单细胞所具备的结构层次_单细胞基因组测序

最近做单细胞分群，总结一下我自己查文献查到的各种组织有哪些细胞，这些细胞的marker gene 是什么。注意这些都是mice中的哦！
推荐两个网站：
CellMarker
http://biocc.hrbmu.edu.cn/CellMarker/
panglaodb
https://panglaodb.se/index.html

一、bladder 膀胱

bladder genes_EC = c("Pecam1", "CD31") #endothelial cells  genes_IC = c("Cd14")#immune cells genes_BEC = c("Epcam","Upk3a","Upk1b")# bladder epithelial cells genes_UIC = c("Grhl3")#umbrella or intermediate cells genes_BC = c("Krt5"," Krt14")# basal cells genes_BC = c("Dcn"," Car3","Scara5")# mesenchymal cells  
  

二、spleen脾脏

spleen genes_B = c("Cd79a", "Ccr2", "Cd19", "Cd45r") genes_T = c("Cd3g") genes_macrophage = c("Itgam", "Fcer1g", "C1qa") genes_Granulocytes=c("Cd11b", "Ly6C", "SiglecF", "Cd49b", "Cd193") genes_Dendritic_cells=c("Cd11c", "MHCII", "XCR1") genes_NKC=c("NKp46")#Natural killer cells  
  

下面是cell 文献Mapping the Mouse Cell Atlas by Microwell-Seq中MCA网站中的细胞类型和marker gene

genes_B = c("Jchain","Iglv2","Ighm")#B cell genes_Dendritic = c("S100a4","Ffar2","Plbd1")#Dendritic cell genes_Erythroid = c("Hba-a1","Car2","Hbb-bs")#Erythroid cell genes_Macrophage = c("C1qc","Hmox1")#Macrophage genes_Marginal = c("Ighd","Ly6d")#Marginal zone B cell genes_Monocyte = c("Lyz2","Ifitm3")#Monocyte  genes_NK = c("Gzma","Klra8")#NK cell genes_Neutrophil = C("Ngp","Camp","S100a8",'S100a9')#Neutrophil genes_PDC = c("Siglech","Bst2")#Plasmacytoid dendritic cell genes_T = c("Trac","Trbc2")#T cell  
  
 
  
 
   
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三、large_intestine大肠

large_intestine genes_EC=c("Krt20", "Slc26a3")#enterocytes genes_GC=c("Atoh1", "Spdef")#goblet cells genes_PTC=c("(Dclk1")#proximal tuft cells genes_CC=c("Chga", "Chgb")#chromaffin cells genes_PSC=c("Lgr5", "Mki67")#Proliferating stem cells  
  
 
  
 
   
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四、tongue舌头

tongue genes_CC=c("Top2a", "Cdc20", "Mki67")#cell cycle related genes genes_BC=c("Krt14", "Krt5", "Krt15")#Basal cells genes_HPC=c("Top2a", "Cdc20", "Mki67")#highly proliferative cells genes_SBC=c("Krt10","Sbsn)")#suprabasal  
  
 
  
 
   
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五、skin皮肤

skin genes_OBC=c("Dkk3")#Outer bulge cells  genes_IBC=c("Fgf18")#Inner bulge cells  genes_ADSC=c("Top2a")#Actively dividing stem cells genes_SC=c("Krt14")#Stem cells genes_BP=c("Krt10")#Bifferentiated progeny genes_HF=c("CD34", "ITGA6").#HF outer bulge stem cells#(CD34high, ITGA6high)  
  
 
  
 
   
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下面是cell 文献Mapping the Mouse Cell Atlas by Microwell-Seq中MCA网站中的细胞类型和marker gene

genes_Adipocyte = c("Retn","Mgst1","Cyp2f2","Car3","Bcat2")#Adipocyte  genes_BAT = c("Cidea","Aco2","mt-Nd5","Cox6a1","Ndufa4","Gm44386")#Brown adipose tissue genes_DM = c("Cd74","Pf4","H2-Aa","Lyz2")#Dermal macrophage genes_Dividing = c("Ube2c","Tuba1b","Birc5",'Pclaf')#Dividing cell genes_Endothelial = c("Cldn5","Tm4sf1","Aqp1")#Endothelial cell  genes_Erythroid = c("Cox5b","S100a1","Gpx3")#Erythroid cell genes_FSMC = c("Tnnc2","Acta1","Mylpf")#Fast skeletal muscle cell genes_Keratinocyte = c("Lgals7","Fxyd3","Perp","Sfn")#Keratinocyte genes_LVEC = c("Lyve1","Mmrn1")#Lymphatic vessel endothelial cell genes_Macrophage = c("Coro1a"," Stfa1")#Macrophage genes_Mast = c("Cma1","Serpinb1a")#Mast cell genes_Melanocyte = c("Dct","Pmel")#Melanocyte  genes_Neuron = c("Mbp","Egfl8")# Neuron genes_Neutrophil = c("S100a9","Ngp")#Neutrophil genes_Osteoblast = c("Ppic","Dlk1","Lum","Wls")#Osteoblast genes_Smooth = c("Lrrc15","Acta2","Myl9")#Smooth muscle genes_Stromal = c("Rnase4","Gas6","Ly6a","Apod")#Stromal cell  
  
 
  
 
    
  
 
  
 
   
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六、diaphragm膈肌

diaphragm genes_MSC= c("Pax7", "Pax3", "Myod1", "Myf5") #muscle stem cell genes genes_FAP = c("Pdgfra") #fibro-adipogenic progenitors genes_EC = c("Pecam1") #endothelial cells genes_BT = c("Cd19", "Cd3d") #B and T cells genes_MC = c("Itgam", "Fcer1g", "C1qa") #macrophages  
  
 
  
 
   
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七、heart 心脏

heart genes_VEC = c("Fabp4", "Cdh5","Cav1") #vascular endothelial cells genes_FC = c("Ddr2","Tcf21","Col3a1","Col1a2","Col1a1") #fibroblasts genes_CC = c( "Nppa", "Myl7","Sln") # cardiomyocytes  genes_EC = c("Npr3", "Pecam1", "Cd14") #endocardial cells genes_IC = c("C1qa","H2-Eb1") #immune cells  genes_MMC = c( "Myh11")#myofibroblasts/smooth muscle cells "Tcf21"  
  
 
  
 
   
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八、livers 肝脏

livers genes_PC=c("Cyp2e1", "Glul", "Oat", "Gulo")#PC hepatocytes genes_PP=c("Cyp2f2", "Pck1", "Hal", "Cdh1")#periportal PP hepatocytes genes_ML=c("Ass1", "Hamp", "Gstp1", "Ubb")# midlobular (ML) hepatocytes genes_EC=c("Pecam1", "Nrp1", "Kdr", "Oit3")#endothelial cells genes_KC=c("Emr1", "Clec4f", "Cd68", "Irf7")#Kupffer cells genes_NKC=c("Zap70", "Il2rb", "Nkg7", "Cxcr6", "Gzma")#NK/NKT cells genes_BC=c("Cd79a", "Cd79b", "Cd74", "Cd19")#B cells genes_check=c("Alb", "Ttr", "Apoa1", "Serpina1c")#hepatocytes  
  
 
  
 
   
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九、lungs 肺

lungs genes_IM=c("Csf1r", "MHCII")#interstitial macrophages genes_AMC=c("Marco", "Itgax", "Mrc1")#Alveolar macrophages genes_LDC=c("Cd24a", "Cd68")#lung dendritic cells genes_IMC=c("Itgam", "Ly6c2", "Cd14")#invading monocytes genes_IC=c("Cxcr4", "Cx3cr1")#immune clusters  
  
 
  
 
   
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十、muscle 肌肉

muscle genes_VEC = c("Fabp4", "Cdh5", "Cav1") #vascular endothelial cells genes_FC = c("Ddr2","Tcf21", "Col3a1", "Col1a2", "Col1a1") #fibroblasts genes_AC = c("Nppa", "Myl7", "Sln") #"Nppa", "Myl7" not found #atrial cardiomyocytes genes_EC = c("Npr3", "Pecam1") #endocardial cells genes_IC = c("C1qa", "H2-Eb1") #immune cells genes_SMSC= c("Myf5", "Myod1","Sox9","Acta2","Chodl") #skeletal muscle satellite cell genes_MSC= c("Pdgfra","Chad") #mesenchymal stem cell genes_endothelialC=c("Atxn1") genes_TmB = c('Ptprc') genes_macrophage=c("Itgam") genes_T=c("Cd3g","Cd4") genes_B=c("Cd19")  
  
 
  
 
   
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十一、pancreas胰腺

pancreas genes_BC=c("Ins1", "Ins2", "Slc2a2", "Nkx61", "Pdx1","Mafa","GLUT2","Mafa","Ngn3","Par6","Pdx1")#Beta cells genes_AC=c("Gcg", "Mafb", "Arx","Hhex", "Ins1", "Ins2", "Nkx6-1","Pax6", "Pdx1", "Sst")#Alpha cells genes_PC=c("Dclk1","Nestin","c-Kit","c-Met")#Progenitor cell genes_DC=c("Sst", "Hhex", "Pdx1") #Delta cells genes_PP=c("Ppy", "Mafbneg", "Spp1") #PP cells genes_aC=c("Amy2b", "Cpa1", "Ptf1a")#Acinar cells genes_DC=c("Krt19" ,"Hnf1b")#Ductal cells genes_EC=c("Pecam1", "Cdh5", "Kdr")#Endothelial cells genes_IC=c("Ptprc")#Immune cells genes_PSC=c("Pdgfra", "Pdgfrb")#Pancreatic stellate cells genes_eC=c("Lectin")#Epithelial cell genes_sc=c("Dclk1","Pdx1","c-Met")#stem cell  
  
 
  
 
   
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下面是cell 文献Mapping the Mouse Cell Atlas by Microwell-Seq中MCA网站中的细胞类型和marker gene

genes_Acinar = c("Ctrb1","Cpa2","Clps")#Acinar cell genes_Ductal = c("Spp1","Cldn3","Adamts1")#Ductal cell  genes_Endocrine = c("Gcg","Pyy","Chgb")#Endocrine cell  genes_Erythroid = c("Hba-x","Mgst3","Tmcc2","Apoa2")#Erythroid cell genes_HepatocyteL = c("Afp","Alb","Apoa2")#Hepatocyte-like cell  genes_LVEC = c("Fabp4","Gng11","S100a16")#Lymphatic vessel endothelial cell genes_Macrophage = c("C1qb","C1qc","Tmsb4x")#Macrophage genes_Mast = c("Mcpt8","Srgn","Ifitm1")#Mast cell  genes_Myeloid = c("Sh3bgrl3","Coro1a","Plac8")#Myeloid cell  genes_Neuron = c("Stmn2","Tuba1a")#Neuron genes_Neutrophil = c("S100a8","Camp","S100a9")#Neutrophil genes_Stromal = c("Col1a2","Cdkn1c","Dcn","S100a6","Cav1")#Stromal cell genes_B = c("Ighm","Jchain","Igkc")#B cell  genes_Dendrtic = c("Retnla","Cd74")#Dendrtic cell  genes_Granulocyte = c("Slpi","Il1b")#Granulocyte genes_SMC = c("Acta2","Rgs5")#Smooth muscle cell  
  
 
  
 
   
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十二、trachea气管

trachea genes_TE = c("Epcam", "Cdh1") #tracheal epithelium genes_CC = c("Foxj1") #ciliated cells genes_SC = c("Scgb1a1") # secretory cells genes_BC = c("Krt15", "Krt14","Krt5") # basal cells genes_MC = c("Pdgfrb") #mesenchymal cells  genes_EC = c("Pecam1")#endothelial cells genes_IC = c("Ptprc")#immune cells genes_NC = c("Cck", "Syp")#neuroendocrine cells  
  
 
  
 
   
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十三、small_intestine小肠

small_intestine gene_MC=c("Lgr5")#Microfold cells (or M cells) gene_SC=c("Lgr5","Ascl2","Stc12a2","Axin2","Olfm4","Gkn3")#Stem cells gene_CC=c("Mki67","Cdk4","Mcm5","Mcm6","Pcna")#Cell cycle gene_EC=c("Alpi","Apoa1","Apoa4","Fabp4")#Enterocyte cells gene_GC=c("Muc2","Clca3","Tff3","Agr2")#Globlet cells  gene_PC=c("Lyz1","Defa17","Defa22","Defa24","Ang4","Mptx2")#Paneth cells gene_EEC=c("Chga","Chgb","Tac1","Tph1","Neurog3","Gpr119")#Enteroendocrine cells(EEC) gene_TC=c("Dclk1","Trpm5","Gfi1b","Il25","Drd3","CD24a")#Tuft cells gene_EECP=c("Neurog3", "Neurod1", "Sox4")# EEC precursors gene_K_cells=c("Cck")#I-cells gene_S_cells=c("Sct")#S-cells gene_L_cells=c("Gcg")#L-cells gene_K_cells=c("GIP")#K-cells  
  
 
  
 
   
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下面是cell 文献Mapping the Mouse Cell Atlas by Microwell-Seq中MCA网站中的细胞类型和marker gene

genes_B = c("Ighd","Igkv12-46","Jchain","Ms4a1")#B cell genes_Dendrtic = c("Cst3","Lyz2","H2-Aa")#Dendrtic cell genes_EnterocyteD = c("Fabp6","Tmigd1","Fabp2")#Enterocyte(mature distal) genes_EnterocyteP = c("Fabp1","Rbp2",'Gstm3')#Enterocyte(mature proximal) genes_Enterocyte = c("Gm23935",'S100g',"mt-Nd1")#Enterocyte genes_Enteroendocrine = c("Chgb","Chga","Gip","Cck")#Enteroendocrine cell genes_Epithelial = c("Kcne3","Clca3b","Ifitm3")#Epithelial cell genes_Erythroid = c("Hbb-bs","Gkn3","Tff2")#Erythroid cell genes_Fibroblast = c("Dcn","Col3a1","Sparc")#Fibroblast  genes_Goblet = c("Tff3",'Zg16',"Fcgbp")#Goblet cell genes_Macrophage = c("Apoe","Cxcl2",'G0s2')#Macrophage genes_Mast = c("Cpa3","Ifitm1","Cd63")#Mast cell genes_Paneth = c("Defa21","Defa17",'Ang4')#Paneth cell genes_PDC = c("Siglech","Cox6a2")#Plasmacytoid dendritic cell genes_Stromal = c("Adamdec1",'Igfbp7',"Dcn","Gpx3")#Stromal cell genes_T = c("Ccl5",'Cd7','Icos','Ms4a4b')#T cell genes_Tuft = c("Sh2d6",'Krt18','Hck')#Tuft cell  
  
 
  
 
   
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十四、stomach胃

stomach gene_FC=c("Col1a1", "Bgn", "Dcn")#Fibroblast gene_EC=c("Epcam","Krt7","Krt14")#epithelial gene_LCA=c("Ptprc","Cd45 ")#leukocyte common antigen gene_MC=c('Cd68', "Cd11b" ,"Itgam", "Cd18" ,"Itgb2") #macrophages. gene_PC=c("Atp4a") # parietal cells,  gene_MNC=c("Muc6") #mucous neck cells  gene_FPC=c("Muc5ac") #foveolar or pit cells  gene_MCC=c("Gif") #mouse chief cells  gene_TC=c("Muc6","Gif")#transitional cells   
  
 
  
 
   
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下面是cell 文献Mapping the Mouse Cell Atlas by Microwell-Seq中MCA网站中的细胞类型和marker gene

genes_Chief = c("Chia1","Pgc","Clps","Pgc","Tmed6")#Chief cell genes_Dendritic = c("Cd74","H2-Ab1","H2-Aa","Srgn")#Dendritic cell genes_Endocrine = c("Gast","Ghrl")#Endocrine cell genes_Endothelial = c("Ly6c1","Cbr2","Krt15","Plvap","Igfbp3")#Endothelial cell genes_Fibrlblast = c ("Dcn","Col1a2")#Fibrlblast genes_Macrophage = c("Lyz2","Cd74","Apoe","H2-Ab1")#Macrophage  genes_Parietal = c("Atp4b","Atp4a","Hamp2","Chia1","Pla2g1b")#Parietal cell genes_Pit = c("C18Rik","Gsdma2","Krt20")#Pit cell  genes_PEC = c("Cdc20","Stmn1","Ube2c","Birc5")#Proliferating epithelial cell genes_SMC = c("Tagln","Mylk",'Cnn1')#Smooth muscle cell  genes_SE = c("Cnfn","Sprr3","Krt10")#Squamous epithelium genes_Stromal = c("Col6a1","Sparc","Lum",'Igfbp7')#Stromal cell genes_Tuft = c("Rgs13","Alox5ap","Dclk1")#Tuft cell  genes_Mast = c("Cma1","Cpa3")#Mast cell  
  
 
  
 
   
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十五、uterus 子宫

uterus genes_IS=c("Bmp7","Nrgn","Cpxm2","Tgfbi") #inner stroma cells genes_OS=c("Wfikkn2","Smoc2","Dpt","Cpe") #outer stroma cells genes_MC=c("Lum","Ptn","Ogn","Thbs2 ")#Myometrium cells genes_IPC=c("Bambi","Unc5b","Fgfr2")#Inhibited Progenitor cells genes_EC=c("Msx2","Cd24","Epcam","Wfdc2","Wnt7a","Cd326")#Epithelium cells genes_PC=c("Hmgb2","Stmn1","Top2a","Mki67")#Proliferating cells genes_VE=c("Cd93","Cdh5","Emcn")#Vascular endothelium genes_SC=c("Lgr5", "Cd133", "Msi1")#stem cell genes_IMC=c("Myh11")#Inner myometrium genes_OMC=c("Thbs2")#Outer myometrium  
  
 
  
 
   
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十六、testis 睾丸

testis genes_SC=c("Glis2","Nanos1","Kit","Stra8")#A1-4 spermatogonia genes_Macrophages=c("Csf1r")#Macrophages genes_Telo=c("Dcn","Cd34","Pdgfra")#Telocytes genes_L/Z=c("Ccnb3","Rhox2d")#Leptotene/Zygotene genes_Ley=c("Cyp11a1")#Leydig genes_Sert=c("Aard","Trim7")#Sertoli genes_eSpd=c("Prm2","Tnp2")#Elongating spermatids genes_rSpd=c("Lrrd1","Fam71b")#Round spermatids genes_uSpg=c("Gfra1","Nanos1","Foxo1","Zbtb16")#Undifferentiated spermatogonia genes_dSpg=c("Esx1","Ctcfl","Prdm9")#Differentiated spermatogonia genes_Pach=c("Piwil1","Ccna1")#Pachytene genes_Acr=c("Acrv1")#Acrosomal genes_MD=c("Ssxb1")#Meiotic division  
  
 
  
 
   
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十七、prostate 前列腺

prostate genes_LC=c("Tacstd2","Ck4","Psca")#Luminal-C genes_LB=c("Fgl1","Mmp7")#Luminal-B genes_Basal=c("Trp63","Ck5","Krt5","Krt14")#basal cell genes_Stromal=c("Col1a2","Col1a1")#stromal cel genes_LA=c("Sbp","Abo")#Luminal-A genes_Neuro=c("Syp","Chga")# neuroendocrine cell genes_SV=c("Svs3a","Svs1")#seminal vesicle epithelial cell genes_Macro_A=c("Ccl4","Retnla")#macrophage-A genes_Macro_B=c("Clec4e","Arg1")#macrophage-B genes_Lymph=c("Ly6c2","Mzb1")#lymphocyte genes_Endo=c("Cdh5","Kdr")#endothelial cell  
  
 
  
 
   
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十八、ovary 卵巢

ovary genes_Germ=c("Ddx4","Oct4","Par6","Slc39a10")#Germ cells genes_Granulosa=c("Amhr2","Serpine2","Kitl","Camta1")#Granulosa cells genes_Stromal=c("Tcf21")#Stromal cells genes_Erythrocytes=c("Alas2")#Erythrocytes  genes_Immune=c("Tyrobp")#Immune cells genes_Endothelial=c("Aplnr")#Endothelial cells genes_Epithelial=c("Tacstd2","Ly6a")#Epithelial cells genes_FO=c("Lhx8","Nobox","Sohlh1")# follicular oocytes genes_MP=c("Prdm9","Stra8")#related to meiotic processes genes_Somatic=c("Nr2f2","Foxl2","Lgr5")#Somatic cell genes_Stem=c("Ddx4","Ifitm3")#Stem cell genes_all=c(genes_Germ,genes_Granulosa,genes_Stromal,genes_Erythrocytes,genes_Immune,genes_Endothelial,genes_Epithelial,genes_FO,genes_MP,genes_Somatic,genes_Stem)  
  
 
  
 
   
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十九、kidneys肾

kidneys肾 genes_1 = c("Cld8", "Slc12a3", "Avpr2", "Aqp2","Slc8a1","Wnk1","Vdr") #distal tubule cells genes_2 = c("Rhcg", "Adgrf5", "Jag1", "Insrr","Ap1s3","Fxyd2","Atp6v1g3","Clcnkb") #intercalated cells genes_3 = c("Ren1", "Trpv4", "Cnn1", "Acta2","Akr1b7") #juxtaglomerular cells genes_4 = c("Osr1", "Pax2", "Eya1", "Cited1","Wt1") #kidney progenitor cells genes_5 = c("Arc", "Gem", "Fga", "Pla2g7","Thbs1","Enc1") #loop of henle cells genes_6 = c("Pdgfrb", "Pde3a", "Fn1", "Arid5b","Itga8") #mesangial cells genes_7 = c("Loxl2","Lrrc49", "Coro2b","Dock5","Adcy1","Crb2","Kank1") #podocytes genes_8 = c("Kcne1","Hes1", "Aqp4","Klk1","Fzd1") #principal cells genes_9 = c("Keg1","G6pc", "Alpl","Slc13a1","Scin") #proximal tubule cells genes_10 = c("Gclc","Enpp5", "Pip4k2c","St14","Slc26a4") #transient cell