Human - PBMC

Overview

Modalities: RNA, ADT, ATAC bridge

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

Label	Expanded Label	OBO Ontology ID	Markers
Mono	Monocyte	monocyte	CTSS, FCN1, NEAT1, LYZ, PSAP, S100A9, AIF1, MNDA, SERPINA1, TYROBP
CD4 T	CD4+ T cell	CD4-positive, alpha-beta T cell	IL7R, MAL, LTB, CD4, LDHB, TPT1, TRAC, TMSB10, CD3D, CD3G
CD8 T	CD8+ T cell	CD8-positive, alpha-beta T cell	CD8B, CD8A, CD3D, TMSB10, HCST, CD3G, LINC02446, CTSW, CD3E, TRAC
NK	natural killer cell	natural killer cell	NKG7, KLRD1, TYROBP, GNLY, FCER1G, PRF1, CD247, KLRF1, CST7, GZMB
B	B cell	mature B cell	CD79A, RALGPS2, CD79B, MS4A1, BANK1, CD74, TNFRSF13C, HLA-DQA1, IGHM, MEF2C
other T	other T cell	mature T cell	CD3D, TRDC, GZMK, KLRB1, NKG7, TRGC2, CST7, LYAR, KLRG1, GZMA
DC	dendritic cell	dendritic cell	CD74, HLA-DPA1, HLA-DPB1, HLA-DQA1, CCDC88A, HLA-DRA, HLA-DMA, CST3, HLA-DQB1, HLA-DRB1

celltype.l2 (default)

Label	Expanded Label	OBO Ontology ID	Markers
B intermediate	Intermediate B cell	mature B cell	MS4A1, TNFRSF13B, IGHM, IGHD, AIM2, CD79A, LINC01857, RALGPS2, BANK1, CD79B
B memory	Memory B cell	memory B cell	MS4A1, COCH, AIM2, BANK1, SSPN, CD79A, TEX9, RALGPS2, TNFRSF13C, LINC01781
B naive	Naive B cell	naive B cell	IGHM, IGHD, CD79A, IL4R, MS4A1, CXCR4, BTG1, TCL1A, CD79B, YBX3
Plasmablast	Plasmablast	plasmablast	IGHA2, MZB1, TNFRSF17, DERL3, TXNDC5, TNFRSF13B, POU2AF1, CPNE5, HRASLS2, NT5DC2
CD4 CTL	CD4+ Cytotoxic T	CD4-positive, alpha-beta cytotoxic T cell	GZMH, CD4, FGFBP2, ITGB1, GZMA, CST7, GNLY, B2M, IL32, NKG7
CD4 Naive	CD4+ Naive T	naive thymus-derived CD4-positive, alpha-beta T cell	TCF7, CD4, CCR7, IL7R, FHIT, LEF1, MAL, NOSIP, LDHB, PIK3IP1
CD4 Proliferating	CD4+ Proliferating T	activated CD4-positive, alpha-beta T cell	MKI67, TOP2A, PCLAF, CENPF, TYMS, NUSAP1, ASPM, PTTG1, TPX2, RRM2
CD4 TCM	CD4+ Central Memory T	CD4-positive, alpha-beta memory T cell	IL7R, TMSB10, CD4, ITGB1, LTB, TRAC, AQP3, LDHB, IL32, MAL
CD4 TEM	CD4+ Effector Memory T	effector CD4-positive, alpha-beta T cell	IL7R, CCL5, FYB1, GZMK, IL32, GZMA, KLRB1, TRAC, LTB, AQP3
Treg	Regulatory T	regulatory T cell	RTKN2, FOXP3, AC133644.2, CD4, IL2RA, TIGIT, CTLA4, FCRL3, LAIR2, IKZF2
CD8 Naive	CD8+ Naive T	naive thymus-derived CD8-positive, alpha-beta T cell	CD8B, S100B, CCR7, RGS10, NOSIP, LINC02446, LEF1, CRTAM, CD8A, OXNAD1
CD8 Proliferating	CD8+ Proliferating T	activated CD8-positive, alpha-beta T cell	MKI67, CD8B, TYMS, TRAC, PCLAF, CD3D, CLSPN, CD3G, TK1, RRM2
CD8 TCM	CD8+ Central Memory T	CD8-positive, alpha-beta memory T cell	CD8B, ANXA1, CD8A, KRT1, LINC02446, YBX3, IL7R, TRAC, NELL2, LDHB
CD8 TEM	CD8+ Effector Memory T	effector CD8-positive, alpha-beta T cell	CCL5, GZMH, CD8A, TRAC, KLRD1, NKG7, GZMK, CST7, CD8B, TRGC2
ASDC	AXL+ Dendritic Cell	dendritic cell	PPP1R14A, LILRA4, AXL, IL3RA, SCT, SCN9A, LGMN, DNASE1L3, CLEC4C, GAS6
cDC1	Conventional Dendritic Cell 1	CD141-positive myeloid dendritic cell	CLEC9A, DNASE1L3, C1orf54, IDO1, CLNK, CADM1, FLT3, ENPP1, XCR1, NDRG2
cDC2	Conventional Dendritic Cell 2	CD1c-positive myeloid dendritic cell	FCER1A, HLA-DQA1, CLEC10A, CD1C, ENHO, PLD4, GSN, SLC38A1, NDRG2, AFF3
pDC	Plasmacytoid Dendritic Cell	plasmacytoid dendritic cell	ITM2C, PLD4, SERPINF1, LILRA4, IL3RA, TPM2, MZB1, SPIB, IRF4, SMPD3
CD14 Mono	CD14+ Monocyte	CD14-positive, CD16-negative classical monocyte	S100A9, CTSS, S100A8, LYZ, VCAN, S100A12, IL1B, CD14, G0S2, FCN1
CD16 Mono	CD16+ Monocyte	CD14-low, CD16-positive monocyte	CDKN1C, FCGR3A, PTPRC, LST1, IER5, MS4A7, RHOC, IFITM3, AIF1, HES4
NK	CD56-dim Natural Killer	CD16-positive, CD56-dim natural killer cell, human	GNLY, TYROBP, NKG7, FCER1G, GZMB, TRDC, PRF1, FGFBP2, SPON2, KLRF1
NK Proliferating	Proliferating Natural Killer	natural killer cell	MKI67, KLRF1, TYMS, TRDC, TOP2A, FCER1G, PCLAF, CD247, CLSPN, ASPM
NK_CD56bright	CD56-bright Natural Killer	CD16-negative, CD56-bright natural killer cell, human	XCL2, FCER1G, SPINK2, TRDC, KLRC1, XCL1, SPTSSB, PPP1R9A, NCAM1, TNFRSF11A
Eryth	Erythroid cell	erythroid lineage cell	HBD, HBM, AHSP, ALAS2, CA1, SLC4A1, IFIT1B, TRIM58, SELENBP1, TMCC2
HSPC	Hematopoietic stem and progenitor cell	hematopoietic precursor cell	SPINK2, PRSS57, CYTL1, EGFL7, GATA2, CD34, SMIM24, AVP, MYB, LAPTM4B
ILC	Innate Lymphoid Cell	innate lymphoid cell	KIT, TRDC, TTLL10, LINC01229, SOX4, KLRB1, TNFRSF18, TNFRSF4, IL1R1, HPGDS
Platelet	Platelet	platelet	PPBP, PF4, NRGN, GNG11, CAVIN2, TUBB1, CLU, HIST1H2AC, RGS18, GP9
dnT	Double-negative T	CD4-negative, CD8-negative, alpha-beta intraepithelial T cell	PTPN3, MIR4422HG, NUCB2, CAV1, DTHD1, GZMA, MYB, FXYD2, GZMK, AC004585.1
gdT	gamma-delta T	gamma-delta T cell	TRDC, TRGC1, TRGC2, KLRC1, NKG7, TRDV2, CD7, TRGV9, KLRD1, KLRG1
MAIT	Mucosal associated invariant T	mucosal invariant T cell	KLRB1, NKG7, GZMK, IL7R, SLC4A10, GZMA, CXCR6, PRSS35, RBM24, NCR3

celltype.l3

Label	Expanded Label	OBO Ontology ID	Markers
ASDC_mDC	AXL+ myeloid dendritic cell	myeloid dendritic cell	AXL, LILRA4, SCN9A, CLEC4C, LTK, PPP1R14A, LGMN, SCT, IL3RA, GAS6
ASDC_pDC	AXL+ plasmacytoid dendritic cell	plasmacytoid dendritic cell	LILRA4, CLEC4C, SCT, EPHB1, AXL, PROC, LRRC26, SCN9A, LTK, DNASE1L3
B intermediate kappa	Intermediate B cell, kappa light chain	mature B cell	MS4A1, IGKC, IGHM, LINC01857, MARCKS, IGHD, TNFRSF13B, CD24, FCRL2, BANK1
B intermediate lambda	Intermediate B cell, lambda light chain	mature B cell	MS4A1, IGLC2, IGHM, CD79A, IGLC3, IGHD, BANK1, TNFRSF13C, CD22, TNFRSF13B
B memory kappa	Memory B cell, kappa light chain	memory B cell	BANK1, IGKC, LINC01781, MS4A1, SSPN, CD79A, RALGPS2, TNFRSF13C, LINC00926
B memory lambda	Memory B cell, lambda light chain	memory B cell	BANK1, IGLC2, MS4A1, IGLC3, COCH, TNFRSF13C, IGHA2, BLK, TNFRSF13B, LINC01781
B naive kappa	Naive B cell, kappa light chain	naive B cell	IGHM, TCL1A, IGHD, IGHG3, CD79A, IL4R, CD37, MS4A1, IGKC
B naive lambda	Naive B cell, lambda light chain	naive B cell	IGHM, IGLC2, IGHD, IGLC3, CD79A, CXCR4, MS4A1, IL4R, TCL1A, CD79B
CD14 Mono	CD14+ Monocyte	CD14-positive, CD16-negative classical monocyte	S100A9, CTSS, LYZ, CTSD, S100A8, VCAN, CD14, FCN1, S100A12, MS4A6A
CD16 Mono	CD16+ Monocyte	CD14-low, CD16-positive monocyte	LST1, YBX1, AIF1, FCGR3A, NAP1L1, MS4A7, FCER1G, TCF7L2, COTL1, CDKN1C
CD4 CTL	CD4+ Cytotoxic T	CD4-positive, alpha-beta cytotoxic T cell	GZMH, CD4, GNLY, FGFBP2, IL7R, S100A4, GZMA, CST7, IL32, CCL5
CD4 Naive	CD4+ Naive T	naive thymus-derived CD4-positive, alpha-beta T cell	TCF7, CD4, NUCB2, LDHB, TRAT1, SARAF, FHIT, LEF1, CCR7, IL7R
CD4 Proliferating	CD4+ Proliferating T	activated CD4-positive, alpha-beta T cell	MKI67, TYMS, PCLAF, TOP2A, CENPF, NUSAP1, CENPM, BIRC5, ZWINT, TPX2
CD4 TCM_1	CD4+ Central Memory T_1	CD4-positive, alpha-beta memory T cell	LTB, CD4, FYB1, IL7R, LIMS1, MAL, TMSB4X, TSHZ2, AP3M2, TRAC
CD4 TCM_2	CD4+ Central Memory T_2	CD4-positive, alpha-beta memory T cell	CTLA4, MIR4435-2HG, TMSB4X, CD28, CDCA7, TMSB10, MAF, ITM2A, TRAC, CD27
CD4 TCM_3	CD4+ Central Memory T_3	CD4-positive, alpha-beta memory T cell	IL7R, ITGB1, LTB, S100A4, AQP3, TNFRSF4, IL32, TOB1, PDE4D, HOPX
CD4 TEM_1	CD4+ Effector Memory T_1	effector CD4-positive, alpha-beta T cell	GZMK, IL7R, IL32, ITGB1, CCL5, GZMA, B2M, DUSP2, KLRB1, SYNE2
CD4 TEM_2	CD4+ Effector Memory T_2	effector CD4-positive, alpha-beta T cell	GZMK, CD4, TIGIT, IFNG-AS1, CD40LG, MALAT1, CD3G, CD3D, TRAC, CD3E
CD4 TEM_3	CD4+ Effector Memory T_3	effector CD4-positive, alpha-beta T cell	IL7R, CCL5, NOSIP, KLRB1, SERINC5, AQP3, ITGA4, IL32, TRAC, LTB
CD4 TEM_4	CD4+ Effector Memory T_4	effector CD4-positive, alpha-beta T cell	CCR9, KDF1, DPP4, CD244, SLC4A4, KLRB1, TMIGD2, CD40LG, IL7R, ODF2L
CD8 Naive	CD8+ Naive T	naive thymus-derived CD8-positive, alpha-beta T cell	CD8B, LDHB, LEF1, LINC02446, CD8A, S100B, ID2, TCF7, VIM, CCR7
CD8 Naive_2	CD8+ Naive T_2	naive thymus-derived CD8-positive, alpha-beta T cell	CD8B, CCR5, CHI3L2, SOX4, CD8A, TNFRSF9, CD38, SIRPG, LRRN3, LEF1
CD8 Proliferating	CD8+ Proliferating T	activated CD8-positive, alpha-beta T cell	PCLAF, CD8B, TYMS, CD3D, CLSPN, CD3G, MKI67, TRAC, CHEK1, TK1
CD8 TCM_1	CD8+ Central Memory T_1	CD8-positive, alpha-beta memory T cell	CD8B, SELL, CD8A, LYAR, ITGB1, NELL2, DUSP2, IL7R, CCL5, LINC01871
CD8 TCM_2	CD8+ Central Memory T_2	CD8-positive, alpha-beta memory T cell	CD8B, C1orf162, IL7R, GATA3, YBX3, KRT1, CD8A, CTSW, INPP4B, LTB
CD8 TCM_3	CD8+ Central Memory T_3	CD8-positive, alpha-beta memory T cell	CD8B, KLRB1, CD8A, HOPX, IL7R, KLRD1, CCL5, SCML4, LINC02446, TRAC
CD8 TEM_1	CD8+ Effector Memory T_1	effector CD8-positive, alpha-beta T cell	GZMK, CD8B, CD8A, CCL5, NKG7, DUSP2, CST7, IL32
CD8 TEM_2	CD8+ Effector Memory T_2	effector CD8-positive, alpha-beta T cell	CD8A, CMC1, CD8B, CD160, GZMH, CST7, KLRD1, CCL5, TIGIT, KLRG1
CD8 TEM_3	CD8+ Effector Memory T_3	effector CD8-positive, alpha-beta T cell	GZMK, CD8A, ITGB1, CD8B, HOPX, CCL5, KLRD1, NKG7, GNLY, YBX3
CD8 TEM_4	CD8+ Effector Memory T_4	effector CD8-positive, alpha-beta T cell	GZMH, THEMIS, GNLY, CD8A, ITGB1, FGFBP2, CD2, GZMB, KLRD1, CD8B
CD8 TEM_5	CD8+ Effector Memory T_5	effector CD8-positive, alpha-beta T cell	GZMH, GNLY, ZNF683, TRAC, KLRC2, TYROBP, CD8B, CD8A, TRGC2, GZMB
CD8 TEM_6	CD8+ Effector Memory T_6	effector CD8-positive, alpha-beta T cell	TRGC2, CD8A, IFNG-AS1, CD8B, ZNF683, KLRC2, NCR3, IKZF2, DUSP2, RTKN2
cDC1	Conventional Dendritic Cell 1	CD141-positive myeloid dendritic cell	WDFY4, C1orf54, CLEC9A, BATF3, CLNK, TSPAN33, FLT3, CADM1, IDO1, DNASE1L3
cDC2_1	Conventional Dendritic Cell 2_1	CD1c-positive myeloid dendritic cell	FCER1A, CD14, CLEC10A, CTSS, ENHO, CD1C, MRC1, FCGR2B, PID1, IL13RA1
cDC2_2	Conventional Dendritic Cell 2_2	CD1c-positive myeloid dendritic cell	FCER1A, BASP1, CD1C, CD74, CLEC10A, HLA-DPA1, ENHO, HLA-DPB1, PLD4, HLA-DQA1
dnT_1	Double-negative T_1	CD4-negative, CD8-negative, alpha-beta intraepithelial T cell	GZMK, NUCB2, CD8B, GPR183, TCF7, LYAR, MALAT1, C12orf57, LEF1, LDHB
dnT_2	Double-negative T_2	CD4-negative, CD8-negative, alpha-beta intraepithelial T cell	AC004585.1, GPR183, FXYD2, NUCB2, CAV1, CD27, MYB, TMSB4X, GZMK, FGFR1
Eryth	Erythroid cell	erythroid lineage cell	HBM, ALAS2, HBD, AHSP, SLC4A1, TRIM58, SELENBP1, CA1, IFIT1B, SNCA
gdT_1	gamma-delta T_1	gamma-delta T cell	TRDC, TRGC1, TRGV9, TRDV2, KLRD1, IL7R, KLRC1, DUSP2, GNLY, KLRG1
gdT_2	gamma-delta T_2	gamma-delta T cell	KLRC2, CD3G, KIR3DL2, CD3D, TRDC, TRDV1, ZNF683, KLRC1, TRGC1, GZMH
gdT_3	gamma-delta T_3	gamma-delta T cell	RTKN2, TRDC, TRGC2, LEF1, IKZF2, SOX4, ZNF331, ARID5B, NUCB2, CRTAM
gdT_4	gamma-delta T_4	gamma-delta T cell	TRDC, TIGIT, KLRC2, TRGC2, IKZF2, GCSAM, FCRL6, TRDV1, CST7, CMC1
HSPC	Hematopoietic stem and progenitor cell	hematopoietic precursor cell	CDK6, SOX4, PRSS57, AC084033.3, ANKRD28, FAM30A, MYB, EGFL7, SPINK2, SMIM24
ILC	Innate Lymphoid Cell	innate lymphoid cell	KIT, TRDC, IL1R1, SOX4, TNFRSF18, TYROBP, TNFRSF4, FCER1G, IL2RA, GATA3
MAIT	Mucosal associated invariant T	mucosal invariant T cell	KLRB1, NKG7, GZMK, SLC4A10, NCR3, CTSW, IL7R, KLRG1, CEBPD, DUSP2
NK Proliferating	Proliferating Natural Killer	natural killer cell	STMN1, KLRF1, TYMS, FCER1G, PCNA, TYROBP, CLSPN, TRDC, PCLAF, SMC2
NK_1	CD56-dim Natural Killer_1	CD16-positive, CD56-dim natural killer cell, human	FGFBP2, KLRC2, GNLY, S100A4, CD3E, CST7, LGALS1, PRF1, NKG7, GZMB
NK_2	CD56-dim Natural Killer_2	CD16-positive, CD56-dim natural killer cell, human	NKG7, FCER1G, PRF1, KLRB1, SPON2, GZMB, FGFBP2, IGFBP7, CST7, B2M
NK_3	CD56-dim Natural Killer_3	CD16-positive, CD56-dim natural killer cell, human	KLRF1, CCL5, TRDC, SYNE2, KLRC1, CMC1, XCL2, KLRB1, KLRD1, IL2RB
NK_4	CD56-dim Natural Killer_4	CD16-positive, CD56-dim natural killer cell, human	XCL2, SELL, XCL1, GZMK, KLRC1, SPTSSB, KLRF1, IL2RB, TCF7, TRDC
NK_CD56bright	CD56-bright Natural Killer	CD16-negative, CD56-bright natural killer cell, human	XCL2, GPR183, SELL, IL2RB, CD44, GZMK, KLRF1, TPT1, KLRC1, XCL1
pDC	Plasmacytoid Dendritic Cell	plasmacytoid dendritic cell	CCDC50, UGCG, TCF4, LILRA4, IRF8, IL3RA, PLD4, IRF7, SERPINF1, ITM2C
Plasma	Plasma cell	plasma cell	MZB1, JCHAIN, TNFRSF17, ITM2C, DERL3, TXNDC5, POU2AF1, IGHA1, TXNDC11, CD79A
Plasmablast	Plasmablast	plasmablast	TYMS, TNFRSF17, SHCBP1, TK1, KNL1, ASPM, TXNDC5, TPX2, RRM2, BIRC5
Platelet	Platelet	platelet	GNG11, PPBP, NRGN, PF4, CAVIN2, TUBB1, HIST1H2AC, PRKAR2B, CLU, F13A1
Treg Memory	Memory Regulatory T	regulatory T cell	RTKN2, B2M, TIGIT, FCRL3, S100A4, AC133644.2, CTLA4, FOXP3, IKZF2, TRAC
Treg Naive	Naive Regulatory T	regulatory T cell	RTKN2, LEF1, FOXP3, C12orf57, IL2RA, TOMM7, CCR7, TRAC, CD4, LDHB

Azimuth References

Human - PBMC

Annotation Details