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)
Written on February 7, 2020