各种组织的marker gene
2024-04-30 00:45:02
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
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
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
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)
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
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
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"
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
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
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")
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
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
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
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
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
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
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("2210407C18Rik","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
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
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
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
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)
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 cellgenes_11 = c("Plvap")#endothelial cells
genes_12 = c("Des", "Vim", "Acta2")#mesangial cells
genes_13 = c("Podxl", "Wt1", "Mme")#podocytes
genes_14 = c("Vil1")#proximal brush border cells
genes_15 =c("Kcne1", "Scnn1a", "Aqp2")# distal collecting duct principal cells
二十、thymus胸腺
thymus
genes_1 = c("Pxk", "Ms4a1", "Cd19", "Cd74","Cd79a","Ighd","Ighm") #B cells
genes_2 = c("Cd7", "Cd40", "Apobec3a", "Hck","Cxcr4","Cd14") #monocytes
genes_3 = c("Lilrb4", "Cpm", "Chit1", "Slamf9","Mgl2","Lilra5","Mrc1","Tgfbr1","Fgd2") #macrophages
genes_4 = c("Trbc2","Cd3d", "Cd3g","Gzmk","Cd3e","Ltb","Il7r") #T cells
genes_5 = c("Flt3","Itgax","Cx3cr1","Cd8a","Itgam") #Dendritic cells
genes_6 = c("CD4","CD69","EZR","CIDEA","BCL6","CD28","UCP2","MS4A4B","NOTCH1","IL2RA") #Thymocytes
genes_7 = c ("Cd44")#DN1 thymocytes
genes_8 = c("Cd8")# the intermediate stages between DN and DP
genes_9 = c("Mki67","Top2a")#proliferating thymocytes
genes_10 = c("Zbtb7b","Runx3")#lymphocyte subset specific differentiation
genes_11 = c ("H2-Aa", "H2-Ab1")# stromal cells
genes_12 = c ("Ptprc","Cd86")#dendritic cells
genes_13 = c("Rag1","Rag2","Dntt")#more mature DN2, DN3, and DN4 thymocytes,lack "Rag1","Rag2","Dntt"
二十一、seminal_vesicle精囊
seminal_vesicle
gene_FC =c("Col1a1", "Bgn", "Dcn","Ddr2","Tcf21", "Col3a1", "Col1a2", "Col1a1")#Fibroblast
genes_TE = c("Epcam", "Cdh1") # epithelium
genes_IC = c("Ptprc")#immune cells
genes_NC = c("Cck", "Syp","Chga")#neuroendocrine cells
genes_SV=c("Svs3a","Svs1")#seminal vesicle epithelial cells
genes_all = unique(c(gene_FC,genes_TE,genes_IC,genes_NC,genes_LB,genes_SV))
二十二、cerebellum小脑
cerebellum
genes_GP = c("Atoh1")#Granule precursors
genes_GC = c("Nhlh1","Reln","Rbfox3")#Granule cells
genes_Ac = c("Aldoc","Aqp4")#Astrocytes
genes_Oc = c("S100b","Olig1")#Oligodendrocytes
genes_PC = c("Gad1","Calb1","Pcp2")#Purkinje cells
genes_EC = c("Pdgfrb","Pecam1")#Endothelial cells
genes_Ic = c("Pax2")#Interneurons
genes_Mc = c("Aldoc","Aqp4")#Microglia
genes_IC = c("Ptprc","C1qa", "H2-Eb1","Cd14")#immune cells
genes_FC = c("Ddr2","Tcf21","Col3a1","Col1a2","Col1a1") #fibroblasts
二十三、cecum盲肠
cecum
gene_EC=c("Alpi","Fabp4","Krt20", "Slc26a3")#Enterocyte cells
gene_GC=c("Muc2","Clca3","Tff3","Agr2","Atoh1", "Spdef")#Globlet cells
gene_EEC=c("Chga","Chgb","Tac1","Tph1")#Enteroendocrine cells(EEC)
gene_TC=c("Dclk1","Cd24a")#Tuft cells
genes_CC=c("Chga", "Chgb")#chromaffin cells
genes_IC = c("Ptprc","C1qa", "H2-Eb1","Cd14")#immune cells
genes_FC = c("Ddr2","Tcf21","Col3a1","Col1a2","Col1a1") #fibroblasts
genes_TE = c("Epcam", "Cdh1") # epithelium
genes_all=unique(c(gene_EC,gene_GC,gene_EEC,gene_TC,gene_EECP,genes_CC,genes_IC,genes_FC))
二十四、Brain脑/cortex
Brain
genes_1 = c("Cx3cr1", "P2ry12", "Tmem119")#Microglia and non-parenchymal macrophages
genes_2 = c("Cd163")#nonparenchymal macrophages
genes_3 = c("Pdgfra", "Susd5","Cspg4")#oligodendrocyte lineage cells
genes_4 = c("Mog", "Mag", "Gjc2")#mature myelinating oligodendrocytes
genes_5 = c("Pecam1", "Cldn5")#pan-endothelial cells
genes_6 = c("Slco1c1", "Ocln")#blood-brain barrier
genes_7 = c("Aldh1l1", "Slc1a3", "Aqp4")#astrocyte
genes_8 = c("Gdf10", "Vim", "Nbl1", "A2m")#Bergman glia
genes_10 = c("Slc17a7", "Neurod6", "Mab21l1")#excitatory neurons
genes_11 = c('Gad1', "Reln", "Calb1")#inhibitory neurons
genes_12 = c("Dcx", "Dlx2", "Ascl1", "Hes5")#neuroprogenitor cells
genes_13 = c("Des", "Mcam", "Pdgfrb")#pericytes
genes_14 = c('Bmx', "Jag1", "Efnb2")#arterioles
genes_15 = c("Nr2f2", 'Flt4', "Vwf") #post-capillary venules
genes_16 = c("Tfrc", "Car4", "Slc16a1")#capillaries
genes_17 = c("Jag1", "Notch1", "Hey1", "Vegfc", "Edn1", "Tmem100")#pro-angiogenic arterioles
genes_18 = c (" Vcam1", "Icam1", "Lcn2","Hif1a", "Vwf", "Csf1")#post-capillary venules and capillaries enriched with inflammatory genes
genes_IC = c("Ptprc", "H2-Eb1","Cd14")#immune cells
genes_all = unique(c(genes_1, genes_2, genes_3, genes_4, genes_5, genes_6, genes_7, genes_8, genes_10, genes_11, genes_12, genes_13, genes_14, genes_15, genes_16, genes_17, genes_18, genes_IC))
二十五、Fat
fat
genes_MPs = c("Pdgfra", "Cd34", "Tek", "Fabp4")#mesenchymal progenitors
genes_ECs = c("Pecam1", "Cdh5", "Cd34") # endothelial cells
genes_ICs = c("Ptprc") #Immune cells
genes_myeloid = c("Itgam", "Cd68", "C1qa", "Lyz2", "Cd14")#myeloid cells
genes_B = c('Cd79a', 'Cd79b', 'Cd74', 'Cd19')#B cells
genes_T = c("Cd3g", "Cd8a", "Cd4") #T cells
genes_Nk = c("Irf8", "Gzma", "Nkg7")#NK cells
genes_AP = c("Cd24a")#adipogenic progenitors
genes_ep = c("Pecam1", "Ptprc")#endothelial progenitor cells of hematopoietic origin
genes_macrophages = c("Mgl2","Lilra5","Mrc1") #macrophages
genes_all=unique(c(genes_MPs,genes_ECs,genes_ICs,genes_myeloid,genes_B,genes_T,genes_Nk,genes_AP,genes_ep,genes_macrophages))
参考文献：
stomach：
1、https://www.nature.com/articles/s41598-019-40809-x
2、https://www.nature.com/articles/s41467-019-14058-5
3、https://gut.bmj.com/content/69/6/1027
small_intestine:
4、https://pubmed.ncbi.nlm.nih.gov/29144463/
5、 https://www.sciencedirect.com/science/article/pii/S2212877817304568
Spleen and Brain：
6、https://www.miltenyibiotec.com/US-en/resources/macs-handbook/mouse-cells-and-organs/mouse-cell-sources/spleen-mouse.html
uterus
7、https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6650247/
8、https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5511104/
testis
9、https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6615865/
prostate
10、https://www.nature.com/articles/s41588-020-0642-1
11、https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7529463/
ovary
12、https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7787681/
cerebellum
13、https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6788728
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