ixxmu
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7 months ago 常用的细胞marker by 东林的扯淡小屋
library(data.table)canonical_markers <- list(Adipocyte = c('ADIPOQ', 'FABP4', 'LEP'),Astrocyte = c('GFAP', 'GJA1'),B_cell = c('MS4A1', 'CD79A', 'CD79B'),Basophil = c('CCR3', 'IL3RA'),Dendritic = c('CCR7', 'CD86', 'CLEC10A'),Endothelial = c('VWF', 'CDH5', 'CLEC14A', 'CLDN5', 'ADGRL4'),Epithelial = c('EPCAM', 'KRT19', 'KRT7', 'MUC1'),Erythrocyte = c('HBA1', 'HBA2', 'HBB'),Fibroblast = c('COL1A1', 'COL1A2', 'COL3A1', 'LUM'),Immune = 'PTPRC',Keratinocyte = c('FLG', 'IVL', 'LORICRIN'),Lymphovascular = c('CCL21', 'TFF3'),Macrophage = c('AIF1', 'CD14', 'CD163'),Mast = c('CPA3', 'MS4A2', 'TPSB2'),Melanocyte = c('DCT', 'MLANA', 'PMEL', 'TYR', 'TYRP1'),Monocyte = c('CCR2', 'CSF1R'),Myocyte = c('ACTA1', 'DES', 'MYL1', 'TTN', 'NEB'),Neuron = c('ENO2', 'RBFOX3'),Neutrophil = c('AZU1', 'CTSG', 'ELANE', 'MPO'),NK_cell = c('NKG7', 'KLRD1', 'GZMB', 'KLRF1'),Oligodendrocyte = c('TF', 'PLP1', 'CLDN11', 'MAG', 'MBP', 'MOG'),OPC = c('OLIG1', 'OLIG2', 'NEU4'),Pericyte = c('RGS5', 'ESAM', 'MEF2C'),Plasma = c('JCHAIN', 'MZB1', 'TNFRSF17'),T_cell = c('CD2', 'CD3D', 'CD3E'))canonical_markers <- rbindlist(lapply(names(canonical_markers), function(ct) data.table(cell_type = ct, gene = canonical_markers[[ct]])))fwrite(canonical_markers, 'canonical_markers.csv')
参考链接：
https://github.com/tiroshlab/3ca/blob/main/canonical_markers.R
pdf("细胞类型注释_patient1-B123.pdf")#T细胞 CD2,CD3D,TRAC,TRBC2FeaturePlot(object = YDL, reduction = "tsne",pt.size = 1.5,features = c("CD2","CD3D","TRAC","TRBC2"),cols = c("gray", "red"))#actin#Plasma细胞：JCHAIN,MZB1,CD79A,IGHG1FeaturePlot(object = YDL, reduction = "tsne",pt.size = 1.5,features = c("JCHAIN","MZB1","CD79A","IGHG1"),cols = c("gray", "red"))#actin#Mononuclear phagocytes：LYZ,CD14,VCAN,C1QA,CD68,CDCFeaturePlot(object = YDL, reduction = "tsne",pt.size = 1.5,features = c("LYZ","CD14","VCAN","CD68","CDC"),cols = c("gray", "red"))#actinFeaturePlot(object = YDL, reduction = "tsne",pt.size = 1.5,features = c("LYZ","CD14","VCAN","C1QA","CD68","CDC"),cols = c("gray", "red"))#actin#Erythrocytes：HBB,HBA1,ALAS2,SNCA,CA1FeaturePlot(object = YDL, reduction = "tsne",pt.size = 1.5,features = c("HBB","HBA1","ALAS2","SNCA"),cols = c("gray", "red"))#actinFeaturePlot(object = YDL, reduction = "tsne",pt.size = 1.5,features = c("HBB","HBA1","ALAS2","SNCA","CA1"),cols = c("gray", "red"))#actin#Neutrophils：CSF3R,CXCR2,FCGR3BFeaturePlot(object = YDL, reduction = "tsne",pt.size = 1.5,features = c("CSF3R","CXCR2","FCGR3B"),cols = c("gray", "red"))#actin#Fibroblasts：DCN,COL1A1,COL1A2FeaturePlot(object = YDL, reduction = "tsne",pt.size = 1.5,features = c("DCN","COL1A1","COL1A2"),cols = c("gray", "red"))#actin#Epithelial cells：EPCAM,CLDN4,CLDN7,TFF3,REG4FeaturePlot(object = YDL, reduction = "tsne",pt.size = 1.5,features = c("EPCAM","CLDN4","CLDN7","TFF3","REG4"),cols = c("gray", "red"))#actin#Granulocytes-monocyte progenitor cells：LYZ,MPO,AZU1,ELANEFeaturePlot(object = YDL, reduction = "tsne",pt.size = 1.5,features = c("LYZ","MPO","AZU1","ELANE"),cols = c("gray", "red"))#actin#Platelets：PPBP,TUBB1,PF4FeaturePlot(object = YDL, reduction = "tsne",pt.size = 1.5,features = c("PPBP","TUBB1","PF4"),cols = c("gray", "red"))#actin#Mast cells：TPSAB1,TPSB2,CPA3FeaturePlot(object = YDL, reduction = "tsne",pt.size = 1.5,features = c("TPSAB1","TPSB2","CPA3"),cols = c("gray", "red"))#actin#Basophils：CLC,GATA2,CPA3FeaturePlot(object = YDL, reduction = "tsne",pt.size = 1.5,features = c("CLC","GATA2","CPA3"),cols = c("gray", "red"))#actindev.off()saveRDS(YDL,"patient1-B123.rds")# 癌细胞：SERPINB3、TP63、CDKN2A、KRT15# 柱状上皮细胞：MUC5B、WFDC2# 平滑肌细胞高表达MYH11、MYLK、ACTG2、COL3A1和COL1A1# 成纤维细胞：COL3A1和COL1A1、LAMA2# 内皮细胞：EMCN、FLT1和EGFLT# 单核细胞（ITGAX、MX4A7）# T细胞（CD3E、CD247）# 浆细胞（MZB1、IGKC）# 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)#T cells (CD2, CD3D), fibroblasts (LUM), macrophages (AIF1, CD68), ductal cells (KRT19), endothelial cells (CDH5), stellate cells (RGS5), acinar cells (PRSS1), B cells (MS4A1), plasma cells (MZB1), mast cells (CPA3), neutrophils (G0S2, S100A8), schwann cells (GAP43), and endocrine cells (CHGA) (Fig. 1B).#参考文献：https://www.sciencedirect.com/science/article/pii/S0304383522003184?via%3DihubFeaturePlot(object = YDL, reduction = "tsne",pt.size = 1.5,features = c("Cd2","Cd3d","Trac","Trbc2"),cols = c("gray", "red"))#actinFeaturePlot(object = YDL, reduction = "tsne",pt.size = 1.5,features = c("Lum"),cols = c("gray", "red"))#actinFeaturePlot(object = YDL, reduction = "tsne",pt.size = 1.5,features = c("Aif1","Cd68"),cols = c("gray", "red"))#actinFeaturePlot(object = YDL, reduction = "tsne",pt.size = 1.5,features = c("Krt19"),cols = c("gray", "red"))#actinFeaturePlot(object = YDL, reduction = "tsne",pt.size = 1.5,features = c("Cdh5"),cols = c("gray", "red"))#actinFeaturePlot(object = YDL, reduction = "tsne",pt.size = 1.5,features = c("Rgs5"),cols = c("gray", "red"))#actin#We characterized the identities of cell types of these groups based on expression of known markers:#AMBP, CFTR, MMP7 (ductal cell 1),38#KRT19, KRT7, TSPAN8, SLPI (ductal cell 2),38,39,68–71#PRSS1, CTRB1, CTRB2, REG1B (acinar),38,69,71#CHGB, CHGA, INS, IAPP (endocrine cell),38,72,73#RGS5, ACTA2, PDGFRB, ADIRF (stellate cell),38,74,75#LUM, DCN, COL1A1 (fibroblast),33,76#CDH5, PLVAP, VWF, CLDN5 (endothelial cell),#AIF1, CD64, CD14, CD68 (macrophage),78–80#CD3D, CD3E, CD4, CD8 (T cell),79,81#MS4A1, CD79A, CD79B, CD52 (B cell).82–84#Sub-clustering of T cells, macrophages, B cells and fibroblasts were further performed with the same approach. In addition, subclusters of T cells without expression of either CD4 or CD8A and subclusters of macrophages without expression of known myeloid markers CD68 and FCER1G were excluded from further analysis.FeaturePlot(object = YDL, reduction = "tsne",pt.size = 1.5,features = c("Ambp","Cftr","Mmp7"),cols = c("gray", "red"))#actinFeaturePlot(object = YDL, reduction = "tsne",pt.size = 1.5,features = c("Krt19","Krt7","Tspan8","Slpi"),cols = c("gray", "red"))#actinFeaturePlot(object = YDL, reduction = "tsne",pt.size = 1.5,features = c("Chgb","Chga","Ins","Iapp"),cols = c("gray", "red"))#actinFeaturePlot(object = YDL, reduction = "tsne",pt.size = 1.5,features = c("Rgs5","Acta2","Pdgfrb","Adirf"),cols = c("gray", "red"))#actinFeaturePlot(object = YDL, reduction = "tsne",pt.size = 1.5,features = c("Lum","Dcn","Col1a1"),cols = c("gray", "red"))#actinFeaturePlot(object = YDL, reduction = "tsne",pt.size = 1.5,features = c("Cdh5","Plvap","Vwf","Cldn5"),cols = c("gray", "red"))#actinFeaturePlot(object = YDL, reduction = "tsne",pt.size = 1.5,features = c("Aif1","Cd64","Cd14","Cd68"),cols = c("gray", "red"))#actinFeaturePlot(object = YDL, reduction = "tsne",pt.size = 1.5,features = c("Cd3d","Cd3e","Cd4","Cd8a"),cols = c("gray", "red"))#actinFeaturePlot(object = YDL, reduction = "tsne",pt.size = 1.5,features = c("Ms4a1","Cd79a","Cd79b","Cd52"),cols = c("gray", "red"))#actin#Alpha cell Normal Hhex, Ins1, Ins2, Nkx6-1, Pax6, Pdx1, SstFeaturePlot(object = YDL, reduction = "tsne",pt.size = 1.5,features = c("Hhex","Ins1","Ins2","Nkx6-1","Pax6","Pdx1","Sst"),cols = c("gray", "red"))#actinFeaturePlot(object = YDL, reduction = "tsne",pt.size = 1.5,features = c("Hhex","Ins1","Ins2","Nkx6-1","Pax6","Pdx1"),cols = c("gray", "red"))#actin#Mouse Pancreas Epithelial cell Normal LectinFeaturePlot(object = YDL, reduction = "tsne",pt.size = 1.5,features = c("Lectin"),cols = c("gray", "red"))#actin# Mouse Pancreas Duct cell Normal CAII# Mouse Pancreas Pancreatic ductal cell Normal CK7FeaturePlot(object = YDL, reduction = "tsne",pt.size = 1.5,features = c("Ck7"),cols = c("gray", "red"))#actin# Mouse Pancreas Beta cell Normal GLUT2, Ngn3, Pdx1# Mouse Pancreatic islet Beta cell Normal Mafa# Mouse Pancreatic islet Beta cell Normal Par6FeaturePlot(object = YDL, reduction = "tsne",pt.size = 1.5,features = c("Mafa"),cols = c("gray", "red"))#actin
小鼠常用的marker：
#T cells (CD2, CD3D), fibroblasts (LUM), macrophages (AIF1, CD68), ductal cells (KRT19), endothelial cells (CDH5), stellate cells (RGS5), acinar cells (PRSS1), B cells (MS4A1), plasma cells (MZB1), mast cells (CPA3), neutrophils (G0S2, S100A8), schwann cells (GAP43), and endocrine cells (CHGA) (Fig. 1B).#参考文献：https://www.sciencedirect.com/science/article/pii/S0304383522003184?via%3DihubFeaturePlot(object = YDL, reduction = "tsne",pt.size = 1.5,features = c("Cd2","Cd3d","Trac","Trbc2"),cols = c("gray", "red"))#actinFeaturePlot(object = YDL, reduction = "tsne",pt.size = 1.5,features = c("Lum"),cols = c("gray", "red"))#actinFeaturePlot(object = YDL, reduction = "tsne",pt.size = 1.5,features = c("Aif1","Cd68"),cols = c("gray", "red"))#actinFeaturePlot(object = YDL, reduction = "tsne",pt.size = 1.5,features = c("Krt19"),cols = c("gray", "red"))#actinFeaturePlot(object = YDL, reduction = "tsne",pt.size = 1.5,features = c("Cdh5"),cols = c("gray", "red"))#actinFeaturePlot(object = YDL, reduction = "tsne",pt.size = 1.5,features = c("Rgs5"),cols = c("gray", "red"))#actin#T cells (CD2, CD3D), fibroblasts (LUM), macrophages (AIF1, CD68), ductal cells (KRT19), endothelial cells (CDH5), stellate cells (RGS5), acinar cells (PRSS1), B cells (MS4A1), plasma cells (MZB1), mast cells (CPA3), neutrophils (G0S2, S100A8), schwann cells (GAP43), and endocrine cells (CHGA) (Fig. 1B).#参考文献：https://www.sciencedirect.com/science/article/pii/S0304383522003184?via%3DihubFeaturePlot(object = YDL, reduction = "tsne",pt.size = 1.5,features = c("Cd2","Cd3d","Trac","Trbc2"),cols = c("gray", "red"))#actinFeaturePlot(object = YDL, reduction = "tsne",pt.size = 1.5,features = c("Lum"),cols = c("gray", "red"))#actinFeaturePlot(object = YDL, reduction = "tsne",pt.size = 1.5,features = c("Aif1","Cd68"),cols = c("gray", "red"))#actinFeaturePlot(object = YDL, reduction = "tsne",pt.size = 1.5,features = c("Krt19"),cols = c("gray", "red"))#actinFeaturePlot(object = YDL, reduction = "tsne",pt.size = 1.5,features = c("Cdh5"),cols = c("gray", "red"))#actinFeaturePlot(object = YDL, reduction = "tsne",pt.size = 1.5,features = c("Rgs5"),cols = c("gray", "red"))#actin#KRASFeaturePlot(object = YDL, reduction = "tsne",pt.size = 1.5,features = c("Kras"),cols = c("gray", "red"))#actinFeaturePlot(object = YDL,split.by = "process", reduction = "tsne",pt.size = 1.5,features = c("Kras"),cols = c("gray", "red"))#actinFeaturePlot(object = YDL,split.by = "process", reduction = "tsne",pt.size = 1.5,features = c("Gsdmd"),cols = c("gray", "red"))#actinFeaturePlot(object = YDL,split.by = "orig.ident", reduction = "tsne",pt.size = 1.5,features = c("Gsdmd"),cols = c("gray", "red"))#actinFeaturePlot(object = YDL, reduction = "tsne",pt.size = 1.5,features = c("Gsdmd"),cols = c("gray", "red"))#actin#acinar cells (PRSS1)FeaturePlot(object = YDL, reduction = "tsne",pt.size = 1.5,features = c("Prss1"),cols = c("gray", "red"))#actin#mast cells (CPA3)FeaturePlot(object = YDL, reduction = "tsne",pt.size = 1.5,features = c("Cpa3"),cols = c("gray", "red"))#actin#neutrophils (G0S2, S100A8)FeaturePlot(object = YDL, reduction = "tsne",pt.size = 1.5,features = c("G0s2","S100a8"),cols = c("gray", "red"))#actin#schwann cells (GAP43)FeaturePlot(object = YDL, reduction = "tsne",pt.size = 1.5,features = c("Gap43"),cols = c("gray", "red"))#actin# endocrine cells (CHGA)FeaturePlot(object = YDL, reduction = "tsne",pt.size = 1.5,features = c("Chga"),cols = c("gray", "red"))#actinpdf("细胞类型注释_patient.pdf")#T细胞 CD2,CD3D,TRAC,TRBC2FeaturePlot(object = YDL, reduction = "tsne",pt.size = 1.5,features = c("Cd2","Cd3d","Trac","Trbc2"),cols = c("gray", "red"))#actin#Plasma细胞：JCHAIN,MZB1,CD79A,IGHG1FeaturePlot(object = YDL, reduction = "tsne",pt.size = 1.5,features = c("Jchain","Mzb1","Cd79a","Ighg1"),cols = c("gray", "red"))#actin#Mononuclear phagocytes：LYZ,CD14,VCAN,C1QA,CD68,CDCFeaturePlot(object = YDL, reduction = "tsne",pt.size = 1.5,features = c("LYZ","CD14","VCAN","CD68","CDC"),cols = c("gray", "red"))#actinFeaturePlot(object = YDL, reduction = "tsne",pt.size = 1.5,features = c("LYZ","CD14","VCAN","C1QA","CD68","CDC"),cols = c("gray", "red"))#actin#Erythrocytes：HBB,HBA1,ALAS2,SNCA,CA1FeaturePlot(object = YDL, reduction = "tsne",pt.size = 1.5,features = c("HBB","HBA1","ALAS2","SNCA"),cols = c("gray", "red"))#actinFeaturePlot(object = YDL, reduction = "tsne",pt.size = 1.5,features = c("HBB","HBA1","ALAS2","SNCA","CA1"),cols = c("gray", "red"))#actin#Neutrophils：CSF3R,CXCR2,FCGR3BFeaturePlot(object = YDL, reduction = "tsne",pt.size = 1.5,features = c("CSF3R","CXCR2","FCGR3B"),cols = c("gray", "red"))#actin#Fibroblasts：DCN,COL1A1,COL1A2FeaturePlot(object = YDL, reduction = "tsne",pt.size = 1.5,features = c("Dcn","Col1a1","Col1a2"),cols = c("gray", "red"))#actin#Epithelial cells：EPCAM,CLDN4,CLDN7,TFF3,REG4FeaturePlot(object = YDL, reduction = "tsne",pt.size = 1.5,features = c("EPCAM","CLDN4","CLDN7","TFF3","REG4"),cols = c("gray", "red"))#actin#Granulocytes-monocyte progenitor cells：LYZ,MPO,AZU1,ELANEFeaturePlot(object = YDL, reduction = "tsne",pt.size = 1.5,features = c("Lyz","Mpo","Azu1","Elane"),cols = c("gray", "red"))#actin#Platelets：PPBP,TUBB1,PF4FeaturePlot(object = YDL, reduction = "tsne",pt.size = 1.5,features = c("Ppbp","Tubb1","Pf4"),cols = c("gray", "red"))#actin#Mast cells：TPSAB1,TPSB2,CPA3FeaturePlot(object = YDL, reduction = "tsne",pt.size = 1.5,features = c("TPSAB1","TPSB2","CPA3"),cols = c("gray", "red"))#actin#Basophils：CLC,GATA2,CPA3FeaturePlot(object = YDL, reduction = "tsne",pt.size = 1.5,features = c("Clc","Gata2","CPA3"),cols = c("gray", "red"))#actinFeaturePlot(object = YDL, reduction = "tsne",pt.size = 1.5,features = c("CD3D","KLRF1","CD79A","COL1A1","CLDN5","LILRA4","TPSAB1","LYZ","EPCAM"),cols = c("gray", "red"))#actin#T/NK cells:3,4,7,9FeaturePlot(object = YDL, reduction = "tsne",pt.size = 1.5,features = c("Cd3e"),cols = c("gray", "red"))#actin#Macrophages:13FeaturePlot(object = YDL, reduction = "tsne",pt.size = 1.5,features = c("Cd68"),cols = c("gray", "red"))#actin#Endothelial cells:1FeaturePlot(object = YDL, reduction = "tsne",pt.size = 1.5,features = c("Dcn"),cols = c("gray", "red"))#actin#Fibroblasts:2,5,8FeaturePlot(object = YDL, reduction = "tsne",pt.size = 1.5,features = c("CD3E"),cols = c("gray", "red"))#actin#B cells:20FeaturePlot(object = YDL, reduction = "tsne",pt.size = 1.5,features = c("Cd79a"),cols = c("gray", "red"))#actin#Epithelial cells:10FeaturePlot(object = YDL, reduction = "tsne",pt.size = 1.5,features = c("Epcam"),cols = c("gray", "red"))#actin#Mast cells:16FeaturePlot(object = YDL, reduction = "tsne",pt.size = 1.5,features = c("Ms4a2"),cols = c("gray", "red"))#actin#Plasma cells:21,22FeaturePlot(object = YDL, reduction = "tsne",pt.size = 1.5,features = c("Mzb1"),cols = c("gray", "red"))#actin#Neutrophils:15FeaturePlot(object = YDL, reduction = "tsne",pt.size = 1.5,features = c("Csf3r"),cols = c("gray", "red"))#actin#Smooth muscle cells:2,14FeaturePlot(object = YDL, reduction = "tsne",pt.size = 1.5,features = c("Actg2"),cols = c("gray", "red"))#actindev.off()
https://mp.weixin.qq.com/s/m0mm8HyLV2U-FctV4Mrpug