01116+ Layer 5 glutamatergic neuronglutamatergic neuronLINC01060, HCRTR2, SEMA3E, DPP4, THEMIS, LINC01116
Exc L5 THEMIS RGPD6THEMIS+ RGPD6+ Layer 5 glutamatergic neuronglutamatergic neuronSEMA3E, TRPC6, SEMA5A, THEMIS, DDR2, RNF152, LINC01060, EGFEM1P, RGPD6
Exc L5 THEMIS SLC22A18THEMIS+ SLC22A18+ Layer 5 glutamatergic neuronglutamatergic neuronKCNG2, GRIN3A, CCBE1, COL21A1, THEMIS, EPHA6, MKX, LDLRAD4, HS3ST2, SLC22A18
Exc L5 THEMIS VILLTHEMIS+ VILL+ Layer 5 glutamatergic neuronglutamatergic neuronTNC, SAMD5, NPFFR2, NELL1, FAP, LRP1B, DACH1, CDH6, THEMIS, VILL
Exc L5-6 FEZF2 C9orf135-AS1FEZF2+ C9orf135-AS1+ Layer 5-6 glutamatergic neuronglutamatergic neuronSEMA3E, OPCML, EGFEM1P, LRRTM4, SEMA5A, RALYL, HS3ST4, PRKD1, FEZF2, C9ORF135-AS1
Exc L5-6 FEZF2 CFTRFEZF2+ CFTR+ Layer 5-6 glutamatergic neuronglutamatergic neuronNR4A2, TMEM244, CTGF, CALCRL, MCTP2, CLDN1, ERG, EPB41L4A, FEZF2, CFTR
Exc L5-6 FEZF2 FILIP1LFEZF2+ FILIP1L+ Layer 5-6 glutamatergic neuronglutamatergic neuronCALCRL, ALDOA, SEMA3E, XIST, SEMA5A, EGFEM1P, FEZF2, FILIP1L
Exc L5-6 FEZF2 IFNG-AS1FEZF2+ IFNG-AS1+ Layer 5-6 glutamatergic neuronglutamatergic neuronCD36, NRXN3, IFNG-AS1, KCNQ5, FER1L6-AS2, PCDH11X, HTR2C, DGKI, NPSR1-AS1, FEZF2
Exc L5-6 FEZF2 LPOFEZF2+ LPO+ Layer 5-6 glutamatergic neuronglutamatergic neuronGADL1, ALCAM, MYHAS, PCED1B, CALCRL, LINC01105, FER1L6-AS2, ZNF385D-AS2, FEZF2, LPO
Exc L5-6 FEZF2 OR1L8FEZF2+ OR1L8+ Layer 5-6 glutamatergic neuronglutamatergic neuronSYT6, KCNC2, MCTP2, CTNND2, SULF1, KIAA1217, RBM20, PLXDC2, FEZF2, OR1L8
Exc L5-6 FEZF2 SH2D1BFEZF2+ SH2D1B+ Layer 5-6 glutamatergic neuronglutamatergic neuronSEMA3E, PRKY, DDR2, USP9Y, DCHS2, NLGN4Y, SEMA5A, DDX3Y, FEZF2, SH2D1B
Exc L5-6 THEMIS SMYD1THEMIS+ SMYD1+ Layer 5-6 glutamatergic neuronglutamatergic neuronNR4A2, KCNMB2, GAS2L3, SEMA6D, ABCC3, TSHZ2, NTNG2, EDIL3, THEMIS, SMYD1
Exc L5-6 THEMIS TNFAIP6THEMIS+ TNFAIP6+ Layer 5-6 glutamatergic neuronglutamatergic neuronTHEMIS, CDH9, HS3ST2, CDH12, MKX, SPOCK1, TSHZ2, KCTD16, RXFP1, TNFAIP6
Exc L6 FEZF2 FFAR4FEZF2+ FFAR4+ Layer 6 glutamatergic neuronglutamatergic neuronSLC15A5, OLFML2B, CTGF, FER1L6-AS2, FEZF2, FFAR4
Exc L6 FEZF2 KLK7FEZF2+ KLK7+ Layer 6 glutamatergic neuronglutamatergic neuronMDFIC, ASIC2, ZFHX3, CHN2, SEMA3D, SDK1, MCTP2, COL24A1, FEZF2, KLK7
Exc L6 FEZF2 PDYNFEZF2+ PDYN+ Layer 6 glutamatergic neuronglutamatergic neuronSLC15A5, ADGRF2, PDYN, CABP7, SYT6, SEMA3D, ERG, FEZF2
Exc L6 FEZF2 POGKFEZF2+ POGK+ Layer 6 glutamatergic neuronglutamatergic neuronCTGF, CHRM2, CDC14A, MGAT4C, SEMA3D, PLCXD3, NPFFR2, KCNK2, FEZF2, POGK
Exc L6 FEZF2 PROKR2FEZF2+ PROKR2+ Layer 6 glutamatergic neuronglutamatergic neuronSLC15A5, CTGF, VCAN, ADD3-AS1, FEZF2, PROKR2
Exc L6 THEMIS LINC00343THEMIS+ LINC00343+ Layer 6 glutamatergic neuronglutamatergic neuronTHEMIS, ROBO1, ADAMTS3, GULP1, ANKRD30B, TRPM3, DCHS2, SEMA3A, SEC24D, LINC00343
Exc L6 THEMIS SLNTHEMIS+ SLN+ Layer 6 glutamatergic neuronglutamatergic neuronTHEMIS, PDE7B, LINCR-0002, LINC01378, GBE1, GRIA4, ARHGEF28, C8orf34, FRMD6, SLN
Exc L6 THEMIS SNTG2THEMIS+ SNTG2+ Layer 6 glutamatergic neuronglutamatergic neuronTHEMIS, THSD7B, EDIL3, SNTG2, TENM4, ADAMTS3, CLSTN2, LY86-AS1, CNTN5, DCHS2
Inh L1 LAMP5 BMP2LAMP5+ BMP2+ Layer 1 GABAergic neuronGABAergic neuronNDNF, SYT1, NPNT, ALK, CXCL14, RBFOX1, RELN, PBX1, LAMP5, BMP2
Inh L1 LAMP5 NMBRLAMP5+ NMBR+ Layer 1 GABAergic neuronGABAergic neuronNDNF, MAGI2, PCDH18, PDE4B, NMBR, PRELID2, NPNT, EPHA6, CXCL14, LAMP5
Inh L1 LAMP5 PVRL2LAMP5+ PVRL2+ Layer 1 GABAergic neuronGABAergic neuronNDNF, UNC13C, MYH11, TMEM132D, KIT, PCDH9, RELN, CLSTN2, LAMP5, PVRL2
Inh L1 LAMP5 RAB11FIP1LAMP5+ RAB11FIP1+ Layer 1 GABAergic neuronGABAergic neuronMYH11, CDH9, KIT, RELN, ADAMTS20, CACNA2D1, KIRREL, CDH11, LAMP5, RAB11FIP1
Inh L1 PAX6 CHRFAM7APAX6+ CHRFAM7A+ Layer 1 GABAergic neuronGABAergic neuronLINC01539, FSTL5, NDNF, CNTNAP4, CXCL14, ZMAT4, NR2F2-AS1, LIMCH1, PAX6, CHRFAM7A
Inh L1 PAX6 MIR101-1PAX6+ MIR101-1+ Layer 1 GABAergic neuronGABAergic neuronTGFBR2, SPHKAP, SP8, ZNF804A, CDH23, PDZRN4, GPC3, ALK, PAX6, MIR101-1
Inh L1 PVALB SST ASIC4PVALB+ SST ASIC4+ Layer 1 GABAergic neuronGABAergic neuronADAM33, RXRG, NDNF, EFEMP1, PVALB, SST ASIC4
Inh L1 SST DEFB108BSST+ DEFB108B+ Layer 1 GABAergic neuronGABAergic neuronPCDH18, ARPP21, NR2F2, THSD7A, SLC10A4, SYNPR, SYT10, CPE, SST, DEFB108B
Inh L1 SST P4HA3SST+ P4HA3+ Layer 1 GABAergic neuronGABAergic neuronCALCB, RXRG, NDNF, ADAM33, SST, P4HA3
Inh L1 VIP KLHDC8BVIP+ KLHDC8B+ Layer 1 GABAergic neuronGABAergic neuronVIP, GPC6, CHRNA2, ST6GALNAC5, NDNF, ADAM12, TRPC7, CNTN5, PROX1-AS1, KLHDC8B
Inh L1-2 PVALB CDK20PVALB+ CDK20+ Layer 1-2 GABAergic neuronGABAergic neuronTAC1, SYT10, SYTL5, NRP2, NDST4, KCNT2, MYO5B, FGD5, PVALB, CDK20
Inh L1-2 SST CCNJLSST+ CCNJL+ Layer 1-2 GABAergic neuronGABAergic neuronCALB1, ALK, DKK2, ALCAM, CMTM8, ERBB4, MYO5B, TMEM132C, SST, CCNJL
Inh L1-2 SST CLIC6SST+ CLIC6+ Layer 1-2 GABAergic neuronGABAergic neuronTAC1, NDST4, NKAIN2, SYTL5, SGCZ, CMTM8, NEDD4, FBN2, SST, CLIC6
Inh L1-2 SST PRRT4SST+ PRRT4+ Layer 1-2 GABAergic neuronGABAergic neuronPENK, PDE4B, CALB1, ARHGAP10, HPGD, ITPR2, SST, ZNF385B, STK32B, PRRT4
Inh L1-2 VIP EXPH5VIP+ EXPH5+ Layer 1-2 GABAergic neuronGABAergic neuronSHISA8, LINGO2, VIP, BTBD11, SLC22A3, ASIC2, FLT1, FAM19A2, ASIC4, EXPH5
Inh L1-2 VIP HTR3AVIP+ HTR3A+ Layer 1-2 GABAergic neuronGABAergic neuronHTR3A, RXFP1, VWA5B1, CSMD1, NR2F2-AS1, EDIL3, EDNRA, INPP4B, COL4A4, VIP
Inh L1-2 VIP PTGER3VIP+ PTGER3+ Layer 1-2 GABAergic neuronGABAergic neuronNPR3, PTGER3, NR2F2, EDNRA, PROX1-AS1, VIP
Inh L1-2 VIP SCML4VIP+ SCML4+ Layer 1-2 GABAergic neuronGABAergic neuronSCML4, ADAMTS19, COL9A1, NELL1, CALB2, SLC6A11, NR2F2, KCNH8, NR2F2-AS1, VIP
Inh L1-2 VIP WNT4VIP+ WNT4+ Layer 1-2 GABAergic neuronGABAergic neuronNR2F2, CCK, CFAP47, CNR1, GABRG1, SORCS3, NECAB2, ROBO1, VIP, WNT4
Inh L1-3 SST FAM20ASST+ FAM20A+ Layer 1-3 GABAergic neuronGABAergic neuronCCDC109B, LINGO2, SST, CDH12, SYTL5, NCAM2, SOX6, TAC1, KIRREL3, FAM20A
Inh L1-3 VIP CBLN1VIP+ CBLN1+ Layer 1-3 GABAergic neuronGABAergic neuronSLC22A3, SOX2-OT, CBLN1, LINC01322, TAC3, ZBTB20, SHISA8, SOX5, HTR2C, VIP
Inh L1-3 VIP CHRNA2VIP+ CHRNA2+ Layer 1-3 GABAergic neuronGABAergic neuronNPR3, DPP6, CHRNA2, CDH20, PPP1R1C, CNTNAP4, CALB2, SLC7A11, VIP, LYPD1
Inh L1-3 VIP FNDC1VIP+ FNDC1+ Layer 1-3 GABAergic neuronGABAergic neuronADAM33, EPHA7, SHISA8, ASIC4, PRR16, LINC01170, ADAMTS19, NPR3, VIP, FNDC1
Inh L1-3 VIP HSPB6VIP+ HSPB6+ Layer 1-3 GABAergic neuronGABAergic neuronSLC22A3, KCNQ5, VIP, CNTN5, SHISA8, SEMA6D, TAC3, NPAS3, PTHLH, HSPB6
Inh L1-5 VIP CD27-AS1VIP+ CD27-AS1+ Layer 1-5 GABAergic neuronGABAergic neuronCALB2, ZDHHC2, IQGAP2, TOX, VIP, KLHL1, NR2E1, FAT3, SMOC1, CD27-AS1
Inh L1-5 VIP LINC01013VIP+ LINC01013+ Layer 1-5 GABAergic neuronGABAergic neuronPTGFR, INPP4B, PCDH18, DAB1, NR2F2, PRELID2, NR2F2-AS1, VIP, LINC01013
Inh L1-5 VIP PHLDB3VIP+ PHLDB3+ Layer 1-5 GABAergic neuronGABAergic neuronTAC3, ASIC4, SLC22A3, CHRNA2, VIP, PHLDB3
Inh L1-5 VIP SMOC1VIP+ SMOC1+ Layer 1-5 GABAergic neuronGABAergic neuronVIP, CNR1, CHRNA2, GULP1, TAC3, LRP1B, SMOC1, SHISA9, SLC22A3, NPR3
Inh L1-6 LAMP5 AARDLAMP5+ AARD+ Layer 1-6 GABAergic neuronGABAergic neuronKIT, CDH13, PKP2, PIP5K1B, EYA4, PRELID2, ROR2, LRP1B, LAMP5, AARD
Inh L1-6 LAMP5 CA1LAMP5+ CA1+ Layer 1-6 GABAergic neuronGABAergic neuronSFRP1, TAC1, KIRREL, OPCML, CA8, PRKG1, NOS1, HS3ST4, LAMP5, CA1
Inh L1-6 LAMP5 NESLAMP5+ NES+ Layer 1-6 GABAergic neuronGABAergic neuronROR2, KCNMB2, KIT, CCBE1, EYA4, MEIS2, PDGFRA, C8orf34, LAMP5, NES
Inh L1-6 PVALB COL15A1PVALB+ COL15A1+ Layer 1-6 GABAergic neuronGABAergic neuronNPNT, HTR1F, COL15A1, GULP1, PTHLH, FSTL5, ADAMTS5, CNTNAP4, FAM19A4, PVALB
Inh L1-6 SST NPYSST+ NPY+ Layer 1-6 GABAergic neuronGABAergic neuronNPY, FAM46A, STAC, OTOF, ANKRD34B, CRHBP, NPY2R, NOS1, CCDC109B, SST
Inh L1-6 VIP SLC7A6OSVIP+ SLC7A6OS+ Layer 1-6 GABAergic neuronGABAergic neuronDYNAP, RASGRF2, FREM2, LINC01539, PBX3, TP53I11, PCP4, VIP, PDLIM5, SLC7A6OS
Inh L2 PAX6 FREM2PAX6+ FREM2+ Layer 2 GABAergic neuronGABAergic neuronSLC17A8, PDE3A, DOCK8, GRIK1, IGFBP7, PCLO, FREM2, YJEFN3, NR1H4, PAX6
Inh L2 PVALB FRZBPVALB+ FRZB+ Layer 2 GABAergic neuronGABAergic neuronCRHBP, ARHGAP42, KAL1, MYO5B, PVALB, FRZB
Inh L2 VIP SLC6A16VIP+ SLC6A16+ Layer 2 GABAergic neuronGABAergic neuronNPR3, CDH8, NR2F2, CALB2, NR2F2-AS1, VIP, SLC6A16
Inh L2-3 SST NMUSST+ NMU+ Layer 2-3 GABAergic neuronGABAergic neuronMYO5B, ERBB4, SOX6, FAM19A2, PIEZO2, MYO16, NOS1, NXPH1, SST, NMU
Inh L2-5 PVALB HHIPL1PVALB+ HHIPL1+ Layer 2-5 GABAergic neuronGABAergic neuronMEPE, EPHA3, PVALB, POU6F2, POSTN, GPR149, PLEKHG1, TAC1, ADAMTS20, HHIPL1
Inh L2-5 PVALB RPH3ALPVALB+ RPH3AL+ Layer 2-5 GABAergic neuronGABAergic neuronBTBD11, LRP1B, ADAMTS17, MSRA, MYO5B, BCL11A, RNF144B, LINC00403, PVALB, RPH3AL
Inh L2-5 VIP BSPRYVIP+ BSPRY+ Layer 2-5 GABAergic neuronGABAergic neuronCHRNA2, ST18, VIP, SFMBT2, SHISA8, CA10, RGS16, PCDH7, SLC22A3, BSPRY
Inh L2-5 VIP SOX11VIP+ SOX11+ Layer 2-5 GABAergic neuronGABAergic neuronPENK, PCDH18, PTGFR, CALB2, VIP, SOX11
Inh L3 PVALB SAMD13PVALB+ SAMD13+ Layer 3 GABAergic neuronGABAergic neuronPVALB, TOX, SULF1, EPHA3, TAC1, HOMER3, POSTN, PHACTR2, RNF144B, SAMD13
Inh L3-5 PVALB ISG20PVALB+ ISG20+ Layer 3-5 GABAergic neuronGABAergic neuronPVALB, PHACTR2, LCNL1, EPHA4, POSTN, GRM8, SULF1, RBMS3, RNF144B, ISG20
Inh L3-5 SST CDH3SST+ CDH3+ Layer 3-5 GABAergic neuronGABAergic neuronLINC01324, IGFBP5, OTOF, POSTN, QRFPR, LINC01399, EDNRA, GDA, SST, CDH3
Inh L3-5 SST GGTLC3SST+ GGTLC3+ Layer 3-5 GABAergic neuronGABAergic neuronADGRG6, ZNF385D, SST, SOX5, EPSTI1, MGAT4C, NMU, ROBO1, GRIK1, GGTLC3
Inh L3-5 SST OR5AH1PSST+ OR5AH1P+ Layer 3-5 GABAergic neuronGABAergic neuronNMU, EPHA6, SST, ADAMTS9-AS2, EDNRA, PCDH9, PAWR, PCSK5, ADAMTS5, OR5AH1P
Inh L3-5 VIP HS3ST3A1VIP+ HS3ST3A1+ Layer 3-5 GABAergic neuronGABAergic neuronSLC22A3, GRM8, IQGAP2, THSD7B, PTHLH, UNC13C, CHRNA2, CDH13, VIP, HS3ST3A1
Inh L3-5 VIP IGDCC3VIP+ IGDCC3+ Layer 3-5 GABAergic neuronGABAergic neuronEREG, NECAB1, TAC3, ANKS1B, SLC22A3, GRIA1, VIP, PTPRD, IQGAP2, IGDCC3
Inh L3-5 VIP TAC3VIP+ TAC3+ Layer 3-5 GABAergic neuronGABAergic neuronTAC3, NBEA, PPP1R1C, ARHGAP18, VIP, EGFEM1P, SLC22A3, NCAM2, IQGAP2, NR2F2-AS1
Inh L3-6 PAX6 LINC01497PAX6+ LINC01497+ Layer 3-6 GABAergic neuronGABAergic neuronSCGN, EGFEM1P, PALMD, TMEM132D, EYA1, C8orf34, TNS3, KCNIP4, PAX6, LINC01497
Inh L3-6 VIP UG0898H09VIP+ UG0898H09+ Layer 3-6 GABAergic neuronGABAergic neuronPCDH18, VIP, CHRNA2, PTGFR, LINC01411, UG0898H09
Inh L3-6 VIP ZIM2-AS1VIP+ ZIM2-AS1+ Layer 3-6 GABAergic neuronGABAergic neuronPENK, PTGFR, VGLL3, ROR2, VIP, ZIM2-AS1
Inh L5 PVALB LRIG3PVALB+ LRIG3+ Layer 5 GABAergic neuronGABAergic neuronHGF, TMTC2, PVALB, ROBO1, GPR149, RIT2, PLCE1, LHFPL3, MEPE, LRIG3
Inh L5 SST RPL35AP11SST+ RPL35AP11+ Layer 5 GABAergic neuronGABAergic neuronSST, ADCY2, EDNRA, GRIK2, QRFPR, DMD, NMU, GRIK1, PAWR, RPL35AP11
Inh L5-6 LAMP5 CRABP1LAMP5+ CRABP1+ Layer 5-6 GABAergic neuronGABAergic neuronSFRP1, COL25A1, FREM2, PRELID2, PDGFRA, KCNIP4, KIRREL, FBN2, LAMP5, CRABP1
Inh L5-6 PVALB FAM150BPVALB+ FAM150B+ Layer 5-6 GABAergic neuronGABAergic neuronFAM150B, GPC5, PALMD, SAMD3, MYBPC1, PDZRN4, ANKRD34B, TMEM200A, GPR149, PVALB
Inh L5-6 PVALB GAPDHP60PVALB+ GAPDHP60+ Layer 5-6 GABAergic neuronGABAergic neuronWNT16, CDH9, MYBPC1, NCAM2, BCHE, KIRREL3, WIF1, PVALB, GAPDHP60
Inh L5-6 PVALB KCNIP2PVALB+ KCNIP2+ Layer 5-6 GABAergic neuronGABAergic neuronNPFFR2, GULP1, THSD7B, CDH8, WIF1, SORCS3, LYPD6, PAWR, PVALB, KCNIP2
Inh L5-6 PVALB MEPEPVALB+ MEPE+ Layer 5-6 GABAergic neuronGABAergic neuronWNT16, PCDH9, MEPE, MCTP1, ANKRD34B, PRKG1, MYBPC1, GALNTL6, CPED1, PVALB
Inh L5-6 PVALB SST CRHR2PVALB+ SST CRHR2+ Layer 5-6 GABAergic neuronGABAergic neuronHPGD, ADAMTS17, FAM89A, CNTNAP4, FLT1, DGKB, TAC1, GHR, PVALB, SST CRHR2
Inh L5-6 PVALB ZFPM2-AS1PVALB+ ZFPM2-AS1+ Layer 5-6 GABAergic neuronGABAergic neuronZFPM2-AS1, WIF1, TMTC2, POSTN, SEMA6D, LYPD6, GRIK2, SULF1, PCDH15, PVALB
Inh L5-6 SST BEAN1SST+ BEAN1+ Layer 5-6 GABAergic neuronGABAergic neuronFBN2, PCDH11X, THSD7B, CDH10, KLHL14, CDH9, SST, DPP10, HGF, BEAN1
Inh L5-6 SST C4orf26SST+ C4orf26+ Layer 5-6 GABAergic neuronGABAergic neuronADAMTS20, LINGO2, FBN2, PLXDC2, KLHL14, PDE1C, DCN, PCDH17, HGF, C4ORF26
Inh L5-6 SST DNAJC14SST+ DNAJC14+ Layer 5-6 GABAergic neuronGABAergic neuronHGF, PLCE1, FBN2, PTPRK, ITGA1, TRPC5, GPR149, LRRC4C, SST, DNAJC14
Inh L5-6 SST FBN2SST+ FBN2+ Layer 5-6 GABAergic neuronGABAergic neuronFBN2, ZNF385D, FAM129A, CSMD1, KLHL14, EFNA5, ADAMTS20, MGAT4C, THSD7B, SST
Inh L5-6 SST ISXSST+ ISX+ Layer 5-6 GABAergic neuronGABAergic neuronSST, CSGALNACT1, NR2F2-AS1, CNTNAP4, DKK2, TRPM3, PREX2, GRM7, SOX6, ISX
Inh L5-6 SST KLHL1SST+ KLHL1+ Layer 5-6 GABAergic neuronGABAergic neuronSLC17A8, ADGRL2, DCN, ROBO1, KLHL14, SOX6, ADAMTS20, NDST4, UNC13C, KLHL1
Inh L5-6 SST PAWRSST+ PAWR+ Layer 5-6 GABAergic neuronGABAergic neuronNDST4, LRRTM4, NMU, PTPRT, DCN, ALCAM, KLHL14, GALNTL6, TMCC3, SST
Inh L5-6 SST PIK3CDSST+ PIK3CD+ Layer 5-6 GABAergic neuronGABAergic neuronADGRG6, NLGN1, KLHL14, LRFN5, NMU, ARHGAP10, NDST4, NEGR1, SST, PIK3CD
Inh L5-6 VIP COL4A3VIP+ COL4A3+ Layer 5-6 GABAergic neuronGABAergic neuronVIP, C11orf1, SLC22A3, GRM8, ABI3BP, CBLN4, NPR3, UNC13C, VCAN, COL4A3
Inh L6 SST THSST+ TH+ Layer 6 GABAergic neuronGABAergic neuronKIAA1024, ERBB4, RAB3B, GPC5, SST, PTPRK, GABRG1, KLHL29, WIF1, TH
Micro L1-6 TYROBP CD74TYROBP+ CD74+ Layer 1-6 microgliamicroglial cellDOCK8, P2RY12, APBB1IP, FYB, TBXAS1, SLCO2B1, CX3CR1, PTPRC, TYROBP, CD74
Oligo L2-6 OPALIN FTH1P3OPALIN+ FTH1P3+ Layer 2-6 oligodendrocyteoligodendrocytePLP1, ANK3, ST18, NLGN1, RNF220, PLXDC2, ENPP2, OPALIN, FRMD4B, FTH1P3
Oligo L2-6 OPALIN MAP6D1OPALIN+ MAP6D1+ Layer 2-6 oligodendrocyteoligodendrocyteOPALIN, FOLH1, ABCA8, MOG, UGT8, SEPP1, LPAR1, ST18, SLCO1A2, MAP6D1
Oligo L3-6 OPALIN ENPP6OPALIN+ ENPP6+ Layer 3-6 oligodendrocyteoligodendrocyteS100B, RBFOX1, CARNS1, RASGRF1, COL4A5, COL18A1, MOG, USH1C, OPALIN, ENPP6
Oligo L3-6 OPALIN LRP4-AS1OPALIN+ LRP4-AS1+ Layer 3-6 oligodendrocyteoligodendrocyteLINC00982, FGFR3, NKAIN3, OPALIN, SLC1A2, TRIM59, RYR3, GJA1, RNF219-AS1, LRP4-AS1
Oligo L5-6 OPALIN LDLRAP1OPALIN+ LDLRAP1+ Layer 5-6 oligodendrocyteoligodendrocytePLP1, ANK3, ST18, NLGN1, RNF220, PLXDC2, ENPP2, OPALIN, FRMD4B, LDLRAP1
OPC L1-6 PDGFRA COL20A1PDGFRA+ COL20A1+ Layer 1-6 oligodendrocyte precursor celloligodendrocyte precursor cellOLIG1, COL9A1, OLIG2, SNX22, NKAIN4, KLRC4-KLRK1, VCAN, PDGFRA, COL20A1, GPR37L1
VLMC L1-5 PDGFRA COLEC12PDGFRA+ COLEC12+ Layer 1-5 vascular lepotomeningeal cellbrain pericyteCOLEC12, COL1A2, TBX18, ITIH5, COL6A2, SRPX2, C7, FMO2, MFAP4, PDGFRA
cross-species cluster
LabelExpanded LabelOBO Ontology IDMarkers
Astro_1Astrocyte_1astrocyteGFAP, FAM189A2, FGFR3, GJA1, SLC14A1, AGT, ID3, RASL12, AQP4, ANGPTL4
Astro_2Astrocyte_2astrocyteFGFR3, GJA1, SLCO1C1, LINC00982, SDC4, NFATC4, GJB6, PRODH, APOE, SLC1A3
ChandelierChandelier neuronGABAergic neuronNPNT, COL15A1, PLEKHH2, NOG, PTHLH, ADAMTS5, COL21A1, FAM19A4, HTR1F, SRGAP1
EndoEndothelial cellendothelial cellEBF1, CLDN5, ABCG2, FLI1, LEF1, IFI27, EMCN, HLA-E, ID3, XAF1
L2/3 ITLayer 2-3 glutamatergic neuron, intratelencephalon-projectingglutamatergic neuronPDZD2, CBLN2, MEIS2, CUX2, KIAA1217, ENC1, DAB1, PVRL3, GNAL, LRRTM4
L5 ET_1Layer 5 glutamatergic neuron, extratelencephalon-projecting_1glutamatergic neuronOR51E2, SORCS1, LINC00922, SEMA6D, FAM84B, TMEM2, LINC01036, ST6GALNAC3, VIM-AS1, PQLC2L
L5 ET_2Layer 5 glutamatergic neuron, extratelencephalon-projecting_2glutamatergic neuronBTNL9, EDNRB, SGCZ, LINC00943, VWC2L, HBE1, PCDH11X, TRAPPC3L, CDH8, LINC01069
L5 IT_1Layer 5 glutamatergic neuron, intratelencephalon-projecting_1glutamatergic neuronRORB, SEMA6D, POU6F2, TMEM196, PLCH1, ALCAM, RMST, CUX1, DCC, TRHDE
L5 IT_2Layer 5 glutamatergic neuron, intratelencephalon-projecting_2glutamatergic neuronCHN2, LRRK1, CAMK2D, FSTL4, PDE1C, DNAH6, PCDH7, PRUNE2, ARSJ, TMSB10
L5 IT_3Layer 5 glutamatergic neuron, intratelencephalon-projecting_3glutamatergic neuronHS3ST3B1, RORB, HES1, CSGALNACT1, CRH, PDZRN3, DRD5, CCDC85A, ARHGAP15, TNNT2
L5/6 NPLayer 5-6 glutamatergic neuron, near-projectingglutamatergic neuronNPSR1-AS1, CBLN2, FER1L6-AS2, LUZP2, TLL1, KIAA1217, CALCRL, TLE4, HTR2C, PDE9A
L6 CT_1Layer 6 glutamatergic neuron, corticothalamic-projecting_1glutamatergic neuronSYT6, FAM189A1, VWA2, SPON1, KL, ASTN2, SEMA5A, WBSCR17, ABO, LGR6
L6 CT_2Layer 6 glutamatergic neuron, corticothalamic-projecting_2glutamatergic neuronVWA2, ERBB4, ABO, PRKD1, SH2D1B, ZNF804B, IL4R, ROBO2, DCHS2, ADAMTSL1
L6 IT_1Layer 6 glutamatergic neuron, intratelencephalon-projecting_1glutamatergic neuronLINC00343, TENM3, WISP1, CDH13, ANKRD30B, MEIS2, FRMD6, RASGRF2, TTC6, SEC24D
L6 IT_2Layer 6 glutamatergic neuron, intratelencephalon-projecting_2glutamatergic neuronSH2D1B, EDIL3, TMEM244, CNTN5, ADAMTS16, PDE1A, MYO1D, TSHZ2, ANO3, PXDN
L6 IT_3Layer 6 glutamatergic neuron, intratelencephalon-projecting_3glutamatergic neuronSMYD1, KCNMB2, OLFML2B, RGS12, NR4A2, SLC24A4, LINC00331, RNF152, GAS2L3, PRLR
L6bLayer 6b glutamatergic neuronglutamatergic neuronZFHX3, C10orf11, MDFIC, MARCH1, SEMA3D, ARSJ, GRIA4, MCTP2, KCNMB2, CTGF
Lamp5_1Lamp5+ GABAergic neuron_1GABAergic neuronNDNF, UNC13C, CPLX3, PCDH9, MYH11, CLSTN2, LINC00298, TMEM132D, FAT1, LAMP5
Lamp5_2Lamp5+ GABAergic neuron_2GABAergic neuronKIT, NTNG1, FBXL7, TOX, NXPH2, NCAM2, PKP2, PTPRG, HAPLN1, LAMP5
Lamp5_3Lamp5+ GABAergic neuron_3GABAergic neuronPDGFD, ITGA8, EYA4, CHST9, SFRP1, SORCS1, KIRREL, UNC5D, PDGFRA, LAMP5
Lamp5_4Lamp5+ GABAergic neuron_4GABAergic neuronSP8, SPHKAP, CDH23, MYO16, NTF3, NXPH1, TGFBR2, ALK, DKFZp686K1684, LAMP5
Lamp5_5Lamp5+ GABAergic neuron_5GABAergic neuronNDNF, COL5A2, CXCL14, HS6ST3, NMBR, ALCAM, BMP6, EPHA6, FAT1, LAMP5
Microglia/PVMmicroglia / perivascular macrophageperivascular macrophageDOCK8, P2RY12, APBB1IP, FYB, TBXAS1, SLCO2B1, CX3CR1, PTPRC, BLNK, CSF1R
Oligo_1oligodendrocyte_1oligodendrocyteS100B, RBFOX1, COL4A5, RASGRF1, CARNS1, COL18A1, MOG, USH1C, ABCA8, FOLH1
Oligo_2oligodendrocyte_2oligodendrocytePLP1, LINC00609, ENPP2, PLXDC2, UGT8, OPALIN, BCAS1, NLGN1, CERCAM, DOCK5
OPColigodendrocyte precursor celloligodendrocyte precursor cellOLIG1, COL9A1, OLIG2, SNX22, NKAIN4, KLRC4-KLRK1, GPR17, VCAN, COL20A1, GPR37L1
Pvalb_1Pvalb+ GABAergic neuron_1GABAergic neuronADAMTS17, GULP1, BTBD11, DPP10, RNF144B, THSD7B, CNTNAP3, TENM4, TMEM132C, PVALB
Pvalb_2Pvalb+ GABAergic neuron_2GABAergic neuronWNT16, SHISA8, MYBPC1, PALMD, FAM150B, TRPC6, GPR149, ANKRD34B, GABRG1, PVALB
Sncg_1Sncg+ GABAergic neuron_1GABAergic neuronLINC01539, SORCS1, DYNAP, DSCAM, SP8, PROX1, CHRFAM7A, PDE7B, HIF3A, SNCG
Sncg_2Sncg+ GABAergic neuron_2GABAergic neuronSLC17A8, YJEFN3, DOCK8, ARHGAP6, IGFBP7, RYR2, FREM2, PCLO, CDH23, SNCG
Sncg_3Sncg+ GABAergic neuron_3GABAergic neuronHTR3A, GRM1, VWA5B1, SYNPR, HGFAC, HDAC9, SLITRK6, PTPRM, PLSCR5, SNCG
Sncg_4Sncg+ GABAergic neuron_4GABAergic neuronRXRG, ARPP21, NDNF, SYNPR, NR2F2, FAM19A1, GNG12, THSD7A, ADAM33, SNCG
Sst ChodlSst+ Chodl+ GABAergic neuronGABAergic neuronNPY, FAM46A, STAC, LINC01014, ANAPC1P1, OTOF, DSP, AOX1, SST, CHODL
Sst_1Sst+ GABAergic neuron_1GABAergic neuronEDNRA, QRFPR, LINC01324, NELL1, PAWR, CDH9, RCAN3, GRIN3A, FLT3, SST
Sst_2Sst+ GABAergic neuron_2GABAergic neuronFAM89A, EPHA6, TPH2, HS6ST3, RCAN3, HTR4, FLT3, VWC2, NMU, SST
Sst_3Sst+ GABAergic neuron_3GABAergic neuronGRIK1, NR2F2-AS1, NMU, THSD7A, EPSTI1, ZNF385D, ELFN1, ZMAT4, DKK2, SST
Sst_4Sst+ GABAergic neuron_4GABAergic neuronNMU, TMTC2, KLHL14, PTPRD, LINC00943, GRID2, C8orf87, MPPED2, PDCL2, SST
Sst_5Sst+ GABAergic neuron_5GABAergic neuronHGF, SEMA5A, ADGRF2, ERBB4, ITGA1, ZNF536, RND3, NEGR1, NXPH1, SST
Sst_6Sst+ GABAergic neuron_6GABAergic neuronKLHL14, L3MBTL4, ADAMTS20, PREX2, FBN2, SLC8A1, DCN, C8orf34, MCAM, SST
Sst_7Sst+ GABAergic neuron_7GABAergic neuronTH, SEMA6A, GABRQ, CACNA2D1, LAYN, TRHDE, SLA, RALYL, PTPRC, SST
Vip_1Vip+ GABAergic neuron_1GABAergic neuronSHISA8, ZMAT4, GPR149, KCNIP4, ASIC4, RYR3, RGS16, KLF12, CBLN1, VIP
Vip_2Vip+ GABAergic neuron_2GABAergic neuronVIP, GRIN2A, PPP1R1C, CDH20, CHRNA2, NRXN1, CALB2, DCC, NPR3, TAC3
Vip_3Vip+ GABAergic neuron_3GABAergic neuronSMOC1, TMEM132D, SLC22A3, EGFEM1P, CHRNA2, FRAS1, TAC3, SLIT2, PPP1R1C, VIP
Vip_4Vip+ GABAergic neuron_4GABAergic neuronPTGFR, CSGALNACT1, PCDH18, PEX5L, CALB2, ADGRL3, LINC01497, KCNC2, PENK, VIP
VLMCvascular lepotomeningeal cellbrain pericyteCOLEC12, COL1A2, TBX18, ITIH5, COL6A2, SRPX2, C7, FMO2, MFAP4, FOXD1

Mouse - Motor Cortex

Overview

Modalities: RNA

Nuclei in Reference: 159,738

Species: Mouse

Reference Dataset(s): Yao, Liu, Xie, Fischer, et al, bioRxiv 2020

Demo Dataset(s): Yao et al, bioRxiv 2020 (Portal) [Seurat Object]

The data used in this reference was generated as part of the effort by Yao, Liu, Xie, Fischer, et al, bioRxiv 2020 to generate an integrated transcriptomic and epigenomic atlas of the primary motor cortex in mouse. To generate the reference used in Azimuth, we applied a reference-based integration strategy to harmonize the 10x v3 snRNA-seq data across 12 individual mice. Annotations are provided at the level of class (e.g. GABAergic), subclass (e.g. L2/3 IT), cluster (e.g. L2/3 IT_3), and cross-species cluster (e.g. Sst_6)


Annotation Details

class
LabelExpanded LabelOBO Ontology IDMarkers
GlutamatergicGlutamatergic neuronglutamatergic neuronCelf2, Ptprd, Arpp21, Sv2b, Pcsk2, Phactr1, Kalrn, Nrg1, Ano3, Satb2
Non-NeuronalNon-neuronal cellanimal cellZbtb20, Qk, Cst3, Nfia, Apoe, Ptn, Maml2, Dock1, Cd81, Gab1
GABAergicGABAergic neuronGABAergic neuronGrip1, Galntl6, Gad1, Gad2, Dlx6os1, Cntnap2, Gm26905, Kcnmb2, Kcnip1, Erbb4
subclass
LabelExpanded LabelOBO Ontology IDMarkers
AstroAstrocyteastrocyteGpc5, Slc1a2, Slc1a3, Apoe, Wdr17, Plpp3, Rorb, Rmst, Slc4a4, Htra1
EndoEndothelial cellendothelial cellFlt1, Slco1a4, Adgrl4, Ly6c1, Slc2a1, Klf2, Mecom, Bsg, Ly6a, Pltp
L2/3 ITLayer 2-3 glutamatergic neuron, intratelencephalon-projectingglutamatergic neuronLingo2, Dscaml1, Gpc6, Fam19a1, Lrrtm4, Slit3, Cux2, Unc5d, Fstl4, Car10
L5 ETLayer 5 glutamatergic neuron, extratelencephalon-projectingglutamatergic neuronFam19a1, Tox, Sgcz, Robo1, Galntl6, Gm2164, Dscaml1, Gm28928, Pex5l, Ralyl
L5 ITLayer 5 glutamatergic neuron, intratelencephalon-projectingglutamatergic neuronCar10, Ncam2, Galntl6, Cdh12, Hs3st4, Gpc6, Unc5d, Tenm4, Ptprd, Hs6st3
L5/6 NPLayer 5-6 glutamatergic neuron, near-projectingglutamatergic neuronTshz2, Gm26883, Nxph1, Vwc2l, Grik1, Olfm3, Kirrel3, Mgat4c, Hs6st3, Dcc
L6 CTLayer 6 glutamatergic neuron, corticothalamic-projectingglutamatergic neuronHs3st4, Chgb, Garnl3, Kctd16, Zfpm2, Foxp2, Mgat4c, Gm28928, Cdh18, Tle4
L6 ITLayer 6 glutamatergic neuron, intratelencephalon-projectingglutamatergic neuronC1ql3, Cdh13, Il1rapl2, Zfp804b, Dscaml1, Slit3, Galnt14, Nell2, Ak5, Cck
L6 IT Car3Layer 6 Car3+ glutamatergic neuron, intratelencephalon-projectingglutamatergic neuronTfap2d, Oprk1, Smoc2, Car12, Nr4a2, Lxn, Gm32647, Col11a1, Sstr2, 6530403H02Rik
L6bLayer 6b glutamatergic neuronglutamatergic neuronCtgf, Cdh18, Hs3st4, Kcnab1, Gm28928, Svil, Inpp4b, Zfpm2, Sdk2, Tle4
Lamp5Lamp5+ GABAergic neuronGABAergic neuronNpy, Nxph1, Fgf13, Ptprm, Reln, Gad2, Unc5d, Alk, Unc5c, Lamp5
Meis2Meis2+ GABAergic neuronGABAergic neuronIgfbpl1, Draxin, Cd1d1, Sp8, Cd24a, Lockd, St8sia2, Gm29260, Gm17750, Meis2
Micro-PVMmicroglia / perivascular macrophageperivascular macrophageInpp5d, Hexb, Tgfbr1, C1qa, Ctss, C1qb, Zfhx3, C1qc, Selplg, Cx3cr1
OligooligodendrocyteoligodendrocytePlp1, Mbp, St18, Prr5l, Mobp, Mal, Mog, Cldn11, Pde4b, Mag
OPColigodendrocyte precursor celloligodendrocyte precursor cellLhfpl3, Vcan, Tnr, Ptprz1, Gm4876, Xylt1, Pdgfra, Epn2, Cacng4, Megf11
Peripericytebrain pericyteAtp13a5, Vtn, Cald1, Ebf1, Abcc9, Dlc1, Pdgfrb, Tbx3os1, Pde8b, Slc38a11
PvalbPvalb+ GABAergic neuronGABAergic neuronKcnc2, Erbb4, Sox5, Il1rapl2, Fam19a2, Cntnap5c, Lrrc4c, Btbd11, Kcnh7, Pvalb
SMCsmooth muscle cellsmooth muscle cellActa2, Map3k7cl, Gm6249, Myh11, Tagln, Pdlim3, Ephx3, Olfr558, Crip1, Tbx2
SncgSncg+ GABAergic neuronGABAergic neuronAdarb2, Cnr1, Megf10, Cadps2, Col25a1, Col19a1, Grip1, Sgcd, Slc44a5, Sncg
SstSst+ GABAergic neuronGABAergic neuronSst, Grin3a, Nxph1, Galntl6, Rgs6, Sox6, Mgat4c, Synpr, Cacna2d3, Grm1
Sst ChodlSst+ Chodl+ GABAergic neuronGABAergic neuronNos1, Crhbp, Ndst4, Tacr1, 9330158H04Rik, Chodl, Fndc1, Stac, Bace2, Gabrg1
VipVip+ GABAergic neuronGABAergic neuronVip, Cacna1a, Adarb2, Limch1, Synpr, Cntn4, Crh, Sdk1, Igf1, Tac2
VLMCvascular lepotomeningeal cellbrain pericytePtgds, Bnc2, Cped1, Slc7a11, Bmp6, Apod, Mgp, Eya2, Ranbp3l, Adam12
cluster
LabelExpanded LabelOBO Ontology IDMarkers
Astro Aqp4_GfapAqp4+ Gfap+ AstrocyteastrocyteGpc5, Myoc, Slc1a2, Fxyd6, Slc1a3, Nrp2, Slc6a6, Apoe, Aqp4, Gfap
Astro Aqp4_Slc7a10Aqp4+ Slc7a10+ AstrocyteastrocyteLsamp, Gpc5, Slc1a2, Luzp2, Slc1a3, Apoe, Cadm2, Rora, Aqp4, Slc7a10
Astro_Top2aTop2a+ AstrocyteastrocyteIgfbpl1, Gpc5, Mki67, Slc1a2, Myt1, Slc1a3, Apoe, E2f2, E2f7, Top2a
EndoEndothelial cellendothelial cellFlt1, Slco1a4, Adgrl4, Ly6c1, Slc2a1, Klf2, Mecom, Bsg, Ly6a, Pltp
L2/3 IT_1Layer 2-3 glutamatergic neuron, intratelencephalon-projecting_1glutamatergic neuronAdamts2, Lingo2, 6530403H02Rik, Dscaml1, Gpc6, Rhbdl3, 5730522E02Rik, Fam19a1, Arhgef28, Lrrtm4
L2/3 IT_2Layer 2-3 glutamatergic neuron, intratelencephalon-projecting_2glutamatergic neuronCntnap5c, Lingo2, Epha6, Dscaml1, Fras1, Gpc6, Fam19a1, Cdh13, Lrrtm4, Lsamp
L2/3 IT_3Layer 2-3 glutamatergic neuron, intratelencephalon-projecting_3glutamatergic neuronLingo2, Cdh12, Dscaml1, Sorcs3, Gpc6, Cntn4, Fam19a1, Pcdh9, Sorcs1, Lrrtm4
L5 ET_1Layer 5 glutamatergic neuron, extratelencephalon-projecting_1glutamatergic neuronSt6galnac5, Fam19a1, Tox, St6galnac3, Pigk, Sgcz, Robo1, Crym, Galntl6, Zfp804b
L5 ET_2Layer 5 glutamatergic neuron, extratelencephalon-projecting_2glutamatergic neuronFam19a1, Vwc2l, Tshz2, Tox, Sgcz, Gm26883, Erg, Robo1, Cdh18, Galntl6
L5 ET_3Layer 5 glutamatergic neuron, extratelencephalon-projecting_3glutamatergic neuronFam19a1, Gpc5, Tox, Galnt17, Lingo2, Sgcz, Stxbp6, Robo1, Spock1, Galntl6
L5 ET_4Layer 5 glutamatergic neuron, extratelencephalon-projecting_4glutamatergic neuronGrin3a, Fam19a1, Olfm3, Tox, Sgcz, Tmtc2, Kctd8, Robo1, Galntl6, Lrp1b
L5 IT Pld5_1Pld5+ Layer 5 glutamatergic neuron, intratelencephalon-projecting_1glutamatergic neuronZfp804a, Car10, Ncam2, Cdh18, Galntl6, Pld5, Cdh12, Ptprt, Arhgap31, Hs3st4
L5 IT Pld5_2Pld5+ Layer 5 glutamatergic neuron, intratelencephalon-projecting_2glutamatergic neuronCar10, Cdh9, Bcl11b, Ncam2, Galntl6, Dscaml1, Cwh43, Cdh12, Rxfp1, Pld5
L5 IT Rspo1_1Rspo1+ Layer 5 glutamatergic neuron, intratelencephalon-projecting_1glutamatergic neuronCar10, Lingo2, Ncam2, Cux2, Galntl6, Cux1, Prr16, Cdh12, Brinp3, Rspo1
L5 IT Rspo1_2Rspo1+ Layer 5 glutamatergic neuron, intratelencephalon-projecting_2glutamatergic neuronCar10, Zfp804b, Ncam2, Cntn5, Cdh8, Galntl6, Cdh12, Cpne4, Tnnc1, Rspo1
L5 IT S100b_1S100b+ Layer 5 glutamatergic neuron, intratelencephalon-projecting_1glutamatergic neuronIl1rapl2, Car10, Deptor, Ncam2, Galntl6, Pde1a, AC129186.1, Cdh12, Grik3, S100b
L5 IT S100b_2S100b+ Layer 5 glutamatergic neuron, intratelencephalon-projecting_2glutamatergic neuronCar10, Cdh9, Ncam2, Rspo2, Galntl6, Blnk, Cdh12, AC129186.1, Gpc6, S100b
L5/6 NP CTLayer 5-6 glutamatergic neuron, near-projecting_CTglutamatergic neuronTshz2, Ephb1, Ankrd33b, Gm26883, Kctd8, Nxph1, Gm28928, Vwc2l, Grik1, Neto1
L5/6 NP_1Layer 5-6 glutamatergic neuron, near-projecting_1glutamatergic neuronHapln1, Tshz2, Gm26883, Cadps2, Nxph1, Rbfox1, Vwc2l, Il1rap, Grik1, Tmem132d
L5/6 NP_2Layer 5-6 glutamatergic neuron, near-projecting_2glutamatergic neuronTshz2, Stxbp6, Gm26883, Sv2c, Zeb2, Nxph1, Vwc2l, Gpc6, Grik1, Sema3e
L5/6 NP_3Layer 5-6 glutamatergic neuron, near-projecting_3glutamatergic neuronCntn6, Tshz2, Gm26883, Inpp4b, Kcnab1, Nxph1, Cntnap5b, Vwc2l, Chrm2, Grik1
L6 CT Cpa6Cpa6+ Layer 6 glutamatergic neuron, corticothalamic-projectingglutamatergic neuronHs3st4, Dscaml1, Chgb, Chrm3, Garnl3, Nfia, Kctd16, Kcnj6, Zfpm2, Cpa6
L6 CT Gpr139Gpr139+ Layer 6 glutamatergic neuron, corticothalamic-projectingglutamatergic neuronHs3st4, Gal, Mdga1, Chgb, Gpr139, Garnl3, Gm26719, Kctd16, Anxa4, Zfpm2
L6 CT GrpGrp+ Layer 6 glutamatergic neuron, corticothalamic-projectingglutamatergic neuronSlc24a3, Hs3st4, Chgb, Ntm, Garnl3, Plcxd3, Kctd16, Tox, Meis2, Grp
L6 CT Kit_1Kit+ Layer 6 glutamatergic neuron, corticothalamic-projecting_1glutamatergic neuronHs3st4, Sostdc1, Nts, Chgb, Garnl3, Rmst, Kctd16, Kit, Zfpm2, Gm29114
L6 CT Kit_2Kit+ Layer 6 glutamatergic neuron, corticothalamic-projecting_2glutamatergic neuronHs3st4, Cobll1, Chgb, Dkk2, Garnl3, Kit, Rmst, Kctd16, Gm26883, Zfpm2
L6 CT Pou3f2Pou3f2+ Layer 6 glutamatergic neuron, corticothalamic-projectingglutamatergic neuronNxph2, Hs3st4, Gm28175, Chgb, Garnl3, Gm10635, Kctd16, Ntm, Kcnc2, Pou3f2
L6 IT Car3Car3+ glutamatergic neuron, intratelencephalon-projectingglutamatergic neuronC1ql3, Cdh13, Il1rapl2, Zfp804b, Dscaml1, Slit3, Galnt14, Nell2, Ak5, Car3
L6 IT_1Layer 6 glutamatergic neuron, intratelencephalon-projecting_1glutamatergic neuronBrinp3, C1ql3, Cdh13, Fst, Il1rapl2, Negr1, Efna5, Zfp804b, Plcxd3, Dscaml1
L6 IT_2Layer 6 glutamatergic neuron, intratelencephalon-projecting_2glutamatergic neuronTfap2d, Cdh9, Pcdh7, Oprk1, Dcc, Smoc2, Cplx2, Car12, Chrm2, Nr4a2
L6b Col6a1Col6a1+ Layer 6b glutamatergic neuronglutamatergic neuronCtgf, Bmpr1b, Cdh18, Foxp2, Egfem1, Hs3st4, Kcnab1, Tcf4, Gm28928, Col6a1
L6b Kcnip1Kcnip1+ Layer 6b glutamatergic neuronglutamatergic neuronCtgf, Gm42557, Cdh18, Rxfp2, Kcnip1, Hs3st4, Kcnab1, 9530026P05Rik, Hcrtr2, Gm28928
L6b Ror1Ror1+ Layer 6b glutamatergic neuronglutamatergic neuronCtgf, Fbxl7, Kirrel3, Cdh18, Hs3st4, Fam19a5, Ptn, Kcnab1, Tox, Ror1
L6b Shisa6_1Shisa6+ Layer 6b glutamatergic neuron_1glutamatergic neuronCtgf, Shisa6, Thsd7b, Cdh18, Hs3st4, Kcnab1, Svil, Gm28928, Zfpm2, Inpp4b
L6b Shisa6_2Shisa6+ Layer 6b glutamatergic neuron_2glutamatergic neuronCtgf, Brinp3, Sema3e, Cdh18, Trhde, Hs3st4, Kcnab1, Il1rapl1, March1, Shisa6
Lamp5 Egln3_1Lamp5+ Egln3+ GABAergic neuron_1GABAergic neuronNpy, Itga8, Nxph1, Egln3, Fgf13, Fam19a1, Ptprm, Fbn2, AC154782.1, Lamp5
Lamp5 Egln3_2Lamp5+ Egln3+ GABAergic neuron_2GABAergic neuronNpy, D030045P18Rik, Nxph1, Crim1, Fgf13, Nrg1, Cdh18, Ptprm, Lamp5, Egln3
Lamp5 Egln3_3Lamp5+ Egln3+ GABAergic neuron_3GABAergic neuronNtn1, Npy, Nxph1, Dcc, Trpc4, Fgf13, Ndst4, Ptprm, Lamp5, Egln3
Lamp5 Lhx6Lamp5+ Lhx6+ GABAergic neuronGABAergic neuronNpy, Lhx6, Cntnap3, Nxph1, Fgf13, Tacr1, Ptprm, Myo5b, Reln, Lamp5
Lamp5 Pax6Lamp5+ Pax6+ GABAergic neuronGABAergic neuronNpy, Pax6, Nxph1, Npsr1, Scrg1, Fgf13, Gm16083, Ptprm, Reln, Lamp5
Lamp5 Pdlim5_1Lamp5+ Pdlim5+ GABAergic neuron_1GABAergic neuronCntn5, Npy, Nxph1, Cntn6, Fgf13, Pde4b, Ptprm, Grid1, Lamp5, Pdlim5
Lamp5 Pdlim5_2Lamp5+ Pdlim5+ GABAergic neuron_2GABAergic neuronNpy, Ndnf, Nxph1, Cntn5, Fgf13, Sema3e, Ptprm, Grik1, Lamp5, Pdlim5
Lamp5 Slc35d3Lamp5+ Slc35d3+ GABAergic neuronGABAergic neuronHtr1f, Npy, Rims1, Nxph1, Ptprm, Fgf13, Reln, Ndst3, Lamp5, Slc35d3
Meis2Meis2+ GABAergic neuronGABAergic neuronIgfbpl1, Draxin, Cd1d1, Sp8, Cd24a, Lockd, St8sia2, Gm29260, Gm17750, Meis2
Meis2_Top2aMeis2+ Top2a+ GABAergic neuronGABAergic neuronIgfbpl1, Dcc, E130114P18Rik, Draxin, Cd1d1, Sp8, Ccnd2, Mdk, Meis2, Top2a
MicroMicrogliamicroglial cellInpp5d, Plxdc2, Tgfbr1, Hexb, Nav2, C1qa, Tanc2, Csmd3, C1qb, Ctss
Oligo Enpp6_1Enpp6+ oligodendrocyte_1oligodendrocytePde9a, Inpp5d, Hexb, Panx1, 4932435O22Rik, Tgfbr1, Gm13179, C1qa, Fam114a1, Enpp6
Oligo Enpp6_2Enpp6+ oligodendrocyte_2oligodendrocyteBmp4, Inpp5d, Hexb, Neu4, 5730559C18Rik, Tgfbr1, Stk32a, C1qa, Ctss, Enpp6
Oligo Enpp6_3Enpp6+ oligodendrocyte_3oligodendrocytePde9a, Inpp5d, Hexb, Carmil1, Tgfbr1, Kcnj12, Egflam, C1qa, Gm38039, Enpp6
Oligo Enpp6_4Enpp6+ oligodendrocyte_4oligodendrocyteGm13883, Plp1, Gm16029, Mbp, Gm26834, St18, Kcnj12, Prr5l, Mobp, Enpp6
Oligo Opalin_1Opalin+ oligodendrocyte_1oligodendrocyteTmem117, Plp1, Mbp, Enpp6, Tln2, St18, Prr5l, Anln, Selenop, Opalin
Oligo Opalin_2Opalin+ oligodendrocyte_2oligodendrocytePlp1, Ptgds, Mbp, Il33, St18, C030029H02Rik, Prr5l, Palm2, Mobp, Opalin
Oligo Opalin_3Opalin+ oligodendrocyte_3oligodendrocyteSynpr, Plp1, Mbp, Man1a, St18, Nckap5, Prr5l, Kank1, Pcdh7, Opalin
Oligo Opalin_4Opalin+ oligodendrocyte_4oligodendrocyteProm1, Plp1, Mbp, Pdzrn3, Thbs3, St18, Cxcl12, Prr5l, Mobp, Opalin
OPC PdgfraPdgfra+ oligodendrocyte precursor celloligodendrocyte precursor cellPlp1, Mbp, St18, Prr5l, Mobp, Mal, Mog, Cldn11, Pde4b, Pdgfra
Peripericytebrain pericytePlp1, Mbp, St18, Prr5l, Mobp, Mal, Mog, Cldn11, Pde4b, Mag
Pvalb Calb1_1Pvalb+ Calb1+ GABAergic neuron_1GABAergic neuronPlp1, Spp1, Trpc6, Mbp, St18, Gm32647, Npy, Prr5l, Pvalb, Calb1
Pvalb Calb1_2Pvalb+ Calb1+ GABAergic neuron_2GABAergic neuronLhfpl3, Tac1, Cntnap5c, Vcan, Tnr, Grm7, Ptprz1, Rbp4, Pvalb, Calb1
Pvalb Egfem1Pvalb+ Egfem1+ GABAergic neuronGABAergic neuronNos1, Atp13a5, 9330158H04Rik, Vtn, Sorcs3, Cald1, Ebf1, Ptprk, Pvalb, Egfem1
Pvalb Gabrg1Pvalb+ Gabrg1+ GABAergic neuronGABAergic neuronKcnc2, Th, Gabrg1, Erbb4, Gpc4, Sox5, Il1rapl2, Gm16685, Pth2r, Pvalb
Pvalb Gpr149Pvalb+ Gpr149+ GABAergic neuronGABAergic neuronKcnc2, Fzd6, Mrvi1, Erbb4, Zfpm2, Sox5, Il1rapl2, Dscam, Pvalb, Gpr149
Pvalb Il1rapl2Pvalb+ Il1rapl2+ GABAergic neuronGABAergic neuronKcnc2, Thsd7a, Pcdh15, Erbb4, Il1rapl2, Sox5, Ncam2, Col25a1, Inpp4b, Pvalb
Pvalb Kank4Pvalb+ Kank4+ GABAergic neuronGABAergic neuronBrinp3, Kcnc2, Erbb4, Sema3e, Lrp1b, Sox5, Il1rapl2, Pcdh9, Pvalb, Kank4
Pvalb RelnPvalb+ Reln+ GABAergic neuronGABAergic neuronKcnc2, Cntn5, Erbb4, Reln, Nlgn1, Sox5, Clstn2, Il1rapl2, Gm46102, Pvalb
Pvalb Vipr2_1Pvalb+ Vipr2+ GABAergic neuron_1GABAergic neuronKcnc2, Crabp1, Prox1, Erbb4, Pcsk6, Sox5, Il1rapl2, Gm37267, Pvalb, Vipr2
Pvalb Vipr2_2Pvalb+ Vipr2+ GABAergic neuron_2GABAergic neuronUnc5b, Kcnc2, Mctp2, Erbb4, Sox5, Pde3a, Il1rapl2, Kit, Pvalb, Vipr2
PVM_1Perivascular macrophageperivascular macrophageF13a1, Kcnc2, Erbb4, Aoah, Ms4a4a, Sox5, Il1rapl2, Colec12, Fam19a2, Gm30489
PVM_2Perivascular macrophageperivascular macrophageKcnc2, Gm49087, Erbb4, Klra2, H2-Eb1, Sox5, Il1rapl2, H2-Ab1, Fam19a2, 4930562F07Rik
PVM_3Perivascular macrophageperivascular macrophageNapsa, Kcnc2, Erbb4, Slamf7, Gpr141, Sox5, Il1rapl2, H2-Eb1, Fam19a2, H2-Aa
SMCsmooth muscle cellsmooth muscle cellActa2, Map3k7cl, Gm6249, Myh11, Tagln, Pdlim3, Ephx3, Olfr558, Crip1, Tbx2
Sncg Calb1_1Sncg+ Calb1+ GABAergic neuron_1GABAergic neuronCpne5, Adarb2, Cnr1, Ror1, Megf10, Oxr1, Lsamp, Cadps2, Sncg, Calb1
Sncg Calb1_2Sncg+ Calb1+ GABAergic neuron_2GABAergic neuronTll1, Adarb2, Calb1, Cnr1, Megf10, Cpne5, Stk32a, Cadps2, Gria3, Sncg
Sncg Col14a1Sncg+ Col14a1+ GABAergic neuronGABAergic neuronLuzp2, Adarb2, Cnr1, Cdh6, Megf10, Npy, Cadps2, Erbb4, Sncg, Col14a1
Sncg Npy2rSncg+ Npy2r+ GABAergic neuronGABAergic neuronPcdh9, Adarb2, Cnr1, Npy2r, Grik4, Megf10, Cadps2, Kirrel3, Col25a1, Sncg
Sncg Slc17a8Sncg+ Slc17a8+ GABAergic neuronGABAergic neuronAdarb2, Slc17a8, Gas2l3, Cnr1, Nr1h4, Megf10, Adamts18, Cadps2, Kctd12, Sncg
Sst C1ql3_1Sst+ C1ql3+ GABAergic neuron_1GABAergic neuronAdarb2, Pard3bos1, Ptprk, Cnr1, Pard3b, Megf10, Cadps2, Crh, Sst, C1ql3
Sst C1ql3_2Sst+ C1ql3+ GABAergic neuron_2GABAergic neuronNdnf, Sst, Crh, Grin3a, Nxph1, Pla2g4a, Galntl6, Gm15584, Ntng1, C1ql3
Sst Calb2Sst+ Calb2+ GABAergic neuronGABAergic neuronSst, Olfm3, Pcsk5, Grin3a, Nkain3, Nxph1, Ptprd, Galntl6, Rgs6, Calb2
Sst ChodlSst+ Chodl+ GABAergic neuronGABAergic neuronSst, Grin3a, Nxph1, Galntl6, Rgs6, Sox6, Mgat4c, Synpr, Cacna2d3, Chodl
Sst Crhr2_1Sst+ Crhr2+ GABAergic neuron_1GABAergic neuronSst, Gm12128, Rspo2, Grin3a, Crtac1, Nxph1, Tmem132d, Galntl6, Alk, Crhr2
Sst Crhr2_2Sst+ Crhr2+ GABAergic neuron_2GABAergic neuronSst, Grm8, Grin3a, Crybg1, Nxph1, Tmem132b, St6galnac5, Galntl6, Rgs6, Crhr2
Sst Etv1_1Sst+ Etv1+ GABAergic neuron_1GABAergic neuronFbn2, Sst, C1qtnf7, Grin3a, Nr2f2, Nxph1, Cnih3, Galntl6, Pcdh7, Etv1
Sst HpseSst+ Hpse+ GABAergic neuronGABAergic neuronHpse, Sst, Ust, Grin3a, Nxph1, Syt6, Galntl6, Pdyn, Rgs6, Tox
Sst Htr1aSst+ Htr1a+ GABAergic neuronGABAergic neuronSst, Pdyn, Gm30835, Grin3a, Ryr3, Nxph1, Elmo1, Galntl6, Cdh9, Htr1a
Sst Myh8_1Sst+ Myh8+ GABAergic neuron_1GABAergic neuronPlpp4, Sst, Il1rapl2, Grin3a, Nxph1, Cdh12, Chsy3, Galntl6, Rgs6, Myh8
Sst Myh8_2Sst+ Myh8+ GABAergic neuron_2GABAergic neuronGulp1, Sst, Pld5, Grin3a, Nxph1, Kcnb2, Gas7, Galntl6, Fat3, Myh8
Sst Myh8_3Sst+ Myh8+ GABAergic neuron_3GABAergic neuronSlc24a2, Sst, Cdh9, Grin3a, Nxph1, Elmo1, Galntl6, Npas3, Rgs6, Myh8
Sst PenkSst+ Penk+ GABAergic neuronGABAergic neuronSst, Cartpt, Grin3a, Zfp521, Nxph1, 9530026P05Rik, Galntl6, Lama3, Baiap3, Penk
Sst Pvalb Calb2Sst+ Pvalb+ Calb2+ GABAergic neuronGABAergic neuronMoxd1, Sst, Grin3a, Klf12, Kcnab1, Nxph1, Galntl6, Col25a1, Pvalb, Calb2
Sst Pvalb Etv1Sst+ Pvalb+ Etv1+ GABAergic neuronGABAergic neuronFbn2, Sst, Grin3a, Etv1, Sgcz, Nxph1, Galntl6, Whrn, Rgs6, Pvalb
Sst Tac2Sst+ Tac2+ GABAergic neuronGABAergic neuronTac2, Sst, Ndnf, Grin3a, Crh, Nxph1, Kcnh8, Galntl6, Myo1b, Rgs6
Sst Th_1Sst+ Th+ GABAergic neuron_1GABAergic neuronSst, Bcl6, Phactr2, Grin3a, Nxph1, Sorcs3, Galntl6, Antxr2, Serpine2, Th
Sst Th_2Sst+ Th+ GABAergic neuron_2GABAergic neuronPnoc, Sst, Grin3a, Nr4a2, Nxph1, Th, Rspo3, Galntl6, Rgs6, Gabrg1
Sst Th_3Sst+ Th+ GABAergic neuron_3GABAergic neuronSst, Corin, Gm36251, Grin3a, Nxph1, Th, Nr4a2, Galntl6, Clec18a, Rgs6
Sst_PappaSst+ Pappa+ GABAergic neuronGABAergic neuronSst, AC129186.1, Grin3a, Layn, Nxph1, Myo5b, Galntl6, Gna14, Rgs6, Pappa
Vip C1ql1Vip+ C1ql1+ GABAergic neuronGABAergic neuronNos1, Ptprk, A830036E02Rik, Crhbp, Ndst4, Lsamp, Tacr1, Pcdh11x, Vip, C1ql1
Vip Chat_1Vip+ Chat+ GABAergic neuron_1GABAergic neuronCreb5, Vip, Vwc2, Cacna1a, Galnt17, Adarb2, Gpc6, Limch1, Chat, Synpr
Vip Chat_2Vip+ Chat+ GABAergic neuron_2GABAergic neuronVip, Lypd1, Cacna1a, Kirrel3, Grik4, Adarb2, Limch1, Grm7, Synpr, Chat
Vip Gpc3Vip+ Gpc3+ GABAergic neuronGABAergic neuronSema6d, Vip, Cacna1a, Lin7a, Alcam, Adarb2, Pcdh11x, Limch1, Synpr, Gpc3
Vip Htr1f_1Vip+ Htr1f+ GABAergic neuron_1GABAergic neuronCdh6, Vip, Cacna1a, Npy, Mlip, Adarb2, Limch1, Vwc2l, Sntg1, Htr1f
Vip Igfbp6_1Vip+ Igfbp6+ GABAergic neuron_1GABAergic neuronVip, Stac, Entpd1, Cacna1a, Adarb2, Plcl1, Ptprr, Limch1, Adgrl2, Igfbp6
Vip Igfbp6_2Vip+ Igfbp6+ GABAergic neuron_2GABAergic neuronReln, Vip, Cacna1a, Cobll1, AC129186.1, Adarb2, Corin, Limch1, Thsd7b, Igfbp6
Vip Mybpc1_1Vip+ Mybpc1+ GABAergic neuron_1GABAergic neuronVip, Gm45321, Cacna1a, Gm2516, Adarb2, 4930555F03Rik, Limch1, C130073E24Rik, Synpr, Mybpc1
Vip Mybpc1_2Vip+ Mybpc1+ GABAergic neuron_2GABAergic neuron5033421B08Rik, Vip, Cacna1a, Slc7a15, Mybpc1, Adarb2, Limch1, Itih5, Synpr, Col15a1
Vip Mybpc1_3Vip+ Mybpc1+ GABAergic neuron_3GABAergic neuronGrm8, Vip, Cacna1a, Dcc, Grik1, Adarb2, Ryr3, Limch1, Synpr, Mybpc1
Vip Serpinf1_1Vip+ Serpinf1+ GABAergic neuron_1GABAergic neuronVip, Sfrp2, Cacna1a, Lmo1, Adarb2, Calcrl, Fam196b, Limch1, Dock2, Serpinf1
Vip Serpinf1_2Vip+ Serpinf1+ GABAergic neuron_2GABAergic neuronVip, Clrn1, Col14a1, Cacna1a, Adarb2, Crtac1, Dpy19l1, Limch1, Gm45680, Serpinf1
Vip Serpinf1_3Vip+ Serpinf1+ GABAergic neuron_3GABAergic neuronRor1, Vip, Arhgef37, Cacna1a, Adarb2, Drd2, Sv2c, Limch1, Synpr, Serpinf1
Vip SncgSncg+ GABAergic neuronGABAergic neuronVip, Cacna1a, Adra1b, Adarb2, Limch1, Synpr, Cntn4, Sorcs1, Crh, Sncg
VLMC_1vascular lepotomeningeal cell_1brain pericytePtgds, Gm30624, Bnc2, Arhgap22, Cped1, Gm47865, Slc7a11, Col15a1, Bmp6, Adgrl3
VLMC_2vascular lepotomeningeal cell_2brain pericyteAox3, Ptgds, Bnc2, Plxna2, Slc7a11, Cped1, Prex2, Vcam1, Bmp6, Coch
VLMC_3vascular lepotomeningeal cell_3brain pericytePkhd1, Ptgds, Rspo2, Bnc2, Cftr, Cped1, Slc7a11, Gm2115, Bmp6, Atp13a5
VLMC_4vascular lepotomeningeal cell_4brain pericytePtgds, Sh3gl3, Bnc2, Aifm3, Ppp1r1a, Cped1, Gm27151, Slc7a11, Atp13a5, Bmp6
VLMC_5vascular lepotomeningeal cell_5brain pericyteSlc47a1, Ptgds, Bnc2, Slc4a10, Cped1, Pcdh7, Slc7a11, Tmeff2, Erc2, Bmp6
VLMC_6vascular lepotomeningeal cell_6brain pericytePtgds, Prg4, Bnc2, Tspan8, Cped1, Msln, Slc7a11, Dapl1, Bmp6, Fn1
VLMC_7vascular lepotomeningeal cell_7brain pericyteCubn, Ptgds, Bnc2, Slc7a14, Sptssb, Cped1, Slc7a11, Dapl1, Igfbp3, Bmp6
cross-species cluster
LabelExpanded LabelOBO Ontology IDMarkers
Astro_1Astrocyte_1astrocyteGfap, Aqp4, Myoc, Pla2g7, Igfbp5, Id4, Mlc1, Ntsr2, Sdc4, Gja1
Astro_2Astrocyte_2astrocyteSlc1a2, Gpc5, Wdr17, Htra1, Slc1a3, Acsl3, Plpp3, Msi2, Dtna, Gabrb1
ChandelierChandelier neuronGABAergic neuronPthlh, Pde3a, Mctp2, Kit, Unc5b, Epb41l4a, Mme, 4933432K03Rik, Gm44129, A830036E02Rik
EndoEndothelial cellendothelial cellFlt1, Sgms1, Adgrl4, Slc2a1, Slco1a4, Bsg, Klf2, Ptprg, Sptbn1, Mecom
L2/3 ITLayer 2-3 glutamatergic neuron, intratelencephalon-projectingglutamatergic neuronCelf2, Rgs6, Lingo2, Dab1, Slit3, Lrrtm4, Camk2a, Dscaml1, Cnksr2, 2010300C02Rik
L5 ET_1Layer 5 glutamatergic neuron, extratelencephalon-projecting_1glutamatergic neuronFam19a1, Cdh13, Gm2164, Kcnt2, Gm19410, Mgat4c, Sgcz, Nav3, Ntng1, Pex5l
L5 ET_2Layer 5 glutamatergic neuron, extratelencephalon-projecting_2glutamatergic neuronNpnt, Vwc2l, Lgr5, Tshz2, Col8a1, Gm26883, Slc26a4, Erg, Trpc7, Gm2164
L5 IT_1Layer 5 glutamatergic neuron, intratelencephalon-projecting_1glutamatergic neuronPtprd, Lrrc4c, Car10, Brinp3, Celf2, Cux2, R3hdm1, Kcnip4, Fhod3, Kcnh5
L5 IT_2Layer 5 glutamatergic neuron, intratelencephalon-projecting_2glutamatergic neuronIl1rapl2, Iqgap2, AC129186.1, Fras1, Grik3, Scube1, Deptor, Dgkb, A830036E02Rik, Sdk2
L5 IT_3Layer 5 glutamatergic neuron, intratelencephalon-projecting_3glutamatergic neuronGrp, Nxph1, Col12a1, Gm26883, Slit1, Wls, Gm28905, Gpc6, Tshz2, Tox
L5/6 NPLayer 5-6 glutamatergic neuron, near-projectingglutamatergic neuronOlfm3, Kirrel3, Vwc2l, Grik1, Tshz2, Kcnip1, Dcc, Lrrc4c, Gm26883, Adcy2
L6 CT_1Layer 6 glutamatergic neuron, corticothalamic-projecting_1glutamatergic neuronHs3st4, Shisa6, Gm28928, Sulf2, Cdh18, Bmpr1b, Zfpm2, Nrxn1, Khdrbs3, Foxp2
L6 CT_2Layer 6 glutamatergic neuron, corticothalamic-projecting_2glutamatergic neuronFoxp2, Kctd16, Hs3st4, Ppp3ca, Garnl3, Nrgn, Zfpm2, Edil3, Nos1ap, Khdrbs3
L6 IT_1Layer 6 glutamatergic neuron, intratelencephalon-projecting_1glutamatergic neuronNell2, Fst, Il1rapl2, Negr1, C1ql3, Brinp3, Satb2, Plcxd3, Bmpr1b, Pou6f2
L6 IT_2Layer 6 glutamatergic neuron, intratelencephalon-projecting_2glutamatergic neuronAk5, Pcdh7, Nell2, Dcc, Cdh9, Pcsk2, Cplx2, Rasgef1b, Chrm2, C1ql3
L6 IT_3Layer 6 glutamatergic neuron, intratelencephalon-projecting_3glutamatergic neuronTfap2d, Nr2f2, Oprk1, Gm45623, Smoc2, Gm15825, Car12, 4930555F03Rik, Nr4a2, Lxn
L6bLayer 6b glutamatergic neuronglutamatergic neuronCtgf, Inpp4b, Cdh18, Tmem163, AC124490.1, Kcnab1, Mmp16, Kcnip4, Erc2, Cplx3
Lamp5_1Lamp5+ GABAergic neuron_1GABAergic neuronKit, Nxph1, Ndnf, Luzp2, Gm30835, Grin2a, Ndst4, Pde11a, Unc5c, Lamp5
Lamp5_2Lamp5+ GABAergic neuron_2GABAergic neuronNyap2, Unc5d, Alk, Grin2a, Fgf13, Gad2, Asph, Rims1, Htr1f, Lamp5
Lamp5_3Lamp5+ GABAergic neuron_3GABAergic neuronDchs2, Lhx6, Nos1, Cntnap3, B020031H02Rik, Gm45680, Ackr3, Tacr1, Cntnap4, Lamp5
Lamp5_4Lamp5+ GABAergic neuron_4GABAergic neuronCol14a1, Luzp2, Pax6, Asph, Frem1, Ralyl, Tnfaip8l3, Dpy19l1, Pnoc, Lamp5
Lamp5_5Lamp5+ GABAergic neuron_5GABAergic neuronReln, Sorcs1, Cxcl14, Npas3, Rxfp1, Nrg1, Ndst4, Galntl6, Nr2f2, Lamp5
Microglia/PVMmicroglia / perivascular macrophageperivascular macrophageInpp5d, Zfhx3, Elmo1, Srgap2, Ccnd3, Tgfbr1, Mef2a, Hexb, Tanc2, Pag1
Oligo_1oligodendrocyte_1oligodendrocytePrr5l, Tmem117, Plp1, Enpp6, Anln, Tln2, Mobp, St18, Selenop, Mog
Oligo_2oligodendrocyte_2oligodendrocytePde4b, Ptgds, Mbp, Erbb4, Plp1, Il33, St18, Kirrel3, Mobp, Nkain2
OPColigodendrocyte precursor celloligodendrocyte precursor cellLhfpl3, Tnr, Vcan, Dscam, Epn2, Xylt1, Ptprz1, Gm4876, Pdgfra, Cacng4
Pvalb_1Pvalb+ GABAergic neuron_1GABAergic neuronKcnc2, Nrg3, Kcnc1, Gria3, Cntnap4, Cntn5, Btbd11, Gm1604a, Erbb4, Pvalb
Pvalb_2Pvalb+ GABAergic neuron_2GABAergic neuronShisa8, Corin, Th, 4930509J09Rik, Tac1, Ptprk, Lama3, Nos1, Rbp4, Pvalb
Sncg_1Sncg+ GABAergic neuron_1GABAergic neuronHtr3a, Cntn4, Sp8, Sorcs1, Pnoc, Dpp10, Tnfaip8l3, Ptprd, Frem1, Sncg
Sncg_2Sncg+ GABAergic neuron_2GABAergic neuronFrem1, Col25a1, Npas1, Eps8, Scml4, 9530059O14Rik, Tac2, Malat1, Rgs16, Sncg
Sncg_3Sncg+ GABAergic neuron_3GABAergic neuronCxcl14, Nell1, Rgs12, Spock1, Npas1, Ppp2r2b, Igf1, Pcdh9, Megf10, Sncg
Sncg_4Sncg+ GABAergic neuron_4GABAergic neuronEgln3, Nrxn3, Col14a1, Cntnap5b, Tnfaip8l3, Itga8, Rxfp1, Fam19a1, Npas1, Sncg
Sst ChodlSst+ Chodl+ GABAergic neuronGABAergic neuronNos1, Crhbp, Ndst4, Tacr1, Chodl, 9330158H04Rik, Fndc1, Stac, Bace2, Sst
Sst_1Sst+ GABAergic neuron_1GABAergic neuronPdyn, Cdh9, Npas1, Cntnap2, AF529169, Ano3, Reln, Zfp804a, Lhx6, Sst
Sst_2Sst+ GABAergic neuron_2GABAergic neuronIl1rapl2, Nebl, Sst, Pcdh7, Reln, Gabrb1, Rab3b, Kctd8, Cntn6, Sst
Sst_3Sst+ GABAergic neuron_3GABAergic neuronGria1, Gpc6, Etl4, Sst, Adgrb3, Grin3a, Pcdh9, Xkr4, Sh3rf3, Sst
Sst_4Sst+ GABAergic neuron_4GABAergic neuronNpas1, Unc5d, 9630002D21Rik, Cdh9, Lhx6, Egfem1, Lypd6, Pou6f2, Sytl5, Sst
Sst_5Sst+ GABAergic neuron_5GABAergic neuron9630002D21Rik, Adgrb3, Crh, Gm20754, Npas1, Kcnc2, Gxylt2, Pard3b, Pard3bos1, Sst
Sst_6Sst+ GABAergic neuron_6GABAergic neuron9630002D21Rik, B3galt1, Crh, Reln, Klhl14, Ptprm, Npas1, Grm1, Gxylt2, Sst
Sst_7Sst+ GABAergic neuron_7GABAergic neuronTh, Cdh9, Corin, Lingo2, Cort, Ncam2, Nxph2, Arpp21, Gm36251, Sst
Vip_1Vip+ GABAergic neuron_1GABAergic neuronVip, Cntnap2, Zfp804a, Kcnip4, Sobp, Gpc6, Sdk1, Brinp3, Sorcs3, Fstl5
Vip_2Vip+ GABAergic neuron_2GABAergic neuronVip, Cxcl14, Adarb2, Clstn2, Synpr, Oxr1, Igf1, Fam19a2, Shisa9, Crh
Vip_3Vip+ GABAergic neuron_3GABAergic neuronVip, Alcam, Igf1, Astn2, Prox1, Pde3a, Grpr, Lin7a, Crh, Pthlh
Vip_4Vip+ GABAergic neuron_4GABAergic neuronPenk, Thsd7a, Gm39185, Nrg3, Npas1, Ccser1, Crh, Thsd7b, Stac, Calb2
VLMCvascular lepotomeningeal cellbrain pericyteCped1, Apod, Ptgds, Atp1a2, Slc6a20a, Colec12, Bmp6, Ranbp3l, Slc7a11, Lama1

Human - Pancreas

This integrated pancreas reference dataset is an aggregate of multiple pancreas single-cell RNA-seq datasets from the literature. It is comprised of data from six different studies, generated using six different single-cell technologies, and integrated into a single reference using Seurat. Details of the integration procedure can be explored in the Snakemake workflow linked above.


Annotation Details

annotation.l1
LabelExpanded LabelOBO Ontology IDMarkers
cyclingcyclingpancreatic endocrine cellUBE2C, TOP2A, CDK1, BIRC5, PBK, CDKN3, MKI67, CDC20, CCNB2, CDCA3
immuneimmuneleukocyteACP5, APOE, HLA-DRA, TYROBP, LAPTM5, SDS, FCER1G, C1QC, C1QB, SRGN
quiescent_stellatequiescent stellatepancreatic stellate cellRGS5, C11orf96, FABP4, CSRP2, IL24, ADIRF, NDUFA4L2, GPX3, IGFBP4, ESAM
endothelialendothelialendothelial cellPLVAP, RGCC, ENG, PECAM1, ESM1, SERPINE1, CLDN5, STC1, MMP1, GNG11
schwannschwannSchwann cellNGFR, CDH19, UCN2, SOX10, S100A1, PLP1, TSPAN11, WNT16, SOX2, TFAP2A
activated_stellateactivated stellatepancreatic stellate cellCOL1A1, COL1A2, COL6A3, COL3A1, TIMP3, TIMP1, CTHRC1, SFRP2, BGN, LUM
epsilonepsilon islet cellpancreatic epsilon cellBHMT, VSTM2L, PHGR1, TM4SF5, ANXA13, ASGR1, DEFB1, GHRL, COL22A1, OLFML3
gammagamma islet cellpancreatic PP cellPPY, AQP3, MEIS2, ID2, GPC5-AS1, CARTPT, PRSS23, ETV1, PPY2, TUBB2A
deltadelta islet cellpancreatic D cellSST, RBP4, SERPINA1, RGS2, PCSK1, SEC11C, HHEX, LEPR, MDK, LY6H
ductalductalpancreatic ductal cellSPP1, MMP7, IGFBP7, KRT7, ANXA4, SERPINA1, LCN2, CFTR, KRT19, SERPING1
acinaracinarpancreatic acinar cellREG1A, PRSS1, CTRB2, CTRB1, REG1B, CELA3A, PRSS2, REG3A, CPA1, CLPS
betabeta islet celltype B pancreatic cellIAPP, INS, DLK1, INS-IGF2, G6PC2, HADH, ADCYAP1, GSN, NPTX2, C12orf75
alphaalpha islet cellpancreatic A cellGCG, TTR, PPP1R1A, CRYBA2, TM4SF4, MAFB, GC, GPX3, PCSK2, PEMT

Human - Fetal Development

Overview

Modalities: RNA

Cells in Reference: 377,456

Species: Human

Reference Dataset(s): Cao et al, Science 2020

Demo Dataset(s): Asp et al, Cell 2019; Enge et al, Cell 2017; Lindstrom et al, Developmental Cell 2018; Cao et al, Science 2020

This reference consists of 378,000 subsampled human fetal cells from Cao et al., 2020. Details of the reference construction procedure can be explored in the Snakemake workflow linked above.


Annotation Details

annotation.l2
LabelMarkers
Adrenal-MegakaryocytesITGA2B, STAR, ITGB3, CYP17A1, PF4, SULT2A1, PLEK, HSPE1, GP1BA, DHCR24
Liver-MegakaryocytesLTBP1, ALB, ITGB3, HBA1, ITGA2B, HBG2, MED12L, HBA2, PF4, AFP
Lung-MegakaryocytesITGB3, PF4, HLA-A, GP9, ITGA2B, CTTN, PPBP, TUBB1, LGALSL, GP1BA
Heart-MegakaryocytesTUBB1, PPBP, KIT, PF4, ACTC1, CPA3, TTN, HDC, CD44, GP9
Placenta-MegakaryocytesAC108463.2, SETP11, ARHGEF19, CTD-2227I18.1, SPOCD1, C6orf25, WDR64, PDYN, AC109829.1, OXSM
Kidney-MegakaryocytesGCSAML, RARB, ITGA2B, TM4SF18, HPSE, CHRM3, PPBP, MYO1B, RP11-556I14.2, CD86
Spleen-MegakaryocytesPF4, PEX16, AC002366.3, RNASET2, RP11-556I14.2, CNTN1, ITGA2B, HSPG2, GP9, SEC24D
Muscle-MegakaryocytesGRXCR2, SLAMF6, GLYATL1P1, RP11-469M7.1, RP11-1006G14.2, MST1R, LY6G6F, RP11-689K5.3, TREML2, GTF2H2C
Eye-Ganglion cellsANK2, CADM2, KCNIP4, ROBO2, NRG3, CTNNA2, MDGA2, EPHA6, RALYL, EBF1
Placenta-Stromal cellsLAMA2, MEG3, PHACTR2, CNTN5, AC011288.2, COL6A2, PRLR, SLIT2, HGF, BMP5
Spleen-Stromal cellsLEPREL1, CTC-535M15.2, GRIK2, ADRA1D, TMTC1, CACNA1D, TSHZ2, HBA1, MAMDC2, CLIC5
Thymus-Stromal cellsPOSTN, IKZF1, CCR9, RP11-94L15.2, DCN, THBS2, CD5, ISLR, CD3E, COL1A1
Adrenal-Stromal cellsCOL1A1, COL1A2, COL3A1, STAR, CYP11A1, CYP17A1, DHCR24, C7, FDX1, COL12A1
Muscle-Stromal cellsCOL3A1, COL1A2, CDH18, COL1A1, POSTN, FNDC1, DCN, RP11-554D15.1, COL5A2, DLK1
Lung-Stromal cellsPIEZO2, FAM155A, SLIT2, CCBE1, FAT3, MEOX2, ARHGAP28, PRKCB, PLEKHH2, A2M
Pancreas-Stromal cellsCOL1A1, RELN, COL3A1, SFRP1, COL1A2, ALDH1A1, IGF2, DCN, HSPB6, COL6A2
Heart-Stromal cellsCOL1A1, TBX20, COL1A2, COL3A1, DCN, COL6A2, FBLN2, COL5A1, ELN, POSTN
Intestine-Stromal cellsHPSE2, THSD4, CDH13, FNDC1, UNC5D, CXCL14, COL1A1, FENDRR, SHANK2, GPC6
Kidney-Stromal cellsPRRX1, MTND4P12, SCARA5, CTNNA2, SFRP2, EBF2, IGFBP5, COL12A1, PPARG, POSTN
Stomach-Stromal cellsPITX1, COL1A2, EGR1, COL3A1, NELL1, COL1A1, NLGN1, POSTN, LPHN3, DCN
Eye-Stromal cellsPI16, SFRP2, CRYAA, CRYBB1, CRYGC, DCN, MFAP5, COL1A1, KCNB2, COL1A2
Adrenal-Adrenocortical cellsSTAR, CYP17A1, SCARB1, DLK1, DHCR24, FDX1, CYP11A1, LDLR, RBM47, SH3BP5
Pancreas-Lymphatic endothelial cellsNTS, CTSS, UBD, SELM, FOXC2, SELE, STAB2, CXCL2, PTGS2, NNMT
Lung-Lymphatic endothelial cellsCCL21, TFPI, PRKG1, STAB2, SEPP1, PROX1, IGFBP7, RELN, IGFBP4, NRP2
Intestine-Lymphatic endothelial cellsRP11-322E11.5, USP20, TSPEAR, ITPR2, P4HA3, CACNA1C, CTC-458G6.2, GPSM2, RP11-451M19.3, NRG1
Muscle-Lymphatic endothelial cellsCCL21, MYL1, MMRN1, TSPEAR, ACTA1, LYVE1, BSCL2, MPP7, CEP19, NFATC1
Heart-Lymphatic endothelial cellsCCL21, DKK3, MMRN1, NTS, NRG3, TFPI, VWF, LYVE1, GUCY1A3, STAB2
Stomach-Lymphatic endothelial cellsPWWP2AP1, RP5-1180C18.1, C3orf55, AC022182.3, IRF4, RP11-799O21.2, WNT16, ABHD17AP6, RP11-77H9.8, CTD-2586B10.1
Adrenal-Myeloid cellsCD74, C1QC, STAR, DLK1, CYP17A1, DHCR24, AOAH, SULT2A1, C1QB, CYP21A2
Heart-Myeloid cellsCD74, TTN, HLA-DRA, TPM1, HLA-DRB1, COL1A1, HLA-DPB1, COL3A1, HLA-DPA1, VIM
Lung-Myeloid cellsCD74, VCAN, HLA-DRB1, MALAT1, HLA-DRA, CLNK, HLA-DPA1, CCSER1, HLA-DPB1, F13A1
Kidney-Myeloid cellsSRGN, MTND4P12, CD74, NR4A3, SAMHD1, LGMN, FOS, CSF1R, PLAUR, HLA-DRA
Muscle-Myeloid cellsF13A1, MYL1, NCF4, TMEM97, HLA-DOA, CTBS, HLA-DMA, TPM2, SIGLEC1, SIRPB2
Liver-Myeloid cellsALB, MS4A7, HBA1, FYB, HBG1, LGMN, HBG2, ADAP2, HBA2, C1QC
Intestine-Myeloid cellsCD74, DNASE1L3, SRGN, SEMA6B, SAMHD1, UTRN, AOAH, XYLT1, HLA-DRB1, PELI1
Placenta-Myeloid cellsCXCL9, GPNMB, F13A1, C1QC, GABRA3, TFEC, TFCP2L1, HLA-DPA1, DNASE2, HLA-DRA
Pancreas-Myeloid cellsCD74, FTH1, HLA-DRA, RPS27, HLA-DPA1, PFN1, SPI1, FOS, PLD4, CLPS
Spleen-Myeloid cellsRP11-1080G15.1, HBA2, CD5L, MALAT1, CR1, TIMD4, VCAM1, CD163, HBA1, CD163L1
Stomach-Myeloid cellsASTL, CDCA4, HLA-DRB5, SUV39H2, HLA-DQA1, IDO1, HLA-DRA, SRP19, RP11-15B24.5, GIPR
Lung-Bronchiolar and alveolar epithelial cellsATP11A, CPM, MECOM, SFTPB, SFTPC, FGFR2, SFTA3, ETV5, ROS1, WIF1
Adrenal-Vascular endothelial cellsLDB2, PPAP2B, FLT1, EMCN, F8, SULT2A1, CYP17A1, DLK1, STAR, IGF2
Lung-Vascular endothelial cellsEPAS1, NCKAP5, CALCRL, KHDRBS2, CD93, VWF, AFF3, APLNR, PDE3B, FENDRR
Muscle-Vascular endothelial cellsCAV1, TNNC2, PRND, FABP4, APLNR, GPIHBP1, COL15A1, IGF2, CDH5, VWF
Heart-Vascular endothelial cellsCAV1, COL15A1, MYL7, SLC9C1, MYH7, FABP4, ACTC1, EMCN, MYL2, CDH5
Pancreas-Vascular endothelial cellsHSPG2, MADCAM1, PLVAP, CLPS, PTRF, COL15A1, IGFBP4, APLNR, CD93, FLT1
Cerebrum-Vascular endothelial cellsIGFBP7, FN1, CLDN5, CDH2, ITM2A, SLC38A5, SLC7A1, CDH11, SLC7A5, ABCB1
Stomach-Vascular endothelial cellsBDKRB2, PLXND1, STK32B, APLNR, ECHDC1, PLEKHG1, KCNN3, ERG, RASGRF2, KANK3
Kidney-Vascular endothelial cellsIGFBP5, MEIS2, CHRM3, LDB2, KCNIP4, PLVAP, ASIC2, PPAP2B, LINC00478, HSPG2
Eye-Vascular endothelial cellsSELP, RP11-89K21.1, CRYAA, SIX3, PKD1L1, CTD-3179P9.1, SGCZ, RP11-187O7.3, SEMA3A, TM4SF18
Liver-Vascular endothelial cellsLDB2, STAB2, PPAP2B, ALB, SLC9A9, ATRNL1, RELN, CRHBP, ACSM3, EDA
Cerebellum-Vascular endothelial cellsIGFBP7, ITM2A, FN1, CLDN5, SLC7A5, MFSD2A, SLC39A10, FLT1, SLC7A1, SLC38A5
Spleen-Vascular endothelial cellsAC010084.1, SNTG1, TGFBR3, FGF12, HBA2, LDB2, DYSF, APLNR, HBG2, PTPRB
Placenta-Vascular endothelial cellsCTD-3006G17.2, MEOX2, HSD17B2, LIN28B, FCGR2B, AC011288.2, IDO2, IGF1, TFPI2, RP11-184E9.1
Intestine-Vascular endothelial cellsMADCAM1, PLVAP, HSPG2, DIAPH2, FLT1, CEL, PTPRM, CALCRL, PLCB1, RASIP1
Thymus-Vascular endothelial cellsRP11-221J22.1, RASA4DP, CD1E, AC005550.4, RP11-306K13.1, TSLP, CTD-3179P9.2, KB-1683C8.1, RP11-103J17.2, RP11-973H7.4
Spleen-STC2_TLX1 positive cellsHBA2, HBA1, HBG2, HBG1, COL1A1, FBLN5, VCAM1, CXCL13, STC2, TLX1
Muscle-Satellite cellsCLCN5, OLFML2A, NEB, MATN2, MEGF10, FLNC, PAX7, FGFR4, CDH15, CALCR
Cerebrum-AstrocytesNPAS3, GPC5, PTPRZ1, CTNNA2, NRXN1, LRP1B, PTN, CADM2, LSAMP, TANC2
Cerebellum-AstrocytesGRID2, PTN, ANKS1B, DACH1, NPAS3, GRIA4, SLC1A3, NRG1, CTNND2, DSCAM
Eye-AstrocytesWIF1, RP11-766N7.4, CPM, RP11-133F8.2, PAX5, CLEC18B, PAX8, SLC1A3, ADAMTS18, RP11-776H12.1
Adrenal-SympathoblastsCHGA, CHGB, DPP6, FGF14, RGS5, AGBL4, CACNA2D3, DBH, SLC24A2, SLC18A1
Kidney-Ureteric bud cellsMECOM, NAALADL2, PKHD1, INADL, PAX8, GATA3, COBLL1, BMPR1B, DCDC2, PAX2
Cerebrum-MicrogliaPLXDC2, PDE4B, DOCK4, ST6GALNAC3, SFMBT2, FRMD4A, EPB41L2, SLC9A9, UTY, SPP1
Cerebellum-MicrogliaPLXDC2, SPP1, PTPRG, DOCK4, RTTN, SFMBT2, RPLP1, SLC9A9, APOE, DOCK8
Eye-MicrogliaOSCAR, KYNU, RP11-480C22.1, ACOT2, TIGD4, SLC9A7, TLR2, PHF5A, LY86, HLA-DPA1
Cerebrum-Limbic system neuronsPTPRD, NTNG1, RNF220, CNTNAP2, NRXN1, TENM2, RIMS2, RBFOX1, ERC2, MEG3
Cerebellum-Inhibitory interneuronsNRXN3, UNC5C, XKR4, NRXN1, NKAIN2, GRID2, CSMD1, ADARB2, ANKS1B, MSRA
Adrenal-Chromaffin cellsRBFOX1, RGS5, STMN2, CACNA2D3, RBMS3, DLC1, CHGB, KCNQ5, ALCAM, CNTNAP2
Intestine-Chromaffin cellsFEV, CACNA1A, MLN, DACH1, CCK, RFX6, DSP, AC018359.1, TPH1, PDE4D
Cerebrum-OligodendrocytesLSAMP, ZBTB20, LHFPL3, DSCAM, CSMD1, NRXN1, PTPRZ1, KCTD16, KCND2, AC007682.1
Cerebellum-OligodendrocytesCSMD1, CNTNAP2, LSAMP, ROBO2, KCND2, CNTNAP5, LHFPL3, NRXN3, PCDH15, XIST
Heart-Endocardial cellsCOL3A1, POSTN, VIM, CDH11, HSPG2, EMCN, FN1, CALCRL, ENG, HMCN1
Eye-Photoreceptor cellsCADM2, MARCH1, SYT1, EYS, RORB, FSTL5, GALNT13, MPPED2, CADPS, ZNF385B
Adrenal-ErythroblastsHBG1, CYP17A1, HBG2, STAR, HBA1, HBA2, SULT2A1, SLC25A37, DLK1, ANK1
Liver-ErythroblastsHBG2, HBA1, NFIA, HBA2, AFP, ANK1, ZDHHC14, SLC25A37, CENPP, HBG1
Spleen-ErythroblastsHBA1, COL3A1, AHSP, COL1A1, HBA2, ELMO1, HBG1, COL6A2, HBG2, AKT3
Pancreas-ErythroblastsSLC25A37, HBG2, HBB, HBA1, HBM, AHSP, UCP2, ALAS2, ANK1, FTH1
Stomach-ErythroblastsAHSP, HIST1H1E, HBM, HBG2, HEMGN, SNX16, RNF224, CIAPIN1, SLC4A1, ALAS2
Kidney-ErythroblastsRNF224, HEMGN, HBG2, HBM, GATC, AHSP, ARHGAP10, SPTA1, TOPORS, ALAS2
Muscle-ErythroblastsRP5-1068B5.3, RP11-737O24.3, AC007317.1, AC007228.5, ADSSL1, RPS20P14, TMEM38A, RP5-890O15.3, TDH, DRP2
Intestine-ErythroblastsHBM, SLC4A1, HBA2, SPTA1, HBG2, AHSP, HBA1, ALAS2, HBG1, HEMGN
Intestine-ENS gliaZNF536, RALYL, CDH19, DLG2, GFRA1, BNC2, PRIMA1, ERBB4, INSC, MALAT1
Pancreas-ENS gliaPLP1, KCTD12, COL20A1, MGAT4C, SOX10, SCN7A, CDH19, RP11-202H2.1, PRIMA1, RPL7A
Stomach-ENS gliaU91328.19, PRIMA1, ATP6AP1, SOX10, ST6GALNAC2, HCFC1R1, CDH19, ABLIM3, RP11-308N19.1, NT5C
Spleen-Lymphoid cellsFAM129C, HBA2, MS4A1, HBG2, BANK1, HBA1, CARD11, RALGPS2, PAX5, ARHGAP24
Heart-Lymphoid cellsSKAP1, TTN, PTPRC, COL3A1, LCP1, COL1A2, LTB, HBA2, CD247, HBG1
Pancreas-Lymphoid cellsRPS3, PFN1, RPS12, PTPRC, RPLP2, HLA-B, RPL32, ARHGDIB, RPS8, ETS1
Lung-Lymphoid cellsARHGAP15, MALAT1, PTPRC, SKAP1, MBNL1, CD247, DPYD, PTPRCAP, ZBTB20, IL7R
Intestine-Lymphoid cellsCD247, ZBTB16, PTPN22, KIT, RUNX3, LZTFL1, LTB, COL23A1, TXK, ADAMTS17
Placenta-Lymphoid cellsGNLY, ENAM, NKG7, CSF1, IGJ, ITGAX, KLRC1, FNDC3B, IL2RB, ITGAD
Kidney-Lymphoid cellsCD69, MTND4P12, CD3E, MTND1P23, RHOH, SRGN, ITK, C1orf21, NKG7, NR4A3
Adrenal-Lymphoid cellsNKG7, PRF1, STAR, LINC00861, SULT2A1, PYHIN1, CYP21A2, GNLY, DHCR24, PTPRC
Liver-Lymphoid cellsIGLL1, PAX5, AFP, FAM129C, ALB, SERPINA1, ARHGAP15, HBG2, HBG1, IKZF3
Stomach-Lymphoid cellsCD6, C22orf34, CD52, NCBP1, RHOH, PKIA, TCF7, TBC1D15, GZMM, PTPRC
Muscle-Lymphoid cellsRTP4, CD2, CD6, SRSF8, CRTAM, ASPH, BATF, CPSF4, CD28, PPIL1
Muscle-Skeletal muscle cellsTTN, MYH3, NEB, ACTN2, MYLPF, MYL1, TPM2, MYBPC1, TNNC2, CA3
Eye-Skeletal muscle cellsCRYAA, MYH3, CRYBA1, TNNT1, CRYBB2, MYL1, BARX2, DUSP13, DACH1, NEB
Stomach-Mesothelial cellsAP000705.7, RP11-74M11.2, DCLRE1B, MSLN, SNTG1, NFATC2, NKAIN3, RP11-275N1.1, ARL17A, RSPO3
Lung-Mesothelial cellsAP000705.7, ELN, C3, TMTC2, ALDH1A2, LINC00842, MALAT1, SBSPON, SYNE1, PTPRQ
Liver-Mesothelial cellsAP000705.7, ALB, PKHD1L1, HBA2, BNC1, HBA1, HHIP, HBG2, RP11-275N1.1, HBG1
Intestine-Mesothelial cellsAP000705.7, ROBO2, HAS1, LRRTM4, LRRN4, LRRC4C, RP11-123O22.1, PCDH7, RP11-404P21.8, AKAP12
Spleen-Mesothelial cellsKLK11, HBG1, PLA2G2A, PRG4, HBG2, MSLN, HBA2, LHX9, HBA1, SLPI
Pancreas-Mesothelial cellsRP11-74M11.2, EGFL6, IL6, MAFF, BDKRB1, POSTN, HAS1, NAMPT, COL8A1, ATP2B1
Cerebellum-SLC24A4_PEX5L positive cellsCNTNAP2, FSTL5, GRM7, LRRTM4, LUZP2, GRM3, CSMD3, NRXN3, SLC24A4, PEX5L
Cerebrum-Excitatory neuronsRBFOX1, PTPRD, ROBO2, LRRC7, NRXN1, DLGAP1, GPM6A, NKAIN2, SOX5, TMEM108
Eye-Retinal progenitors and Muller gliaRORB, LGR4, SORCS1, GALNT13, CLVS1, CRB1, ILDR2, FAM184B, ADAMTS18, RP11-89K21.1
Cerebrum-SKOR2_NPSR1 positive cellsDAB1, GRID2, RORA, BAI3, FOXP2, AUTS2, DMD, NRG1, SKOR2, NPSR1
Liver-HepatoblastsALB, AFP, APOA1, APOA2, SERPINA1, APOB, HBA1, AHSG, IGF2, HBG2
Thymus-ThymocytesLEF1, BCL11B, CALN1, TFDP2, ARHGAP15, THEMIS, SATB1, IKZF2, RUNX1, TCF7
Cerebellum-Purkinje neuronsDAB1, GRID2, RORA, AUTS2, BAI3, NRG1, EBF1, GRIK1, FOXP2, LPHN2
Placenta-Syncytiotrophoblasts and villous cytotrophoblastsTENM3, FBN2, ARL15, EGFR, KANK1, ZFAT, SVEP1, RHOBTB1, RP11-30J20.1, MBNL3
Kidney-Mesangial cellsGPC3, KIAA1217, PALLD, MEIS2, MEIS1, FLRT2, TNC, NR2F2, KIF26B, CCBE1
Intestine-Smooth muscle cellsMYH11, FOXP2, TAGLN, ACTG2, DES, SORBS1, ACTA2, TMTC2, CNN1, KCNIP4
Pancreas-Smooth muscle cellsBGN, IGF2, NOTCH3, PDGFRB, ZFP36L1, PCDH18, EGR1, THBS4, FOS, NDUFA4L2
Heart-Smooth muscle cellsRGS5, PLA2G5, HBA2, ACTA2, HBG2, CYGB, HBG1, PDGFRB, HBA1, ABCC9
Placenta-Smooth muscle cellsHGF, FLT1, AC011288.2, AGTR1, LAMC3, PLCB1, ADAMTS18, LAMA2, TBX5, AFF2
Muscle-Smooth muscle cellsACTA2, MYLPF, EGFLAM, NOTCH3, DLGAP1, EBF2, MYH11, NCKAP5, ABCC9, BMP5
Eye-Smooth muscle cellsTYRP1, PMEL, TYR, TRPM1, MLANA, TEX41, MET, PAX3, TFAP2A, HR
Intestine-Intestinal epithelial cellsPCSK5, APOA1, C10orf112, RAB11FIP1, LGALS3, ARID3A, THRB, CPS1, MYH14, HNF4A
Cerebellum-Granule neuronsERBB4, GRIK2, RELN, NRG1, KCND2, CNTN5, NRXN1, SYT1, ROBO2, NELL2
Eye-Horizontal cellsNRXN3, RORB, CNTN4, ONECUT1, TNR, MEGF10, MEGF11, ONECUT2, CACNG3, TFAP2B
Cerebrum-Inhibitory neuronsNRXN3, CCSER1, CTNNA2, RBFOX1, LRRC7, MYT1L, GRIN2B, GRM5, RP11-85M11.2, MIR137HG
Heart-Schwann cellsMPZ, ROBO2, CDH19, INSC, XKR4, S100B, NPPA, RP11-141M1.3, BICD1, PLP1
Muscle-Schwann cellsMPZ, FSTL5, CDH19, POU3F1, TNNC2, FOXD3, PLP1, MYLPF, SOX10, MYH3
Adrenal-Schwann cellsOLFML2A, PLP1, APOE, MPZ, CYP17A1, FOXD3, DHCR24, CDH19, DLK1, SOX10
Pancreas-Islet endocrine cellsCHGA, PCSK1N, GNAS, ERO1LB, CPE, INS, CADPS, TTR, MEIS2, MAFB
Eye-Amacrine cellsNRXN3, MEIS2, CADM2, ZNF385D, RORB, DCC, SYT1, DSCAM, MIR181A1HG, RP11-689K5.3
Cerebellum-Unipolar brush cellsERBB4, NRXN1, LRP1B, NLGN1, LPHN3, CCSER1, PCDH9, UNC5C, STXBP5L, GRIA2
Stomach-MUC13_DMBT1 positive cellsDMBT1, CEA, KRT20, MUC13, FER1L6, PHGR1, HNF4G, ABCC3, HNF4A, CDH17
Pancreas-Acinar cellsCEL, SPINK1, CPA1, CTRB2, CLPS, SYCN, CPA2, GP2, CTRB1, DLK1
Kidney-Metanephric cellsDACH1, PAX2, EYA1, HMGA2, GPC3, TRABD2B, ITGA8, PTPN14, WT1, BMPER
Pancreas-Ductal cellsIGF2, SLC4A4, DLK1, ATP1B1, CFTR, FXYD2, JUN, CLU, SPINK1, H3F3B
Eye-Retinal pigment cellsTRPM1, TYR, COL8A1, SLC38A11, LINC00276, BEST1, RP11-690J15.1, RPE65, TYRP1, PMEL
Heart-CardiomyocytesTTN, MYL7, TNNT2, TPM1, ACTC1, SLC8A1, TNNC1, MYL4, MYH7, TNNI1
Stomach-Squamous epithelial cellsKRT19, PDE4D, KRT13, FOS, RAB11FIP1, PARD3, S100A6, CSMD1, ANXA1, EGR1
Lung-Squamous epithelial cellsSPRR3, TACSTD2, KRT13, KRT78, LGALS3, S100A9, TMPRSS11B, MT2A, IL1RN, ECM1
Stomach-Goblet cellsCLDN18, SPINK1, RAB11FIP1, AGR2, MUC6, LYZ, ELF3, GPRC5A, PPARG, PIK3C2G
Placenta-Extravillous trophoblastsFN1, FLT1, ISM2, NOTUM, PAPPA2, PRG2, ADAM12, FSTL3, QSOX1, SERPINE2
Pancreas-ENS neuronsCHRNA3, RNASE1, PHOX2B, GAL, CD81, VIP, NFIX, HMX2, TUBA1A, TLX2
Intestine-ENS neuronsKCNQ5, DPP6, EML5, FAM155A, PHOX2B, AUTS2, RP11-348J24.2, IQCJ-SCHIP1, FAM163A, KCND2
Stomach-ENS neuronsVIP, MRPS31P4, RP11-457K10.1, NAT9, SCG2, PIGO, ALK, FAM124A, CTA-481E9.3, ATP2B3
Heart-Visceral neuronsPRPH, RGS5, SST, CALM2, SLC5A7, RBMS3, C10orf85, ALCAM, NPY2R, STMN2
Lung-Visceral neuronsSLC18A3, RUNX1T1, PRPH, NELL2, VIP, ROBO2, GAL, NKAIN3, CHRNA3, SGCZ
Lung-Ciliated epithelial cellsCDHR3, TPPP3, CAPS, RPLP1, DNAH12, AGR3, LRRIQ1, OSBPL6, C4orf22, AGR2
Stomach-Ciliated epithelial cellsDNAH9, PSCA, DNAH12, PLCG2, C9orf117, S100A6, DNAH3, CLPS, AC079354.1, MUC16
Heart-Epicardial fat cellsC3, PRG4, CCDC80, SULF1, ITLN1, RP11-572C15.6, MSLN, CFH, AP000705.7, PLA2G2A
Stomach-Parietal and chief cellsESRRG, IGFBP5, FGD4, ATP4B, ATP4A, CLDN18, GIF, ARHGEF28, CLIC6, IGFBP2
Liver-Stellate cellsCOL25A1, IGFBP3, ALB, NR1H4, HHIP, CCBE1, HGF, COLEC11, COLEC10, PTH1R
Placenta-IGFBP1_DKK1 positive cellsLUM, IGFBP1, CD248, SCARA5, DKK1, APOD, GAS1, CHRDL1, SERPINE1, CFD
Eye-Bipolar cellsGRIK1, FSTL5, ZNF385B, ZNF804B, CA10, ZPBP, FAM19A4, VSX2, TRPC7, SLC1A7
Lung-Neuroendocrine cellsGRP, SEC11C, IGFBP5, ASCL1, NRG1, TFF3, NKAIN2, GHRL, HEPACAM2, RALYL
Stomach-Neuroendocrine cellsTPH1, GHRL, HS6ST3, CHGA, SLC38A11, CLDN18, LINC00261, HS3ST4, RFX6, DIP2B
Placenta-PAEP_MECOM positive cellsPAEP, AC073218.2, C1orf186, CP, MUC16, RP11-98L5.2, RP11-510D19.1, DEFB1, AC104654.1, MECOM
Eye-Corneal and conjunctival epithelial cellsS100A9, LYPD2, LCN2, MUC4, SLPI, KRT4, CP, MUC16, CEACAM6, MUC15
Liver-Hematopoietic stem cellsMPO, ALB, RNF220, ITGA4, RP5-964N17.1, RUNX1, ANGPT1, ARHGAP15, IQGAP2, GPR141
Adrenal-CSH1_CSH2 positive cellsCGB, MAGEA10, CGA, INSL4, PAGE4, KISS1, XAGE3, PSG9, CSH1, CSH2
Eye-Lens fibre cellsCRYBB1, CRYAA, CRYBB2, CRYBA4, CRYBA1, CRYGC, BFSP1, LIM2, MIP, BFSP2
Pancreas-CCL19_CCL21 positive cellsCCL19, FDCSP, CCL21, PTGDS, C1S, TNFSF11, CXCL13, CXCL12, PRRX1, SLC22A3
Placenta-Trophoblast giant cellsCSH1, PAPPA, ADAM12, CYP19A1, TFPI2, CSH2, CGA, PSG1, KISS1, FBLN1
Adrenal-SLC26A4_PAEP positive cellsSLC26A4, HSD3B2, RP11-328J2.1, LL0XNC01-16G2.1, BPIFB1, IL1A, MAP3K15, LINC00086, ASB4, PAEP
Placenta-AFP_ALB positive cellsRP4-794H19.1, BAAT, SLCO1B3, AHSG, SERPINA5, FGB, DUSP9, KNG1, AFP, ALB
Spleen-AFP_ALB positive cellsMBL2, HBA1, CFHR1, HBA2, RBP4, HBG2, FGG, SERPINA7, AFP, ALB
Thymus-Thymic epithelial cellsRP11-114G22.1, PRSS16, TBATA, FAM163A, AC005042.5, FOXN1, PAX1, MIR205HG, LY75, NEURL2
Eye-PDE11A_FAM19A2 positive cellsADAMTS18, MEGF10, PDE11A, POU6F2, PTPRR, CHAT, RP11-689K5.3, KCNAB1, RELN, FAM19A2
Thymus-Antigen presenting cellsRAG1, CCL19, HLA-DRA, CD74, CLNK, HLA-DRB1, HLA-DPB1, BIRC3, WDFY4, CIITA
Heart-SATB2_LRRC7 positive cellsFOXG1, NEUROD2, CDK5R1, SATB2, RBFOX1, GRIN2B, NKAIN2, FABP7, ARPP21, LRRC7
Heart-ELF3_AGBL2 positive cellsPLN, MYL3, MYL2, MYL7, MYH7, TNNC1, MB, TNNI1, ELF3, AGBL2
Heart-CLC_IL5RA positive cellsCLC, MS4A3, IL5RA, MYL3, HAND1, PLN, HSPB7, TNNT2, MYL7, MYH7
Stomach-PDE1C_ACSM3 positive cellsFOXI1, TFCP2L1, HEPACAM2, STAC2, ST14, CLNK, ATP6V0D2, BMPR1B, PDE1C, ACSM3
Cerebrum-MegakaryocytesPF4, PPBP, TUBB1, C6orf25, GP9, GP6, LY6G6F, TREML1, GP5, GP1BA
Heart-ErythroblastsLINC00705, SPRR2A, RPL24P2, SPATA41, RP11-389C8.3, SERPINB7, LY6K, PGBD4, RP11-215A21.2, EIF3C
Lung-CSH1_CSH2 positive cellsCSH1, CSH2, PSG1, PSG2, PSG3, PSG4, PSG11, ENDOU, XAGE3, KISS1
annotation.l1
LabelMarkers
MegakaryocytesLTBP1, ITGB3, ITGA2B, PF4, THBS1, PLEK, MED12L, PRKAR2B, RUNX1, ARHGAP6
Ganglion cellsANK2, CADM2, KCNIP4, ROBO2, NRG3, CTNNA2, MDGA2, EPHA6, RALYL, EBF1
Stromal cellsCOL1A1, COL3A1, COL1A2, DCN, COL6A2, COL5A1, COL5A2, IGF2, SPARC, VCAN
Adrenocortical cellsSTAR, CYP17A1, SCARB1, DLK1, DHCR24, FDX1, CYP11A1, LDLR, RBM47, SH3BP5
Lymphatic endothelial cellsCCL21, TFPI, STAB2, PROX1, RELN, EFNA5, IGFBP7, CD36, MMRN1, LYVE1
Myeloid cellsCD74, SRGN, SAMHD1, CST3, AOAH, SLC9A9, CTSB, RBM47, LGMN, FTL
Bronchiolar and alveolar epithelial cellsATP11A, CPM, MECOM, SFTPB, SFTPC, FGFR2, SFTA3, ETV5, ROS1, WIF1
Vascular endothelial cellsLDB2, FLT1, COL4A2, COL4A1, PTPRM, IGFBP7, HSPG2, TCF4, PTPRB, EPAS1
STC2_TLX1 positive cellsHBA2, HBA1, HBG2, HBG1, COL1A1, FBLN5, VCAM1, CXCL13, STC2, TLX1
Satellite cellsCLCN5, OLFML2A, NEB, MATN2, MEGF10, FLNC, PAX7, FGFR4, CDH15, CALCR
AstrocytesNPAS3, PTN, GRID2, LSAMP, GPM6A, SLC1A3, QKI, BAI3, CTNND2, PTPRZ1
SympathoblastsCHGA, CHGB, DPP6, FGF14, RGS5, AGBL4, CACNA2D3, DBH, SLC24A2, SLC18A1
Ureteric bud cellsMECOM, NAALADL2, PKHD1, INADL, PAX8, GATA3, COBLL1, BMPR1B, DCDC2, PAX2
MicrogliaPLXDC2, SPP1, DOCK4, SFMBT2, FRMD4A, SLC9A9, ITPR2, DOCK8, APBB1IP, IPCEF1
Limbic system neuronsPTPRD, NTNG1, RNF220, CNTNAP2, NRXN1, TENM2, RIMS2, RBFOX1, ERC2, MEG3
Inhibitory interneuronsNRXN3, UNC5C, XKR4, NRXN1, NKAIN2, GRID2, CSMD1, ADARB2, ANKS1B, MSRA
Chromaffin cellsRBFOX1, RGS5, STMN2, CACNA2D3, CHGB, KCNQ5, ALCAM, BMPR1B, CHGA, DBH
OligodendrocytesLSAMP, CSMD1, LHFPL3, KCND2, PCDH15, CADM2, PTPRZ1, LRRC4C, OPCML, LRP1B
Endocardial cellsCOL3A1, POSTN, VIM, CDH11, HSPG2, EMCN, FN1, CALCRL, ENG, HMCN1
Photoreceptor cellsCADM2, MARCH1, SYT1, EYS, RORB, FSTL5, GALNT13, MPPED2, CADPS, ZNF385B
ErythroblastsHBG2, HBA1, HBA2, HBG1, SLC25A37, ANK1, TFRC, CD36, EPB41, SPTA1
ENS gliaSLC35F1, ZNF536, GFRA1, CDH19, PLP1, PRIMA1, COL20A1, SOX10, MPZ, INSC
Lymphoid cellsPTPRC, ARHGAP15, B2M, PABPC1, SKAP1, LCP1, HLA-B, FAM65B, ETS1, CD247
Skeletal muscle cellsTTN, MYH3, NEB, MYLPF, TPM2, MYL1, ACTC1, ACTA1, TNNC2, TNNT3
Mesothelial cellsAP000705.7, C3, SULF1, ALDH1A2, HHIP, MSLN, LINC00842, TFPI2, PTPRQ, SBSPON
SLC24A4_PEX5L positive cellsCNTNAP2, FSTL5, GRM7, LRRTM4, LUZP2, GRM3, CSMD3, NRXN3, SLC24A4, PEX5L
Excitatory neuronsRBFOX1, PTPRD, ROBO2, LRRC7, NRXN1, DLGAP1, GPM6A, NKAIN2, SOX5, TMEM108
Retinal progenitors and Muller gliaRORB, LGR4, SORCS1, GALNT13, CLVS1, CRB1, ILDR2, FAM184B, ADAMTS18, RP11-89K21.1
SKOR2_NPSR1 positive cellsDAB1, GRID2, RORA, BAI3, FOXP2, AUTS2, DMD, NRG1, SKOR2, NPSR1
HepatoblastsALB, AFP, APOA1, APOA2, SERPINA1, APOB, HBA1, AHSG, IGF2, HBG2
ThymocytesLEF1, BCL11B, CALN1, TFDP2, ARHGAP15, THEMIS, SATB1, IKZF2, RUNX1, TCF7
Purkinje neuronsDAB1, GRID2, RORA, AUTS2, BAI3, NRG1, EBF1, GRIK1, FOXP2, LPHN2
Syncytiotrophoblasts and villous cytotrophoblastsTENM3, FBN2, ARL15, EGFR, KANK1, ZFAT, SVEP1, RHOBTB1, RP11-30J20.1, MBNL3
Mesangial cellsGPC3, KIAA1217, PALLD, MEIS2, MEIS1, FLRT2, TNC, NR2F2, KIF26B, CCBE1
Smooth muscle cellsCOL4A2, COL3A1, COL1A1, CALD1, NOTCH3, COL6A3, BGN, RGS5, PDGFRB, ITGA1
Intestinal epithelial cellsPCSK5, APOA1, C10orf112, RAB11FIP1, LGALS3, ARID3A, THRB, CPS1, MYH14, HNF4A
Granule neuronsERBB4, GRIK2, RELN, NRG1, KCND2, CNTN5, NRXN1, SYT1, ROBO2, NELL2
Horizontal cellsNRXN3, RORB, CNTN4, ONECUT1, TNR, MEGF10, MEGF11, ONECUT2, CACNG3, TFAP2B
Inhibitory neuronsNRXN3, CCSER1, CTNNA2, RBFOX1, LRRC7, MYT1L, GRIN2B, GRM5, RP11-85M11.2, MIR137HG
Schwann cellsMPZ, OLFML2A, PLP1, CDH19, SOX10, FOXD3, S100B, INSC, ABCA8, NGFR
Islet endocrine cellsCHGA, PCSK1N, GNAS, ERO1LB, CPE, INS, CADPS, TTR, MEIS2, MAFB
Amacrine cellsNRXN3, MEIS2, CADM2, ZNF385D, RORB, DCC, SYT1, DSCAM, MIR181A1HG, RP11-689K5.3
Unipolar brush cellsERBB4, NRXN1, LRP1B, NLGN1, LPHN3, CCSER1, PCDH9, UNC5C, STXBP5L, GRIA2
MUC13_DMBT1 positive cellsDMBT1, CEA, KRT20, MUC13, FER1L6, PHGR1, HNF4G, ABCC3, HNF4A, CDH17
Acinar cellsCEL, SPINK1, CPA1, CTRB2, CLPS, SYCN, CPA2, GP2, CTRB1, DLK1
Metanephric cellsDACH1, PAX2, EYA1, HMGA2, GPC3, TRABD2B, ITGA8, PTPN14, WT1, BMPER
Ductal cellsIGF2, SLC4A4, DLK1, ATP1B1, CFTR, FXYD2, JUN, CLU, SPINK1, H3F3B
Retinal pigment cellsTRPM1, TYR, COL8A1, SLC38A11, LINC00276, BEST1, RP11-690J15.1, RPE65, TYRP1, PMEL
CardiomyocytesTTN, MYL7, TNNT2, TPM1, ACTC1, SLC8A1, TNNC1, MYL4, MYH7, TNNI1
Squamous epithelial cellsKRT19, KRT13, RAB11FIP1, ANXA1, S100A6, DSP, ELF3, PITX1, AQP3, KRT5
Goblet cellsCLDN18, SPINK1, RAB11FIP1, AGR2, MUC6, LYZ, ELF3, GPRC5A, PPARG, PIK3C2G
Extravillous trophoblastsFN1, FLT1, ISM2, NOTUM, PAPPA2, PRG2, ADAM12, FSTL3, QSOX1, SERPINE2
ENS neuronsKCNQ5, EML5, ELAVL4, PHOX2B, MIR137HG, RP11-348J24.2, CNGB1, PRPH, FAM163A, NOS1
Visceral neuronsPRPH, SLC5A7, SLC18A3, PIRT, SST, RP11-466P24.7, CHRNA3, GAL, RGS4, PHOX2B
Ciliated epithelial cellsCDHR3, DNAH12, CAPS, TPPP3, LRRIQ1, C4orf22, STK33, DNAH9, AGBL4, RP11-56A10.1
Epicardial fat cellsC3, PRG4, CCDC80, SULF1, ITLN1, RP11-572C15.6, MSLN, CFH, AP000705.7, PLA2G2A
Parietal and chief cellsESRRG, IGFBP5, FGD4, ATP4B, ATP4A, CLDN18, GIF, ARHGEF28, CLIC6, IGFBP2
Stellate cellsCOL25A1, IGFBP3, ALB, NR1H4, HHIP, CCBE1, HGF, COLEC11, COLEC10, PTH1R
IGFBP1_DKK1 positive cellsLUM, IGFBP1, CD248, SCARA5, DKK1, APOD, GAS1, CHRDL1, SERPINE1, CFD
Bipolar cellsGRIK1, FSTL5, ZNF385B, ZNF804B, CA10, ZPBP, FAM19A4, VSX2, TRPC7, SLC1A7
Neuroendocrine cellsGRP, SEC11C, ASCL1, GHRL, TPH1, HEPACAM2, TFF3, MS4A8, LINC00261, DDC
PAEP_MECOM positive cellsPAEP, AC073218.2, C1orf186, CP, MUC16, RP11-98L5.2, RP11-510D19.1, DEFB1, AC104654.1, MECOM
Corneal and conjunctival epithelial cellsS100A9, LYPD2, LCN2, MUC4, SLPI, KRT4, CP, MUC16, CEACAM6, MUC15
Hematopoietic stem cellsMPO, ALB, RNF220, ITGA4, RP5-964N17.1, RUNX1, ANGPT1, ARHGAP15, IQGAP2, GPR141
CSH1_CSH2 positive cellsCGB, MAGEA10, CGA, INSL4, PAGE4, KISS1, XAGE3, PSG9, CSH1, CSH2
Lens fibre cellsCRYBB1, CRYAA, CRYBB2, CRYBA4, CRYBA1, CRYGC, BFSP1, LIM2, MIP, BFSP2
CCL19_CCL21 positive cellsCCL19, FDCSP, CCL21, PTGDS, C1S, TNFSF11, CXCL13, CXCL12, PRRX1, SLC22A3
Trophoblast giant cellsCSH1, PAPPA, ADAM12, CYP19A1, TFPI2, CSH2, CGA, PSG1, KISS1, FBLN1
SLC26A4_PAEP positive cellsSLC26A4, HSD3B2, RP11-328J2.1, LL0XNC01-16G2.1, BPIFB1, IL1A, MAP3K15, LINC00086, ASB4, PAEP
AFP_ALB positive cellsFGB, AHSG, VTN, KNG1, ITIH2, APOA2, APOC3, FGG, AFP, ALB
Thymic epithelial cellsRP11-114G22.1, PRSS16, TBATA, FAM163A, AC005042.5, FOXN1, PAX1, MIR205HG, LY75, NEURL2
PDE11A_FAM19A2 positive cellsADAMTS18, MEGF10, PDE11A, POU6F2, PTPRR, CHAT, RP11-689K5.3, KCNAB1, RELN, FAM19A2
Antigen presenting cellsRAG1, CCL19, HLA-DRA, CD74, CLNK, HLA-DRB1, HLA-DPB1, BIRC3, WDFY4, CIITA
SATB2_LRRC7 positive cellsFOXG1, NEUROD2, CDK5R1, SATB2, RBFOX1, GRIN2B, NKAIN2, FABP7, ARPP21, LRRC7
ELF3_AGBL2 positive cellsPLN, MYL3, MYL2, MYL7, MYH7, TNNC1, MB, TNNI1, ELF3, AGBL2
CLC_IL5RA positive cellsCLC, MS4A3, IL5RA, MYL3, HAND1, PLN, HSPB7, TNNT2, MYL7, MYH7
PDE1C_ACSM3 positive cellsFOXI1, TFCP2L1, HEPACAM2, STAC2, ST14, CLNK, ATP6V0D2, BMPR1B, PDE1C, ACSM3

Human - Lung

Overview

Modalities: RNA

Cells in Reference: 65,662

Species: Human

Reference Dataset(s): Travaglini et al, Nature 2020

Demo Dataset(s): Vieira-Braga et al, Nature Medicine 2019 [Seurat Object]

This reference consists of 65,662 human lung cells (10x Genomics v2) from Travaglini et al. 2020. Cells were sourced from three donor patients and from all lung tissue compartments (bronchi, bronchiole, alveoli) as well as circulating blood.


Annotation Details

annotation.l1
LabelOBO Ontology IDMarkers
Alveolar Epithelial Type 1type I pneumocyteEMP2, AGER, GPRC5A, LMO7, RTKN2, ARHGEF26, LAMA3, DST, SPOCK2, SCEL
BB cellMS4A1, BANK1, LINC00926, CD79A, BLK, CD79B, VPREB3, SP140, CD22, ADAM28
Basalbasal cellKRT15, S100A2, KRT17, KRT5, KRT19, PERP, CLDN1, FHL2, DST, ITGA2
CD14+ MonocyteCD14-positive, CD16-negative classical monocyteS100A9, S100A12, S100A8, VCAN, FCN1, CD300E, CTSS, CD99, CSF3R, METTL9
CD4 TCD4-positive, alpha-beta T cellCD2, IL7R, TRAT1, BCL11B, ITK, CAMK4, CD6, LEF1, MALAT1, MAL
Ciliatedciliated cellRSPH1, CAPS, FAM92B, CDHR3, CCDC170, SNTN, C20orf85, ZMYND10, DNAH6, FANK1
Dendriticdendritic cellHLA-DPB1, FCGR2B, HLA-DMB, CLEC10A, CSF2RA, MS4A6A, HLA-DQA1, RGS1, GPR183, FPR3
FibroblastfibroblastFBLN1, ADH1B, DCN, LUM, C1S, C1R, SLIT2, C3, CFD, ABLIM1
Lymphaticlymphatic vesselCCL21, MMRN1, PROX1, PPFIBP1, TFF3, TBX1, PKHD1L1, IGFBP7, TFPI, TIMP3
MacrophagemacrophageACP5, C1QA, C1QB, VSIG4, MARCO, OLR1, APOC1, SLCO2B1, GPD1, ITGAX
Natural Killernatural killer cellPRF1, NKG7, KLRF1, CD247, GNLY, PYHIN1, KLRD1, SPON2, FCGR3A, GZMB
Plasmaplasma cellMZB1, DERL3, SEC11C, XBP1, TNFRSF17, SSR4, POU2AF1, HSP90B1, PRDX4, MANF
Alveolar Epithelial Type 2type II pneumocyteSFTPA1, SFTPA2, NAPSA, SFTPB, SFTPD, SFTPC, SLC34A2, ABCA3, LAMP3, LPCAT1
Basophil/Mastmyeloid leukocyteKIT, CPA3, TPSAB1, HPGDS, VWA5A, MS4A2, HDC, CD44, GATA2, GRAP2
CD16+ MonocyteCD14-low, CD16-positive monocyteLST1, LILRB2, AIF1, COTL1, SAT1, FCN1, FCGR3A, RPS19, RHOC, IFITM2
CapillarycapillaryFCN3, EPAS1, RAMP3, CDH5, PODXL, BTNL9, NOSTRIN, FLNB, CDC42EP1, CD81
CD8 TCD8-positive, alpha-beta T cellCCL5, CD3D, NKG7, GZMH, CD3G, CD8A, GZMA, CD8B, RPS27, RPL34
Clubclub cellSCGB3A2, CYB5A, SFTPB, PIGR, C16orf89, CTSE, KIAA1324, CEACAM6, WFDC2, DSTN
Myofibroblastmyofibroblast cellCOL1A1, COL1A2, COL3A1, COL6A3, ASPN, LTBP1, ITGBL1, CALD1, POSTN, BGN
Plasmacytoid Dendriticplasmacytoid dendritic cellPPP1R14B, IRF4, GZMB, IL3RA, IRF7, PLD4, SEC61B, PTPRE, NPC2, TYROBP
Proliferating MacrophagemacrophageH2AFZ, CDK1, UBE2C, ANLN, BIRC5, NUSAP1, STMN1, TPX2, TYMS, KPNA2
Proliferating NK/TlymphocyteNUSAP1, TOP2A, HMGB2, BIRC5, H2AFV, SMC4, CENPF, AURKB, UBE2C, KIF2C
Bronchial Vesselbronchial epithelial cellPLVAP, ZNF385D, SPRY1, POSTN, SPARCL1, VWF, EMCN, COL15A1, INHBB, ENPP2
Mucousmucus secreting cellSCGB3A1, BPIFB1, SLPI, LCN2, WFDC2, SAA1, SCGB1A1, RARRES1, MUC5B, MSMB
VeinveinVWF, SELP, SLCO2A1, LIFR, PLA1A, PTPRB, PRSS23, CPE, TGM2, SRPX
Pericytepericyte cellCOX4I2, PDGFRB, TACC1, CALD1, NID1, COL4A1, COL4A2, LAMB1, LAMC3, CHN1
Smooth Musclesmooth muscle cellTPM2, ACTA2, MYL9, MYH11, CALD1, DSTN, CNN1, DES, PLN, CSRP1
ArteryarteryDKK2, PTPRB, EFNB2, EPAS1, GJA5, HEY1, ARGLU1, FBLN5, SEMA3G, BMX
Capillary Aerocytecapillary endothelial cellHPGD, APP, EDNRB, EMCN, ESAM, STXBP6, CLDN5, CYP3A5, SOSTDC1, TBX2
Capillary Intermediatecapillary endothelial cellEPAS1, SH3BP5, RALA, PECAM1, WWTR1, GALNT18, ACVRL1, SRSF11, VAT1, IPO7
LipofibroblastfibroblastWT1, STEAP1, MEDAG, OSR1, CPXM1, FGF7, CCDC71L, HAS1, C3, C7
Mesothelialmesothelial cellGALNT9, ITLN1, WT1, PRG4, MGARP, C3, ALDH1A3, DMKN, SLPI, DSC3
Platelet/Megakaryocytemyeloid cellTUBB1, CMTM5, ACRBP, PF4, GP9, TMEM40, ITGA2B, GRAP2, GP6, CABP5
Natural Killer Tmature NK T cellGNLY, CD7, CTSW, CCL5, CD2, ZFP36L2, CXCR4, LGALS1, CEBPB, S100A6
Fibromyocytesmooth muscle cellSCX, FAM150A, HSPB3, RAMP1, CSRP1, CNN1, CST5, IGF1, CLU, MET
Gobletgoblet cellS100P, FAM3D, CXCL17, GABRP, WFDC2, PSCA, AGR2, TXN, CLIC1, COX5A
IonocyteionocytePHGR1, ASCL3, HEPACAM2, FOXI1, TMPRSS11E, ATP6V1B1, BSND, TFF3, STAC2, MFSD6L
Neuroendocrineneuroendocrine cellPCSK1N, BEX1, SEC11C, CPE, NENF, PRDX2, CHGA, EGR1, FAM46A, SCGN
Serousserous secreting cellZG16B, LYZ, PRB4, PRB3, PRH2, PRR4, TCN1, LPO, PHB, TESC
annotation.l2
LabelOBO Ontology IDMarkers
Adventitial FibroblastfibroblastFBLN1, C3, CCDC80, DCN, SFRP2, IGFBP6, SCARA5, PIK3R1, LAMA2, USP53
Alveolar Epithelial Type 1type I pneumocyteEMP2, AGER, LMO7, GPRC5A, RTKN2, ARHGEF26, LAMA3, DST, SPOCK2, SCEL
Alveolar FibroblastfibroblastA2M, SCN7A, GPC3, ADH1B, MYH10, RARRES2, LUM, AOC3, C7, CFD
BB cellMS4A1, BANK1, LINC00926, CD79A, BLK, CD79B, CD22, SP140, VPREB3, ADAM28
CD4+ Memory/Effector TCD4-positive, alpha-beta T cellCD2, CD3D, CD96, IL7R, ITK, PTPRC, CD3E, MALAT1, PDCD4, GPR171
Ciliatedciliated cellRSPH1, FANK1, CDHR3, CAPS, C20orf85, FAM92B, MS4A8, MALAT1, ANKRD36C, SLCO3A1
Classical Monocyteclassical monocyteS100A9, S100A8, S100A12, VCAN, FCN1, MNDA, FPR1, SELL, ZFP36L2, MYO1F
Lymphaticlymphatic vesselCCL21, MMRN1, PROX1, PPFIBP1, TBX1, TFF3, PKHD1L1, IGFBP7, TIMP3, TFPI
MacrophagemacrophageACP5, MARCO, OLR1, APOC1, MSR1, VSIG4, CYP27A1, SLCO2B1, GPD1, ITGAX
Natural Killernatural killer cellNKG7, PRF1, KLRF1, CD247, GNLY, PYHIN1, KLRD1, TXK, SPON2, SH2D1B
Plasmaplasma cellMZB1, DERL3, SEC11C, XBP1, TNFRSF17, SSR4, POU2AF1, HSP90B1, PRDX4, MANF
Alveolar Epithelial Type 2type II pneumocyteNAPSA, SFTPD, ABCA3, SFTPA1, SFTPA2, SFTPB, SLC34A2, MAP7D1, GPRC5A, CLDN1
OLR1+ Classical Monocyteclassical monocyteIL1B, SOD2, CXCL8, G0S2, EREG, CCL20, SRGN, CXCL3, CXCL2, C15orf48
CapillarycapillaryFCN3, EPAS1, RAMP3, CDH5, PODXL, BTNL9, IL7R, CD81, ATP6V0B, THBD
Clubclub cellSCGB3A2, SFTPB, CYB5A, PIGR, C16orf89, CTSE, KIAA1324, CEACAM6, WFDC2, DSTN
Intermediate Monocyteintermediate monocyteCOTL1, LILRA2, ADGRE2, FCN1, FGR, LILRB2, AIF1, BACH1, TRABD, MFNG
Myeloid Dendritic Type 1myeloid dendritic cellCSF2RA, CCL22, CCR7, FSCN1, DAPP1, BIRC3, LAMP3, TXN, ID2, GSN
Myeloid Dendritic Type 2myeloid dendritic cellCD1C, HLA-DPB1, HLA-DPA1, HLA-DQA1, HLA-DQB1, HLA-DRA, FCER1A, IL2RG, CD1E, PKIB
Myofibroblastmyofibroblast cellCOL1A1, COL1A2, COL3A1, ASPN, LTBP1, COL6A3, ITGBL1, COL12A1, CTHRC1, TGFBI
Plasmacytoid Dendriticplasmacytoid dendritic cellPPP1R14B, IRF4, GZMB, IL3RA, IRF7, SMPD3, PLD4, PTPRE, NPC2, TYROBP
Proliferating MacrophagemacrophageH2AFZ, CDK1, UBE2C, ANLN, NUSAP1, RHEB, TYMS, TPX2, BIRC5, KPNA2
Proliferating NK/TlymphocyteNUSAP1, TOP2A, HMGB2, BIRC5, H2AFV, SMC4, CENPF, AURKB, UBE2C, KIF2C
Basalbasal cellKRT15, S100A2, KRT17, KRT5, KRT19, LAMB3, SFN, TNS1, CCND2, DST
Bronchial Vessel 1bronchial epithelial cellPLVAP, ZNF385D, POSTN, SPRY1, SPARCL1, VWF, EMCN, COL15A1, ENPP2, INHBB
CD8+ Naive Tnaive thymus-derived CD8-positive, alpha-beta T cellCCL5, CD3D, GZMA, NKG7, CD3E, GZMB, CD2, ITGB1, LGALS1, CLIC3
Mucousmucus secreting cellSCGB3A1, BPIFB1, LCN2, SLPI, WFDC2, SCGB1A1, SAA1, RARRES1, MUC5B, MSMB
VeinveinVWF, SELP, SLCO2A1, LIFR, PLA1A, PTPRB, PRSS23, C7, CPE, ACKR1
Airway Smooth Musclerespiratory system smooth muscleTPM2, DSTN, ACTA2, FLNA, MYH11, MYL9, PLN, CASQ2, KCNAB1, RERGL
EREG+ Dendriticdendritic cellAREG, PLAUR, MXD1, GPR183, EREG, CSF2RA, RAB31, HLA-DPB1, HLA-DQA1, HLA-DRA
Pericytepericyte cellCOX4I2, PDGFRB, CALD1, TACC1, COL4A1, NID1, COL4A2, LAMC3, PTN, KCNK3
ArteryarteryDKK2, PTPRB, EFNB2, EPAS1, GJA5, HEY1, ARGLU1, FBLN5, SEMA3G, BMX
Basophil/Mast 1myeloid leukocyteCPA3, KIT, HPGDS, TPSAB1, SLC18A2, MS4A2, RGS13, GNPTAB, KIF13B, HIPK2
Capillary Aerocytecapillary endothelial cellHPGD, APP, EDNRB, EMCN, ESAM, STXBP6, PRX, CYP3A5, SOSTDC1, TBX2
Capillary Intermediate 2capillary endothelial cellEPAS1, SH3BP5, WWTR1, RALA, PECAM1, GALNT18, ARHGAP29, VAT1, SRSF11, YWHAB
Bronchial Vessel 2bronchial epithelial cellTM4SF1, SOX17, SOCS3, EMP1, ITPRIP, ARID5A, ESAM, RGCC, CD200, LPAR6
IGSF21+ Dendriticdendritic cellFOLR2, MS4A6A, STAB1, F13A1, FCGR2A, C1QA, CTSB, LGMN, MAF, CCL13
Proliferating Basalbasal cellNMU, PTTG1, TOP2A, BIRC5, CENPF, TPX2, CKAP2, MKI67, HMGB2, CENPE
Nonclassical Monocytenon-classical monocyteLST1, AIF1, FCGR3A, LILRB2, BID, CTSS, COTL1, NAAA, SPN, LYPD2
CD8+ Memory/Effector TCD8-positive, alpha-beta T cellDUSP2, CCL5, CD8A, CST7, NKG7, CD3E, IL32, RPL34, IL7R, TC2N
CD4+ Naive Tnaive thymus-derived CD4-positive, alpha-beta T cellMAL, LTB, CCR7, SIRPG, NOSIP, LEF1, IL23A, TSHZ2, TSR1, ATF7IP2
Differentiating Basalbasal cellPERP, GPR87, AQP3, PROM2, RAB25, KRT19, BAG1, KRT7, XBP1, PLA2G10
LipofibroblastfibroblastWT1, STEAP1, FGF7, MEDAG, OSR1, CPXM1, CCDC71L, PTMA, DMKN, PPA1
Mesothelialmesothelial cellGALNT9, ITLN1, WT1, MGARP, PRG4, ALDH1A3, C3, C1S, SERPING1, GFPT2
Platelet/Megakaryocytemyeloid cellTUBB1, CMTM5, ACRBP, PF4, GP9, CABP5, ITGA2B, WRB, MAP3K7CL, GRAP2
TREM2+ Dendriticdendritic cellAPOE, CHIT1, PLA2G2D, SLAMF8, PLA2G7, LILRB4, CAPG, CSTB, PDXK, APOC1
Signaling Alveolar Epithelial Type 2type II pneumocyteSFTPC, SFTPA1, SFTPA2, NAPSA, SLC34A2, SFTPB, SELENBP1, SLPI, FABP5, ARC
Natural Killer Tmature NK T cellGNLY, CD7, CTSW, CCL5, CD2, ZFP36L2, CXCR4, LGALS1, DUSP4, S100A6
Capillary Intermediate 1capillary endothelial cellEDNRB, AQP1, HPGD, CNN3, HLA-E, CLDN5, TMEM204, FCN3, EDN1, VWF
Vascular Smooth Musclevascular associated smooth muscle cellREM1, TPM1, ACTA2, TAGLN, CALD1, NEXN, MYH11, FSTL1, THY1, CFH
Basophil/Mast 2myeloid leukocyteGPR65, SRGN, TNFRSF9, TPSAB1, CD69, BIRC3, GATA2, AREG, ICAM1, KDM6B
Fibromyocytesmooth muscle cellSCX, CNN1, FAM150A, PDLIM7, HSPB3, MYLK, RAMP1, SCUBE1, CSDC2, TBC1D10A
Gobletgoblet cellS100P, CXCL17, FAM3D, WFDC2, GABRP, LCN2, PSCA, C3, MSMB, ZG16B
IonocyteionocyteASCL3, HEPACAM2, FOXI1, TMPRSS11E, ATP6V1B1, BSND, TMEM61, SMIM11, PSMG1, BIK
Neuroendocrineneuroendocrine cellPCSK1N, BEX1, SEC11C, CPE, NENF, PRDX2, CHGA, EGR1, FAM46A, SCGN
Proximal Basalbasal cellSERPINB13, SERPINB4, KRT19, CLCA2, KRT5, PERP, ADH7, TSPAN8, SUSD4, CLCA4
Proximal Ciliatedciliated cellC1orf189, LINC01571, CALML4, CH17-340M24.3, AKAP14, CD24, HCG14, TP53AIP1, MRPL41, UCP2
Serousserous secreting cellZG16B, LYZ, PRB4, PRB3, PRH2, PRR4, TCN1, LPO, PHB, TESC