细胞类型鉴定--单细胞marker基因（持续修正）

细胞类型	marker基因
T Cells	CD3D, CD3E
Th	CD3D, CD3E, CD40LG
Tc	CD3D, CD3E, CD8A, CD8B
gdT	TRDV2, TRGV9
B cells	CD19, CD79A, CD79B, MS4A1 [CD20]
Plasma cells	IGHG1, MZB1, SDC1, CD79A
Monocytes and DCs	CST3, LYZ
Monocytes and macrophages	CST3, LYZ, CD68, CD163, CD14
NK Cells	FGFBP2, FCG3RA, CX3CR1, GNLY, NKG7, TYOBP, PRF1
Neutrophils	CST3, LYZ, FCGR3B, CSF3R
Photoreceptor cells	RCVRN
Megakaryocytes	CST3, PF4, PPBP
Fibroblasts	FGF7, MME
Endothelial cells	PECAM1, VWF
epi or tumor	EPCAM, KRT18, KRT19, PROM1, ALDH1A1, CD24
immune	CD45,PTPRC
epithelial/cancer	EpCAM+,EPCAM
stromal	CD10+,MME,fibo or CD31+,PECAM1,endo
mast cell	CST3, KIT, CPA3
RBC	HBA1, HBA2, HBB, HBD, HBE1, HBG1, HBG2, HBM, HBQ1, HBZ（用于细胞过滤）

文献：dropClust: efficient clustering of ultra-large scRNA-seq data

Potential cell type	Markers
Naive T cells	CD27, CCR7, CD8A, CD8B
CD4+ memory cells	IL7R, CD27, CCR7
NKT cells	ZNF683, CD8A, CD8B
B cells	CD79A, CD37
CD8+ T cells	GZMK, CD8A, CD8B
NK cells	CD160, NKG7, GNLY, CD247, CCL3, GZMB
CD16+ and CD14+ monocytes	CD68, CD16(FCGR3A), CD14, S100A12
Regulatory T cells	CCR10, CD25(IL2RA), CD52, CMTM7, FOXP3
Monocyte derived dendritic cells	CST3, CD1C, FCER1A
Megakaryocyte progenitors	PF4, PPBP, PLA2G12A
Progenitor-NK cells	ID2
Plasmacytoid dendritic cells	GZMB, CD123(IL3RA)

library(ggplot2) 
genes_to_check = c('PTPRC', 'CD3D', 'CD3E', 'CD8A','CD19', 'CD79A', 'MS4A1' ,
                   'IGHG1', 'MZB1', 'SDC1',
                   'CD68', 'CD163', 'CD14', 
                   'RCVRN',
                   'FGF7','MME',
                   'PECAM1', 'VWF', 
                   'EPCAM' , 'KRT19', 'PROM1', 'ALDH1A1' )
library(stringr)  
p <- DotPlot(sce.all, features = genes_to_check,
             assay='RNA'  )  + coord_flip()

p
ggsave(plot=p, filename="check_marker_by_seurat_cluster.pdf")

张泽民老师的文章里对各类细胞的注释极为详细，可以参考。

出自Single-Cell Analyses Inform Mechanisms of Myeloid- Targeted Therapies in Colon Cancer

出自COVID-19 immune features revealed by a large-scale single-cell transcriptome atlas

亚群细分时不必拘泥于现有分类，可以使用marker基因来对细胞群命名，后续查看这些细胞群是否有生物学意义。

PBMC的注释：

文献：Temporally integrated single cell RNA sequencing analysis of PBMC from experimental and natural primary human DENV-1 infections

文献：A single-cell map for the transcriptomic signatures of peripheral blood mononuclear cells in end-stage renal disease

文献：Single-cell RNA sequencing reveals the sustained immune cell dysfunction in the pathogenesis of sepsis secondary to bacterial pneumonia

• 先分大群

T/NK cells (CD3D+ IL32+ NKG7+), myeloid cells (CD14+ FCGR3A+ S100A9+) and B cells (CD79B+ CD79A+ IGHM+)

• 再细分亚群