A Incomplete Summary of Immune Cell Markers from scRNA-Seq Literature
Systematic comparative analysis of single cell RNA-sequencing methods
Their cell type assignment is based on the difference between average expression of positive marker and average expression of negative markers.
Cell Type | Markers |
---|---|
CD4+ T cell | CD3D, CD3E, CD3G, TRAC, CD4, TCF7, CD27, IL7R(CD127), CD8A-, CD8B-, GNLY-, NKG7-, CST7- |
Cytotoxic T cell | CD3D, CD3E, CD3G, TRAC, CD8A, CD8B, GZMK, CCL5, NKG7, CD4-, FCER1G-(CD23-) |
B cell | CD19, MS4A1(CD20), CD79A, CD79B, MZB1, IGHD, IGHM |
NK cell | NCAM1(CD56), NKG7, KLRB1, KLRD1, KLRF1, KLRC1, KLRC2, KLRC3, KLRC4, FCGR3A(CD16), FCGR3B(CD16), FCER1G(CD23), ITGAL(CD11A), ITGAM(CD11B), CD3D-, CD3E-, CD3G-, CD14-, TRAC- |
CD14+ monocyte | VCAN, FCN1, S100A8, S100A9, S100A12, CD14, ITGAL, ITGAM, CSF3R, CSF1R, CX3CR1, TYROBP, LYZ, FCGR3A-, FCGR3B-, CD3D-, CD3E-, TRAC-, NKG7-, KLRB1-, KLRD1- |
CD16+ monocyte | FCN1, FCGR3A(CD16), FCGR3B(CD16), ITGAL(CD11A), ITGAM(CD11B), CSF3R(CD114), CSF1R(CD115), CX3CR1, CDKN1C, MS4A7, S100A8-, S100A9-, S100A12-, CD14-, CD3D-, CD3E-, CD3G-, TRAC-, NKG7-, KLRB1-, KLRD1- |
Dendritic cell | HLA-DPA1, HLA-DPB1, HLA-DQA1, ITGAX(CD11C), CD1C, CD1E, FCER1A, FCGR2B(CD32), CLEC10A(CD301), CD3D-, CD3E-, CD3G-, NCAM1-(CD56-), CD19-, CD14-, MS4A1-, CD79A-, CD79B- |
Plasmacytoid dendritic cell | IL3RA(CD123), GZMB, JCHAIN, IRF7, TCF4, LILRA4(CD85g), CLEC4C(CD303), ITGAX-(CD11C-), CD3D-, CD3E-, CD3G-, NCAM1-(CD56-), CD19-, CD14-, MS4A1-(CD20-), CD79A-, CD79B- |
Plasma cell | IGHA1, IGHA2, IGHG1, IGHG2, IGHG3, IGHG4, CD38, XBP1, CD27, SLAMF7(CD319), CD19-, MS4A1-(CD20-), CD3D-, CD3E-, CD3G- |
Megakaryocyte | PF4, PPBP, GP5(CD42d), ITGA2B(CD41), NRGN, TUBB1, SPARC, RGS18, MYL9, GNG11 |
Massively parallel digital transcriptional profiling of single cells
Citation: Zheng, G.X., et al. Nat Commun 2017;8:14049.
Platform: ~68K Human in 10X, and also bead-enriched sub-populations of PBMCs in V1 chemistry.
Cell Type | Markers |
---|---|
CD34+ cells | |
CD14+ Monocytes | |
CD19+ B cells | |
CD56+ NK cells | |
CD8+ Cytotoxic T cells | |
CD8+/CD45RA+ Naive Cytotoxic T cells | |
Cd4+/CD45RO+ Memory T cells | |
CD4+/CD45RA+/CD25- Naive T cells | |
CD4+/CD25+ Regulatory T cells | |
CD4+ Helper T |
Single-cell RNA sequencing unveils the shared and the distinct cytotoxic hallmarks of human TCRVdelta1 and TCRVdelta2 gammadelta T lymphocytes.
Citation: Pizzolato, G., et al. Proc Natl Acad Sci U S A 2019;116(24):11906-11915.
Platform: ~13K Human PBMC in 10x Genomics platform, including PBMC4K and PBMC8K by 3’ V2 chemistry in 10X’s website
Note: In their analysis, CD4 and CD8 can only be seperated with a higher resolution parameter, 0.6 -> 1.2
Cell Type | Markers |
---|---|
Intermediate monocytes | CD14-, LYZ, S100A9, FCGR3A |
Dendertic cells (DC) | LYZ, S100A9, FCER1A |
B cells | CD79A, CD79B, CD19 |
Naive and central memory CD4 T cells | CD3E, CD4, SELL, CD27 |
Naive and central memory CD8 T cells | CD3E, CD8A, SELL, CD27 |
Effector memory CD4 T cells | CD3E, CD4, CD27, PRF1, GNLY |
Effector memory CD8 T cells | CD3E, CD8A, CD27, PRF1, GNLY |
NK | CD3E-, NKG7 |
Seurat PBMC3K Tutorial
Platform: ~3K Human PBMC in 10X platform, may be in V1 chemistry
Cell Type | Markers |
---|---|
CD14+ Mono | CD14, LYZ |
FCGR3A+ Mono | FCGR3A(CD16), MS4A7 |
DC | FCER1A, CST3 |
B | MS4A1(CD20) |
Naive CD4+ T | IL7R(CD127), CCR7 |
Memory CD4+ T | IL7R(CD127), S100A4 |
CD8+ T | CD8A |
NK | GNLY, NKG7 |
Platelet | PPBP |
Garnett Human PBMC Classifiers
Platform: ~100K PBMC in 10X platform, from Zheng’s 2017 Nature Communication Paper.
https://www.biolegend.com/essential_markers
Cell Type | Markers |
---|---|
CD34+ | CD34, THY1(CD90), ENG, KIT(CD117), PROM1(CD133) |
Monocytes | CD14, FCGR1A(CD64), CD68, S100A12 |
Dendritic cells | IL3RA(CD123), CD1C, BATF3, THBD(CD141), CD209 |
B cells | CD19, MS4A1(CD20), CD79A |
T cells | CD3D, CD3E, CD3G |
CD4 T cells | CD4, FOXP3, IL2RA(CD25), IL7R(CD127) |
CD8 T cells | CD8A, CD8B |
NK cells | NCAM1(CD56), FCGR3A(CD16) |