Azimuth References
Human - Bone Marrow
Overview
Modalities: RNA, ATAC bridge
Cells in Reference: 297,627
Species: Human
Reference Dataset(s): [Oetjen et al., 2018], [Granja, Klemm, McGinnis, et al. 2019], [Human Cell Atlas Immune Cell Census]
Demo Dataset(s): Stuart et al., Cell 2019 [Seurat Object]
This reference consists of 297,627 bone marrow cells from 39 donors and 3 different studies: Oetjen et al., 2018, Granja, Klemm, McGinnis, et al. 2019, and the Human Cell Atlas Immune Cell Census. All samples, which were generated using 10x Genomics v2, were integrated together and used to define a reference UMAP visualization and list of cell type annotations.
Annotation Details
celltype.l2(detailed)
| Label | Label | OBO Ontology ID | Markers |
|---|---|---|---|
| ASDC | AXL+ Dendritic Cell | dendritic cell | AXL,SCT,LILRA4,PPP1R14A,TGFBI,UPK3A,SCN9A,CLEC10A,PROC,PLD4 |
| BaEoMa | Basophil Eosinophil Mast Progenitor | basophil mast progenitor cell | HDC,MS4A2,TPSAB1,TPSB2,CLC,CPA3,MS4A3,IL1RL1,PRG2,HPGDS |
| CD14 Mono | CD14 Monocyte | CD14-positive monocyte | FOLR3,CLEC4E,MCEMP1,RBP7,CDA,FPR1,CD300E,C5AR1,CD93,APOBEC3A |
| CD16 Mono | CD16 Monocyte | CD14-low, CD16-positive monocyte | LYPD2,VMO1,TPPP3,C1QA,C5AR1,CD300E,GPBAR1,LILRA1,HES4,APOBEC3A |
| CD4 Effector | CD4 Effector | effector CD4-positive, alpha-beta T cell | TNFRSF4,AQP3,TNFRSF25,MAL,IL7R,TRAT1,RORA,FLT3LG,KLRB1,CD6 |
| CD4 Memory | CD4 Memory | CD4-positive, alpha-beta memory T cell | MAL,TRAT1,AP3M2,CAMK4,AQP3,IL7R,RCAN3,BCL11B,LEF1,FLT3LG |
| CD4 Naive | CD4 Naive | naive thymus-derived CD4-positive, alpha-beta T cell | TSHZ2,MAL,CCR7,CAMK4,LEF1,BCL11B,FHIT,RCAN3,SH3YL1,PIK3IP1 |
| CD8 Effector 1 | CD8 Effector 1 | effector CD8-positive, alpha-beta T cell | CRTAM,IFNG,CD8A,XCL1,GZMK,TIGIT,CCL4L2,CD8B,CD160,XCL2 |
| CD8 Effector 2 | CD8 Effector 2 | effector CD8-positive, alpha-beta T cell | ZNF683,PRSS23,KLRC2,FCRL6,S1PR5,GZMH,FGFBP2,PATL2,TRGC2,CD3G |
| CD8 Effector 3 | CD8 Effector 3 | effector CD8-positive, alpha-beta T cell | GZMK,CD160,CD8A,KLRB1,LAG3,CCL4,XCL2,GZMM,XCL1,CCL3 |
| CD8 Memory | CD8 Memory | CD8-positive, alpha-beta memory T cell | CD8B,CD8A,GZMK,IL7R,BCL11B,CD3E,PIK3IP1,CD6,TRAC,SPOCK2 |
| CD8 Naive | CD8 Naive | naive thymus-derive CD8-positive, alpha-beta T cell | NELL2,CD8B,S100B,TRABD2A,CCR7,OXNAD1,FLT3LG,MAL,LEF1,CAMK4 |
| cDC1 | Conventional Dendritic Cell 1 | CD141-positive myeloid dendritic cell | IDO1,XCR1,TACSTD2,CLEC9A,WFDC21P,CLNK,CADM1,DNASE1L3,BATF3,LGALS2 |
| cDC2 | Conventional Dendritic Cell 2 | CD1c-positive myeloid dendritic cell | ENHO,CLEC10A,CD1C,IL13RA1,PLBD1,LGALS2,CD33,IGSF6,IFI30,FCER1A |
| CLP | Common Lymphoid Progenitor | common lymphoid progenitor | ACY3,PRSS2,C1QTNF4,SPINK2,SMIM24,NREP,CD34,DNTT,FLT3,SPNS3 |
| Early Eryth | Early Erythroid | erythroid lineage cell | CNRIP1,GATA2,ITGA2B,TFR2,GATA1,KLF1,CYTL1,MAP7,FSCN1,APOC1 |
| EMP | Erythroid Megakaryocyte Progenitor | megakaryocyte-erythroid progenitor cell | MYCT1,CRHBP,NPR3,AVP,GATA2,HPGDS,CYTL1,CRYGD,IGSF10,PBX1 |
| GMP | Granulocyte Monocyte Progenitor | granulocyte monocyte progenitor cell | SERPINB10,RNASE3,MS4A3,PRTN3,ELANE,AZU1,CTSG,RNASE2,RETN,NPW |
| HSC | Hematopoeitic Stem Cell | hematopoeitic stem cell | CRHBP,AVP,MYCT1,BEX1,NPR3,CRYGD,MSRB3,CD34,NPDC1,MLLT3 |
| ILC | Innate Lymphoid Cell | mature natural killer cell | LDB2,CD160,XCL2,KLRB1,XCL1,KLRF1,KLRD1,KLRC1,TRDC,GZMM |
| Late Eryth | Late Erythroid | erythroid lineage cell | CTSE,TSPO2,IFIT1B,TMEM56,RHCE,RHAG,SPTA1,ADD2,EPCAM,HBG1 |
| LMPP | Lymphoid Primed Multipotent Progenitor | hematopoeitic multipotent progenitor cell | AVP,CRHBP,C1QTNF4,BEX1,NPR3,CD34,NPW,SMIM24,CSF3R,NPDC1 |
| Macrophage | Macrophage | macrophage | SPIC,FABP3,CD5L,CCL18,C1QC,C1QB,FABP4,C1QA,APOE,SELENOP |
| MAIT | Mucosal associated invariant T | mucosal invariant T cell | KLRB1,IL7R,TNFRSF25,SPOCK2,RORA,NCR3,GZMK,KLRG1,TRGC2,CD6 |
| Memory B | Memory B | memory B cell | FCRL2,TNFRSF13B,ARHGAP24,PNOC,FCER2,FCRLA,BLK,HLA-DOB,MS4A1,TNFRSF13C |
| Naive B | Naive B | naive B cell | FCRL2,FCRL1,ARHGAP24,FCRL5,FCER2,FCRLA,PAX5,CD19,HLA-DOB,CD22 |
| NK | Natural Killer | CD16-positive, CD56-dim natural killer cell, human | SH2D1B,PRSS23,S1PR5,LAIR2,KLRC1,PTGDR,FGFBP2,FCRL6,TBX21,KLRC2 |
| NK CD56+ | Natural Killer CD56+ | CD16-negative, CD56-bright natural killer cell, human | SPTSSB,NCAM1,KLRC1,XCL1,IL18RAP,XCL2,IL2RB,KLRF1,TNFRSF18,KLRD1 |
| NK Proliferating | Proliferating Natural Killer | mature natural killer cell | GZMA,GZMB,TRDC,PRF1,TYMS,FGFBP2,KLRF1,CD247,GZMH,CCL4 |
| pDC | Plasmacytoid Dendritic Cell | plasmacytoid dendritic cell | ASIP,CLEC4C,SCAMP5,PROC,PTCRA,SCT,SHD,PPM1J,LILRA4,LRRC26 |
| Plasma | Plasma | plasma cell | SDC1,IGLC6,IGLV6-57,TNFRSF17,IGLV3-1,TNFRSF13B,IGLC7,JSRP1,FCRL5,IGKV1-5 |
| Platelet | Platelet | platelet | RGS18,C2orf88,TMEM40,GP9,PF4,PPBP,DAB2,SPARC,RUFY1,F13A1 |
| pre B | Precursor B | precursor B cell | NPY,LCN6,RAG2,HMHB1,ARPP21,AKAP12,RAG1,C10orf10,CYGB,SLC8A1-AS1 |
| pre-mDC | Precursor Myeloid Dendritic Dell | common dendritic progenitor | ENHO,CLEC10A,RNASE2,PLBD1,FCER1A,IGSF6,MNDA,SAMHD1,ALDH2,PAK1 |
| pre-pDC | Precursor Plasmacytoid Dendritic Cell | immature CD11c-negative plasmacytoid dendritic cell | SCT,SHD,LILRA4,LILRB4,PTPRS,TNNI2,PLD4,SPIB,IRF8,TNFRSF21 |
| pro B | Progenitor B | pro-B cell | CYGB,UMODL1,EBF1,MME,VPREB1,DNTT,IGLL1,UHRF1,BLNK,AGPS |
| Prog Mk | Progenitor Megakaryocyte | megakaryocyte progenitor cell | CLEC1B,SPX,WFDC1,ANXA3,CMTM5,SELP,RBPMS2,ARHGAP6,GP9,LTBP1 |
| Stromal | Stromal | stromal cell | IGFBP5,CP,TF,DCN,LUM,COL1A2,CRH,TNC,SPARCL1,BMP5 |
| T proliferating | Proliferating T | T cell | RRM2,MKI67,BIRC5,LCK,SH2D1A,CLSPN,CDT1,TK1,TOP2A,TRAC |
| transitional B | Transitional B | transitional stage B cell | BMP3,CFAP73,ARPP21,IGLC5,APBB2,HRK,DTX1,AKAP12,IGLC6,MME |
celltype.l1
| Label | Expanded Label | OBO Ontology ID | Markers |
|---|---|---|---|
| B | B | lymphocyte of B lineage | FCRL1,FCRL2,CD22,ARHGAP24,BANK1,MS4A1,RALGPS2,CD37,SWAP70,CD79A |
| CD4 T | CD4 T | CD4-positive, alpha-beta T cell | MAL,LEF1,IL7R,TCF7,LTB,LEPROTL1,CD3E,CD3D,CD3G,CD27 |
| CD8 T | CD8 T | CD8-positive, alpha-beta T cell | CD8B,CD8A,NELL2,CD3D,CD3E,S100B,GZMH,CD3G,TRGC2,CCL5 |
| DC | Dendritic Cell | dendritic cell | CLEC4C,PROC,SCT,SCN9A,SHD,PPM1J,ENHO,CLEC10A,LILRA4,DNASE1L3 |
| HSPC | Hematopoeitic stem and progenitor cell | hematopoietic precursor cell | ARPP21,CFAP73,AVP,SPTA1,EPCAM,RHCE,AKAP12,RHAG,C1QTNF4,CYTL1 |
| Mono | Monocyte | monocyte | LYPD2,FOLR3,CLEC4E,LILRA1,CDA,RBP7,CD300LF,FPR1,CD93,MTMR11 |
| NK | Natural Killer | mature NK cell | NCR1,SH2D1B,KLRC1,PRSS23,CD160,B3GNT7,IL2RB,IL18RAP,XCL1,KLRF1 |
| Other T | Other T | T cell | SLC4A10,KLRB1,IL7R,TNFRSF25,RORA,SPOCK2,MAF,GZMK,ZFP36L2,LYAR |