T细胞marker
CD4+ T cell：CD3E+ CD4+
CD4+ naive T cell：CCR7+ 、SELL+、CD5、HLA-
CD4+ memory T cell：CD44、IFNG、S100A4+、GPR183+
CD4+ effector T cell：CD4、FASLG、 IFNG、CD44hi、FAS
CD4+ Th1：IL-2（IL2）、IFN-γ(IFNG)
CD4+ Th2：IL-4(IL4)、IL-5(IL5)、IL-13(IL13)
CD4+ Th17：IL-17(IL17A)、IL-22(IL22)
CD4+ Th9：IL-9(IL9)、
CD4+ Th22：IL-22(IL22)
CD4+ Tfh：CXCR5(CXCR5)、ICOS(ICOS)、PD-1(PDCD1)、IL-21(IL21)、Bcl-6(BCL6)
CD4+ regulatory T (Treg) cell ：FOXP3+、IL2RA+
CD8+ T cell：CD3E+ CD8A+
CD8+ naïve：CCR7+ SELL+
CD8+ effector ：CD8A 、FASLG、 CD44、 FAS
γδT cell ：TRGV9+、TRDV2+
# T Cells (CD3D, CD3E, CD8A),
# B cells (CD19, CD79A, MS4A1 [CD20]),
# Plasma cells (IGHG1, MZB1, SDC1, CD79A),
# Monocytes and macrophages (CD68, CD163, CD14),
# NK Cells (FGFBP2, FCG3RA, CX3CR1),
# Photoreceptor cells (RCVRN),
# Fibroblasts (FGF7, MME),
# Endothelial cells (PECAM1, VWF).
# epi or tumor (EPCAM, KRT19, PROM1, ALDH1A1, CD24).
# immune (CD45+,PTPRC), epithelial/cancer (EpCAM+,EPCAM),
# stromal (CD10+,MME,fibo or CD31+,PECAM1,endo)
各类白细胞百分比为：
中性粒细胞60～70％，
嗜酸性粒细胞0.5～5％，
嗜碱性粒细胞0～1％，
淋巴细胞20～40％，
单核细胞3～8％。
# mast cells, TPSAB1 and TPSB2
# B cell, CD79A and MS4A1 (CD20)
# naive B cells, such as MS4A1 (CD20), CD19, CD22, TCL1A, and CD83,
# plasma B cells, such as CD38, TNFRSF17 (BCMA), and IGHG1/IGHG4
genes_to_check = c('CD3D','MS4A1','CD79A',
'CD19', 'CD22', 'TCL1A', 'CD83', # naive B cells
'CD38','TNFRSF17','IGHG1','IGHG4', # plasma B cells,
'TPSAB1' , 'TPSB2', # mast cells,
'PTPRC' )
colnames(sce@meta.data)
p <- DotPlot(sce, features = genes_to_check,
assay='RNA' ,group.by = "RNA_snn_res.0.1" ) + coord_flip()
p
genes_to_check = c('PTPRC', 'CD3D', 'CD3E', 'CD4','CD8A',
'CCR7', 'SELL' , 'TCF7','CXCR6' , 'ITGA1',
'FOXP3', 'IL2RA', 'CTLA4','GZMB', 'GZMK','CCL5',
'IFNG', 'CCL4', 'CCL3' ,
'PRF1' , 'NKG7')
colnames(sce@meta.data)
p <- DotPlot(sce, features = genes_to_check,
assay='RNA' ,group.by = "CCA_snn_res.0.1" ) + coord_flip()
p
# epi or tumor (EPCAM, KRT19, PROM1, ALDH1A1, CD24).
# - alveolar type I cell (AT1; AGER+)
# - alveolar type II cell (AT2; SFTPA1)
# - secretory club cell (Club; SCGB1A1+)
# - basal airway epithelial cells (Basal; KRT17+)
# - ciliated airway epithelial cells (Ciliated; TPPP3+)
genes_to_check = c( 'EPCAM' , 'KRT19', 'PROM1', 'ALDH1A1' ,
'AGER','SFTPA1','SCGB1A1','KRT17','TPPP3',
'KRT4','KRT14','KRT8','KRT18',
'CD3D','PTPRC' )
colnames(sce@meta.data)
p <- DotPlot(sce, features = genes_to_check,
assay='RNA' ,group.by = "RNA_snn_res.0.1" ) + coord_flip()
p
cell marker
