Tabula Sapiens Tabula Tissue Cell Track Settings
 
Tabula sapiens RNA by tissue and cell type

Track collection: Tabula Sapiens single cell RNA data from many tissues

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Label: Name or ID of item    Alternative name for item   
Log10(x+1) transform:    View limits maximum: parts per million (range 0-10000)

color cluster count tissue cell_class cell_type
   
adipose tissue B cell 23 adipose tissue immune B cell
   
adipose tissue endothelial cell 3748 adipose tissue endothelial endothelial cell
   
adipose tissue fibroblast 8459 adipose tissue stromal fibroblast
   
adipose tissue leukocyte 160 adipose tissue immune leukocyte
   
adipose tissue macrophage 2807 adipose tissue immune macrophage
   
adipose tissue mast cell 4 adipose tissue immune mast cell
   
adipose tissue mature NK T cell 572 adipose tissue immune mature NK T cell
   
adipose tissue mesenchymal stem cell 1311 adipose tissue stromal mesenchymal stem cell
   
adipose tissue myofibroblast cell 982 adipose tissue stromal myofibroblast cell
   
adipose tissue neutrophil 440 adipose tissue immune neutrophil
   
adipose tissue plasma cell 26 adipose tissue immune plasma cell
   
adipose tissue smooth muscle cell 16 adipose tissue stromal smooth muscle cell
   
adipose tissue T cell 1715 adipose tissue immune T cell
   
bladder organ B cell 251 bladder organ immune B cell
   
bladder organ bladder urothelial cell 2873 bladder organ epithelial bladder urothelial cell
   
bladder organ capillary endothelial cell 66 bladder organ endothelial capillary endothelial cell
   
bladder organ endothelial cell of lym... 73 bladder organ endothelial endothelial cell of lymphatic vessel
   
bladder organ fibroblast 4927 bladder organ stromal fibroblast
   
bladder organ macrophage 4876 bladder organ immune macrophage
   
bladder organ mast cell 991 bladder organ immune mast cell
   
bladder organ mature NK T cell 485 bladder organ immune mature NK T cell
   
bladder organ myofibroblast cell 1989 bladder organ stromal myofibroblast cell
   
bladder organ pericyte cell 708 bladder organ stromal pericyte cell
   
bladder organ plasma cell 1141 bladder organ immune plasma cell
   
bladder organ plasmacytoid dendritic ... 18 bladder organ immune plasmacytoid dendritic cell
   
bladder organ smooth muscle cell 227 bladder organ stromal smooth muscle cell
   
bladder organ T cell 2626 bladder organ immune T cell
   
bladder organ vein endothelial cell 266 bladder organ endothelial vein endothelial cell
   
blood alpha-beta T cell 31 blood immune alpha-beta T cell
   
blood basophil 29 blood immune basophil
   
blood CD4-positive, alpha-beta memory... 949 blood immune CD4-positive, alpha-beta memory T cell
   
blood CD4-positive, alpha-beta T cell 2863 blood immune CD4-positive, alpha-beta T cell
   
blood CD8-positive, alpha-beta cytoki... 1493 blood immune CD8-positive, alpha-beta cytokine sec...
   
blood CD8-positive, alpha-beta T cell 1322 blood immune CD8-positive, alpha-beta T cell
   
blood CD141-positive myeloid dendriti... 15 blood immune CD141-positive myeloid dendritic cell
   
blood classical monocyte 7211 blood immune classical monocyte
   
blood common myeloid progenitor 3 blood immune common myeloid progenitor
   
blood erythrocyte 10484 blood immune erythrocyte
   
blood granulocyte 2 blood immune granulocyte
   
blood hematopoietic stem cell 70 blood immune hematopoietic stem cell
   
blood macrophage 488 blood immune macrophage
   
blood mature NK T cell 2948 blood immune mature NK T cell
   
blood memory B cell 854 blood immune memory B cell
   
blood monocyte 8972 blood immune monocyte
   
blood naive B cell 2239 blood immune naive B cell
   
blood naive thymus-derived CD4-positi... 412 blood immune naive thymus-derived CD4-positive, al...
   
blood neutrophil 8456 blood immune neutrophil
   
blood non-classical monocyte 8 blood immune non-classical monocyte
   
blood plasma cell 488 blood immune plasma cell
   
blood plasmablast 10 blood immune plasmablast
   
blood plasmacytoid dendritic cell 11 blood immune plasmacytoid dendritic cell
   
blood platelet 239 blood immune platelet
   
blood type I NK T cell 518 blood immune type I NK T cell
   
bone marrow CD4-positive, alpha-beta ... 2025 bone marrow immune CD4-positive, alpha-beta T cell
   
bone marrow CD8-positive, alpha-beta ... 1147 bone marrow immune CD8-positive, alpha-beta T cell
   
bone marrow common myeloid progenitor 287 bone marrow immune common myeloid progenitor
   
bone marrow erythrocyte 87 bone marrow immune erythrocyte
   
bone marrow erythroid progenitor cell 757 bone marrow immune erythroid progenitor cell
   
bone marrow granulocyte 853 bone marrow immune granulocyte
   
bone marrow hematopoietic stem cell 617 bone marrow immune hematopoietic stem cell
   
bone marrow macrophage 265 bone marrow immune macrophage
   
bone marrow mature NK T cell 678 bone marrow immune mature NK T cell
   
bone marrow memory B cell 310 bone marrow immune memory B cell
   
bone marrow monocyte 1389 bone marrow immune monocyte
   
bone marrow naive B cell 142 bone marrow immune naive B cell
   
bone marrow neutrophil 2911 bone marrow immune neutrophil
   
bone marrow plasma cell 825 bone marrow immune plasma cell
   
bone marrow plasmablast 4 bone marrow immune plasmablast
   
eye B cell 102 eye immune B cell
   
eye CD4-positive, alpha-beta T cell 23 eye immune CD4-positive, alpha-beta T cell
   
eye CD8-positive, alpha-beta T cell 8 eye immune CD8-positive, alpha-beta T cell
   
eye conjunctival epithelial cell 4587 eye epithelial conjunctival epithelial cell
   
eye corneal epithelial cell 1488 eye epithelial corneal epithelial cell
   
eye dendritic cell 182 eye immune dendritic cell
   
eye endothelial cell 105 eye endothelial endothelial cell
   
eye epithelial cell of lacrimal sac 52 eye epithelial epithelial cell of lacrimal sac
   
eye erythroid lineage cell 30 eye immune erythroid lineage cell
   
eye eye photoreceptor cell 891 eye epithelial eye photoreceptor cell
   
eye fat cell 44 eye stromal fat cell
   
eye fibroblast 95 eye stromal fibroblast
   
eye keratocyte 595 eye epithelial keratocyte
   
eye macrophage 108 eye immune macrophage
   
eye mast cell 5 eye immune mast cell
   
eye melanocyte 144 eye stromal melanocyte
   
eye microglial cell 209 eye immune microglial cell
   
eye monocyte 44 eye immune monocyte
   
eye Muller cell 360 eye stromal Muller cell
   
eye pigmented ciliary epithelial cell 17 eye epithelial pigmented ciliary epithelial cell
   
eye plasma cell 46 eye immune plasma cell
   
eye radial glial cell 195 eye stromal radial glial cell
   
eye retina horizontal cell 6 eye stromal retina horizontal cell
   
eye retinal bipolar neuron 34 eye stromal retinal bipolar neuron
   
eye retinal blood vessel endothelial ... 466 eye endothelial retinal blood vessel endothelial cell
   
eye retinal ganglion cell 5 eye stromal retinal ganglion cell
   
eye retinal pigment epithelial cell 49 eye epithelial retinal pigment epithelial cell
   
eye stem cell 144 eye epithelial stem cell
   
eye stromal cell 325 eye stromal stromal cell
   
eye surface ectodermal cell 54 eye epithelial surface ectodermal cell
   
eye T cell 237 eye immune T cell
   
heart cardiac endothelial cell 2665 heart endothelial cardiac endothelial cell
   
heart cardiac muscle cell 7205 heart stromal cardiac muscle cell
   
heart fibroblast 250 heart stromal fibroblast
   
heart hepatocyte 1089 heart epithelial hepatocyte
   
heart macrophage 74 heart immune macrophage
   
heart smooth muscle cell 222 heart stromal smooth muscle cell
   
kidney B cell 341 kidney immune B cell
   
kidney CD4-positive helper T cell 181 kidney immune CD4-positive helper T cell
   
kidney CD8-positive, alpha-beta T cell 241 kidney immune CD8-positive, alpha-beta T cell
   
kidney endothelial cell 95 kidney endothelial endothelial cell
   
kidney kidney epithelial cell 8331 kidney epithelial kidney epithelial cell
   
kidney macrophage 321 kidney immune macrophage
   
kidney mature NK T cell 131 kidney immune mature NK T cell
   
large intestine B cell 497 large intestine immune B cell
   
large intestine CD4-positive, alpha-b... 2872 large intestine immune CD4-positive, alpha-beta T cell
   
large intestine CD8-positive, alpha-b... 2147 large intestine immune CD8-positive, alpha-beta T cell
   
large intestine enterocyte 1464 large intestine epithelial enterocyte
   
large intestine enterocyte 2764 large intestine epithelial enterocyte
   
large intestine fibroblast 953 large intestine stromal fibroblast
   
large intestine goblet cell 166 large intestine epithelial goblet cell
   
large intestine goblet cell 385 large intestine epithelial goblet cell
   
large intestine gut endothelial cell 53 large intestine endothelial gut endothelial cell
   
large intestine intestinal crypt stem... 143 large intestine epithelial intestinal crypt stem cell
   
large intestine intestinal crypt stem... 114 large intestine epithelial intestinal crypt stem cell
   
large intestine intestinal enteroendo... 55 large intestine epithelial intestinal enteroendocrine cell
   
large intestine intestinal tuft cell 33 large intestine epithelial intestinal tuft cell
   
large intestine mast cell 38 large intestine immune mast cell
   
large intestine monocyte 543 large intestine immune monocyte
   
large intestine neutrophil 27 large intestine immune neutrophil
   
large intestine paneth cell of colon 888 large intestine epithelial paneth cell of colon
   
large intestine plasma cell 330 large intestine immune plasma cell
   
large intestine transit amplifying cell 208 large intestine epithelial transit amplifying cell
   
liver endothelial cell of hepatic sin... 421 liver endothelial endothelial cell of hepatic sinusoid
   
liver endothelial cell 267 liver endothelial endothelial cell
   
liver erythrocyte 108 liver immune erythrocyte
   
liver fibroblast 76 liver stromal fibroblast
   
liver hepatocyte 1558 liver epithelial hepatocyte
   
liver intrahepatic cholangiocyte 42 liver epithelial intrahepatic cholangiocyte
   
liver liver dendritic cell 34 liver immune liver dendritic cell
   
liver macrophage 1381 liver immune macrophage
   
liver mature NK T cell 245 liver immune mature NK T cell
   
liver monocyte 612 liver immune monocyte
   
liver neutrophil 83 liver immune neutrophil
   
liver plasma cell 34 liver immune plasma cell
   
liver T cell 146 liver immune T cell
   
lung adventitial cell 373 lung stromal adventitial cell
   
lung B cell 87 lung immune B cell
   
lung basal cell 2188 lung epithelial basal cell
   
lung basophil 686 lung immune basophil
   
lung blood vessel endothelial cell 47 lung endothelial blood vessel endothelial cell
   
lung bronchial smooth muscle cell 81 lung stromal bronchial smooth muscle cell
   
lung capillary endothelial cell 1534 lung endothelial capillary endothelial cell
   
lung CD4-positive, alpha-beta T cell 543 lung immune CD4-positive, alpha-beta T cell
   
lung CD8-positive, alpha-beta T cell 552 lung immune CD8-positive, alpha-beta T cell
   
lung classical monocyte 1487 lung immune classical monocyte
   
lung club cell 1038 lung epithelial club cell
   
lung dendritic cell 316 lung immune dendritic cell
   
lung effector CD4-positive, alpha-bet... 132 lung immune effector CD4-positive, alpha-beta T cell
   
lung effector CD8-positive, alpha-bet... 80 lung immune effector CD8-positive, alpha-beta T cell
   
lung endothelial cell of artery 187 lung endothelial endothelial cell of artery
   
lung endothelial cell of lymphatic ve... 47 lung endothelial endothelial cell of lymphatic vessel
   
lung fibroblast 336 lung stromal fibroblast
   
lung intermediate monocyte 252 lung immune intermediate monocyte
   
lung lung ciliated cell 602 lung epithelial lung ciliated cell
   
lung lung microvascular endothelial cell 485 lung endothelial lung microvascular endothelial cell
   
lung macrophage 12160 lung immune macrophage
   
lung mature NK T cell 132 lung immune mature NK T cell
   
lung mesothelial cell 17 lung epithelial mesothelial cell
   
lung myofibroblast cell 10 lung stromal myofibroblast cell
   
lung neutrophil 174 lung immune neutrophil
   
lung non-classical monocyte 1005 lung immune non-classical monocyte
   
lung pericyte cell 213 lung stromal pericyte cell
   
lung plasma cell 134 lung immune plasma cell
   
lung plasmacytoid dendritic cell 18 lung immune plasmacytoid dendritic cell
   
lung pulmonary ionocyte 19 lung epithelial pulmonary ionocyte
   
lung respiratory goblet cell 762 lung epithelial respiratory goblet cell
   
lung serous cell of epithelium of bro... 15 lung epithelial serous cell of epithelium of bronchus
   
lung smooth muscle cell 25 lung stromal smooth muscle cell
   
lung type I pneumocyte 211 lung epithelial type I pneumocyte
   
lung type II pneumocyte 9146 lung epithelial type II pneumocyte
   
lung vascular associated smooth muscl... 80 lung stromal vascular associated smooth muscle cell
   
lung vein endothelial cell 508 lung endothelial vein endothelial cell
   
lymph node B cell 15249 lymph node immune B cell
   
lymph node CD1c-positive myeloid dend... 90 lymph node immune CD1c-positive myeloid dendritic cell
   
lymph node CD4-positive, alpha-beta m... 1434 lymph node immune CD4-positive, alpha-beta memory T cell
   
lymph node CD8-positive, alpha-beta m... 864 lymph node immune CD8-positive, alpha-beta memory T cell
   
lymph node CD141-positive myeloid den... 101 lymph node immune CD141-positive myeloid dendritic cell
   
lymph node classical monocyte 246 lymph node immune classical monocyte
   
lymph node effector CD4-positive, alp... 6908 lymph node immune effector CD4-positive, alpha-beta T cell
   
lymph node effector CD8-positive, alp... 5860 lymph node immune effector CD8-positive, alpha-beta T cell
   
lymph node endothelial cell 158 lymph node endothelial endothelial cell
   
lymph node erythrocyte 24 lymph node immune erythrocyte
   
lymph node hematopoietic stem cell 34 lymph node immune hematopoietic stem cell
   
lymph node innate lymphoid cell 2420 lymph node immune innate lymphoid cell
   
lymph node intermediate monocyte 306 lymph node immune intermediate monocyte
   
lymph node macrophage 1148 lymph node immune macrophage
   
lymph node mast cell 143 lymph node immune mast cell
   
lymph node mature conventional dendri... 17 lymph node immune mature conventional dendritic cell
   
lymph node mature NK T cell 683 lymph node immune mature NK T cell
   
lymph node memory B cell 3319 lymph node immune memory B cell
   
lymph node naive B cell 1335 lymph node immune naive B cell
   
lymph node naive thymus-derived CD4-p... 1499 lymph node immune naive thymus-derived CD4-positive, al...
   
lymph node neutrophil 107 lymph node immune neutrophil
   
lymph node non-classical monocyte 31 lymph node immune non-classical monocyte
   
lymph node plasma cell 2687 lymph node immune plasma cell
   
lymph node plasmacytoid dendritic cell 6 lymph node immune plasmacytoid dendritic cell
   
lymph node regulatory T cell 889 lymph node immune regulatory T cell
   
lymph node stromal cell 111 lymph node stromal stromal cell
   
lymph node T cell 3848 lymph node immune T cell
   
lymph node type I NK T cell 3758 lymph node immune type I NK T cell
   
mammary gland B cell 43 mammary gland immune B cell
   
mammary gland basal cell 476 mammary gland epithelial basal cell
   
mammary gland endothelial cell of artery 168 mammary gland endothelial endothelial cell of artery
   
mammary gland endothelial cell of lym... 32 mammary gland endothelial endothelial cell of lymphatic vessel
   
mammary gland fibroblast 2066 mammary gland stromal fibroblast
   
mammary gland luminal epithelial cell... 5378 mammary gland epithelial luminal epithelial cell of mammary gland
   
mammary gland macrophage 219 mammary gland immune macrophage
   
mammary gland mast cell 16 mammary gland immune mast cell
   
mammary gland mature NK T cell 19 mammary gland immune mature NK T cell
   
mammary gland pericyte cell 106 mammary gland stromal pericyte cell
   
mammary gland plasma cell 194 mammary gland immune plasma cell
   
mammary gland T cell 2324 mammary gland immune T cell
   
mammary gland vascular associated smo... 71 mammary gland stromal vascular associated smooth muscle cell
   
mammary gland vein endothelial cell 263 mammary gland endothelial vein endothelial cell
   
muscle tissue capillary endothelial cell 2015 muscle tissue endothelial capillary endothelial cell
   
muscle tissue CD4-positive, alpha-bet... 221 muscle tissue immune CD4-positive, alpha-beta T cell
   
muscle tissue CD8-positive, alpha-bet... 536 muscle tissue immune CD8-positive, alpha-beta T cell
   
muscle tissue endothelial cell of artery 133 muscle tissue endothelial endothelial cell of artery
   
muscle tissue endothelial cell of lym... 134 muscle tissue endothelial endothelial cell of lymphatic vessel
   
muscle tissue endothelial cell of vas... 3602 muscle tissue endothelial endothelial cell of vascular tree
   
muscle tissue erythrocyte 20 muscle tissue immune erythrocyte
   
muscle tissue fast muscle cell 266 muscle tissue stromal fast muscle cell
   
muscle tissue macrophage 1989 muscle tissue immune macrophage
   
muscle tissue mast cell 46 muscle tissue immune mast cell
   
muscle tissue mature NK T cell 137 muscle tissue immune mature NK T cell
   
muscle tissue mesenchymal stem cell 14148 muscle tissue stromal mesenchymal stem cell
   
muscle tissue mesothelial cell 12 muscle tissue epithelial mesothelial cell
   
muscle tissue pericyte cell 1794 muscle tissue stromal pericyte cell
   
muscle tissue skeletal muscle satelli... 4831 muscle tissue stromal skeletal muscle satellite stem cell
   
muscle tissue slow muscle cell 163 muscle tissue stromal slow muscle cell
   
muscle tissue smooth muscle cell 58 muscle tissue stromal smooth muscle cell
   
muscle tissue T cell 407 muscle tissue immune T cell
   
muscle tissue tendon cell 234 muscle tissue stromal tendon cell
   
pancreas B cell 144 pancreas immune B cell
   
pancreas endothelial cell 2100 pancreas endothelial endothelial cell
   
pancreas fibroblast 47 pancreas stromal fibroblast
   
pancreas mast cell 53 pancreas immune mast cell
   
pancreas mature NK T cell 47 pancreas immune mature NK T cell
   
pancreas myeloid cell 1862 pancreas immune myeloid cell
   
pancreas pancreatic A cell 71 pancreas epithelial pancreatic A cell
   
pancreas pancreatic acinar cell 5534 pancreas epithelial pancreatic acinar cell
   
pancreas pancreatic D cell 9 pancreas epithelial pancreatic D cell
   
pancreas pancreatic ductal cell 2431 pancreas epithelial pancreatic ductal cell
   
pancreas pancreatic PP cell 71 pancreas epithelial pancreatic PP cell
   
pancreas pancreatic stellate cell 393 pancreas stromal pancreatic stellate cell
   
pancreas plasma cell 63 pancreas immune plasma cell
   
pancreas T cell 573 pancreas immune T cell
   
pancreas type B pancreatic cell 99 pancreas epithelial type B pancreatic cell
   
prostate gland basal cell of prostate... 3298 prostate gland epithelial basal cell of prostate epithelium
   
prostate gland CD8-positive, alpha-be... 1081 prostate gland immune CD8-positive, alpha-beta T cell
   
prostate gland club cell 1078 prostate gland epithelial club cell
   
prostate gland endothelial cell 585 prostate gland endothelial endothelial cell
   
prostate gland epithelial cell 6848 prostate gland epithelial epithelial cell
   
prostate gland erythroid progenitor cell 86 prostate gland immune erythroid progenitor cell
   
prostate gland fibroblast 223 prostate gland stromal fibroblast
   
prostate gland luminal cell of prosta... 1092 prostate gland epithelial luminal cell of prostate epithelium
   
prostate gland macrophage 317 prostate gland immune macrophage
   
prostate gland mast cell 9 prostate gland immune mast cell
   
prostate gland mature NK T cell 430 prostate gland immune mature NK T cell
   
prostate gland monocyte 33 prostate gland immune monocyte
   
prostate gland myeloid cell 365 prostate gland immune myeloid cell
   
prostate gland neutrophil 16 prostate gland immune neutrophil
   
prostate gland smooth muscle cell 285 prostate gland stromal smooth muscle cell
   
prostate gland sperm 11 prostate gland germ line sperm
   
prostate gland stromal cell 32 prostate gland stromal stromal cell
   
prostate gland T cell 586 prostate gland immune T cell
   
saliva-secreting gland acinar cell of... 10147 saliva-secreting gland epithelial acinar cell of salivary gland
   
saliva-secreting gland adventitial cell 442 saliva-secreting gland stromal adventitial cell
   
saliva-secreting gland B cell 137 saliva-secreting gland immune B cell
   
saliva-secreting gland basal cell 922 saliva-secreting gland epithelial basal cell
   
saliva-secreting gland CD4-positive h... 1221 saliva-secreting gland immune CD4-positive helper T cell
   
saliva-secreting gland CD4-positive, ... 182 saliva-secreting gland immune CD4-positive, alpha-beta T cell
   
saliva-secreting gland CD8-positive, ... 1979 saliva-secreting gland immune CD8-positive, alpha-beta T cell
   
saliva-secreting gland duct epithelia... 1693 saliva-secreting gland epithelial duct epithelial cell
   
saliva-secreting gland endothelial ce... 320 saliva-secreting gland endothelial endothelial cell of lymphatic vessel
   
saliva-secreting gland endothelial cell 323 saliva-secreting gland endothelial endothelial cell
   
saliva-secreting gland fibroblast 2169 saliva-secreting gland stromal fibroblast
   
saliva-secreting gland ionocyte 87 saliva-secreting gland epithelial ionocyte
   
saliva-secreting gland macrophage 1761 saliva-secreting gland immune macrophage
   
saliva-secreting gland mature NK T cell 317 saliva-secreting gland immune mature NK T cell
   
saliva-secreting gland memory B cell 2879 saliva-secreting gland immune memory B cell
   
saliva-secreting gland monocyte 426 saliva-secreting gland immune monocyte
   
saliva-secreting gland myoepithelial ... 196 saliva-secreting gland epithelial myoepithelial cell
   
saliva-secreting gland naive B cell 1120 saliva-secreting gland immune naive B cell
   
saliva-secreting gland neutrophil 115 saliva-secreting gland immune neutrophil
   
saliva-secreting gland pericyte cell 146 saliva-secreting gland stromal pericyte cell
   
saliva-secreting gland plasma cell 345 saliva-secreting gland immune plasma cell
   
saliva-secreting gland salivary gland... 45 saliva-secreting gland epithelial salivary gland cell
   
saliva-secreting gland T cell 227 saliva-secreting gland immune T cell
   
skin of body CD1c-positive myeloid de... 165 skin of body immune CD1c-positive myeloid dendritic cell
   
skin of body CD4-positive helper T cell 59 skin of body immune CD4-positive helper T cell
   
skin of body CD4-positive, alpha-beta... 339 skin of body immune CD4-positive, alpha-beta memory T cell
   
skin of body CD8-positive, alpha-beta... 129 skin of body immune CD8-positive, alpha-beta cytotoxic T ...
   
skin of body CD8-positive, alpha-beta... 857 skin of body immune CD8-positive, alpha-beta memory T cell
   
skin of body CD141-positive myeloid d... 17 skin of body immune CD141-positive myeloid dendritic cell
   
skin of body cell of skeletal muscle 10 skin of body stromal cell of skeletal muscle
   
skin of body endothelial cell 1309 skin of body endothelial endothelial cell
   
skin of body epithelial cell 106 skin of body epithelial epithelial cell
   
skin of body Langerhans cell 36 skin of body immune Langerhans cell
   
skin of body macrophage 846 skin of body immune macrophage
   
skin of body mast cell 645 skin of body immune mast cell
   
skin of body mature NK T cell 605 skin of body immune mature NK T cell
   
skin of body melanocyte 64 skin of body stromal melanocyte
   
skin of body memory B cell 9 skin of body immune memory B cell
   
skin of body muscle cell 437 skin of body stromal muscle cell
   
skin of body naive B cell 7 skin of body immune naive B cell
   
skin of body naive thymus-derived CD4... 71 skin of body immune naive thymus-derived CD4-positive, al...
   
skin of body naive thymus-derived CD8... 88 skin of body immune naive thymus-derived CD8-positive, al...
   
skin of body plasma cell 24 skin of body immune plasma cell
   
skin of body regulatory T cell 126 skin of body immune regulatory T cell
   
skin of body smooth muscle cell 13 skin of body stromal smooth muscle cell
   
skin of body stromal cell 2943 skin of body stromal stromal cell
   
skin of body T cell 519 skin of body immune T cell
   
small intestine B cell 519 small intestine immune B cell
   
small intestine CD4-positive, alpha-b... 5257 small intestine immune CD4-positive, alpha-beta T cell
   
small intestine CD8-positive, alpha-b... 2323 small intestine immune CD8-positive, alpha-beta T cell
   
small intestine duodenum glandular cell 44 small intestine epithelial duodenum glandular cell
   
small intestine enterocyte 942 small intestine epithelial enterocyte
   
small intestine enterocyte 1100 small intestine epithelial enterocyte
   
small intestine fibroblast 113 small intestine stromal fibroblast
   
small intestine goblet cell 61 small intestine epithelial goblet cell
   
small intestine goblet cell 300 small intestine epithelial goblet cell
   
small intestine gut endothelial cell 46 small intestine endothelial gut endothelial cell
   
small intestine intestinal crypt stem... 102 small intestine epithelial intestinal crypt stem cell
   
small intestine intestinal crypt stem... 71 small intestine epithelial intestinal crypt stem cell
   
small intestine intestinal enteroendo... 58 small intestine epithelial intestinal enteroendocrine cell
   
small intestine intestinal tuft cell 160 small intestine epithelial intestinal tuft cell
   
small intestine mast cell 65 small intestine immune mast cell
   
small intestine monocyte 61 small intestine immune monocyte
   
small intestine neutrophil 68 small intestine immune neutrophil
   
small intestine paneth cell of epithe... 647 small intestine epithelial paneth cell of epithelium of small in...
   
small intestine plasma cell 303 small intestine immune plasma cell
   
small intestine transit amplifying cell 227 small intestine epithelial transit amplifying cell
   
spleen CD1c-positive myeloid dendriti... 51 spleen immune CD1c-positive myeloid dendritic cell
   
spleen CD4-positive, alpha-beta memor... 1771 spleen immune CD4-positive, alpha-beta memory T cell
   
spleen CD8-positive, alpha-beta memor... 4301 spleen immune CD8-positive, alpha-beta memory T cell
   
spleen CD8-positive, alpha-beta T cell 43 spleen immune CD8-positive, alpha-beta T cell
   
spleen CD141-positive myeloid dendrit... 51 spleen immune CD141-positive myeloid dendritic cell
   
spleen classical monocyte 4443 spleen immune classical monocyte
   
spleen endothelial cell 596 spleen endothelial endothelial cell
   
spleen erythrocyte 170 spleen immune erythrocyte
   
spleen hematopoietic stem cell 73 spleen immune hematopoietic stem cell
   
spleen innate lymphoid cell 117 spleen immune innate lymphoid cell
   
spleen intermediate monocyte 131 spleen immune intermediate monocyte
   
spleen macrophage 1335 spleen immune macrophage
   
spleen mature NK T cell 2439 spleen immune mature NK T cell
   
spleen memory B cell 6460 spleen immune memory B cell
   
spleen naive B cell 1044 spleen immune naive B cell
   
spleen naive thymus-derived CD4-posit... 1261 spleen immune naive thymus-derived CD4-positive, al...
   
spleen naive thymus-derived CD8-posit... 610 spleen immune naive thymus-derived CD8-positive, al...
   
spleen neutrophil 4539 spleen immune neutrophil
   
spleen plasma cell 3171 spleen immune plasma cell
   
spleen plasmacytoid dendritic cell 43 spleen immune plasmacytoid dendritic cell
   
spleen platelet 29 spleen immune platelet
   
spleen regulatory T cell 288 spleen immune regulatory T cell
   
spleen type I NK T cell 1038 spleen immune type I NK T cell
   
thymus B cell 1919 thymus immune B cell
   
thymus capillary endothelial cell 1362 thymus endothelial capillary endothelial cell
   
thymus CD4-positive helper T cell 7611 thymus immune CD4-positive helper T cell
   
thymus CD8-positive, alpha-beta cytot... 501 thymus immune CD8-positive, alpha-beta cytotoxic T ...
   
thymus CD8-positive, alpha-beta T cell 349 thymus immune CD8-positive, alpha-beta T cell
   
thymus dendritic cell 35 thymus immune dendritic cell
   
thymus DN1 thymic pro-T cell 985 thymus immune DN1 thymic pro-T cell
   
thymus DN3 thymocyte 1788 thymus immune DN3 thymocyte
   
thymus DN4 thymocyte 32 thymus immune DN4 thymocyte
   
thymus endothelial cell of artery 536 thymus endothelial endothelial cell of artery
   
thymus endothelial cell of lymphatic ... 271 thymus endothelial endothelial cell of lymphatic vessel
   
thymus erythrocyte 47 thymus immune erythrocyte
   
thymus fast muscle cell 86 thymus stromal fast muscle cell
   
thymus fibroblast 3924 thymus stromal fibroblast
   
thymus immature natural killer cell 44 thymus immune immature natural killer cell
   
thymus innate lymphoid cell 2594 thymus immune innate lymphoid cell
   
thymus macrophage 461 thymus immune macrophage
   
thymus mast cell 11 thymus immune mast cell
   
thymus mature NK T cell 274 thymus immune mature NK T cell
   
thymus medullary thymic epithelial cell 166 thymus epithelial medullary thymic epithelial cell
   
thymus memory B cell 1845 thymus immune memory B cell
   
thymus mesothelial cell 12 thymus epithelial mesothelial cell
   
thymus monocyte 434 thymus immune monocyte
   
thymus myeloid dendritic cell 3 thymus immune myeloid dendritic cell
   
thymus naive B cell 874 thymus immune naive B cell
   
thymus naive regulatory T cell 761 thymus immune naive regulatory T cell
   
thymus plasma cell 1554 thymus immune plasma cell
   
thymus T follicular helper cell 398 thymus immune T follicular helper cell
   
thymus thymocyte 553 thymus immune thymocyte
   
thymus vascular associated smooth mus... 2130 thymus stromal vascular associated smooth muscle cell
   
thymus vein endothelial cell 2104 thymus endothelial vein endothelial cell
   
tongue basal cell 6281 tongue epithelial basal cell
   
tongue capillary endothelial cell 101 tongue endothelial capillary endothelial cell
   
tongue endothelial cell of artery 40 tongue endothelial endothelial cell of artery
   
tongue endothelial cell of lymphatic ... 44 tongue endothelial endothelial cell of lymphatic vessel
   
tongue epithelial cell 2114 tongue epithelial epithelial cell
   
tongue fibroblast 251 tongue stromal fibroblast
   
tongue keratinocyte 3667 tongue epithelial keratinocyte
   
tongue leukocyte 2109 tongue immune leukocyte
   
tongue pericyte cell 117 tongue stromal pericyte cell
   
tongue Schwann cell 10 tongue stromal Schwann cell
   
tongue tongue muscle cell 60 tongue stromal tongue muscle cell
   
tongue vein endothelial cell 226 tongue endothelial vein endothelial cell
   
trachea B cell 462 trachea immune B cell
   
trachea basal cell 4198 trachea epithelial basal cell
   
trachea CD4-positive, alpha-beta T cell 65 trachea immune CD4-positive, alpha-beta T cell
   
trachea CD8-positive, alpha-beta T cell 464 trachea immune CD8-positive, alpha-beta T cell
   
trachea ciliated cell 317 trachea epithelial ciliated cell
   
trachea connective tissue cell 249 trachea stromal connective tissue cell
   
trachea double-positive, alpha-beta t... 6 trachea immune double-positive, alpha-beta thymocyte
   
trachea endothelial cell 257 trachea endothelial endothelial cell
   
trachea fibroblast 1239 trachea stromal fibroblast
   
trachea goblet cell 84 trachea epithelial goblet cell
   
trachea ionocyte 13 trachea epithelial ionocyte
   
trachea macrophage 541 trachea immune macrophage
   
trachea mast cell 69 trachea immune mast cell
   
trachea mucus secreting cell 64 trachea epithelial mucus secreting cell
   
trachea neutrophil 758 trachea immune neutrophil
   
trachea plasma cell 138 trachea immune plasma cell
   
trachea secretory cell 253 trachea epithelial secretory cell
   
trachea serous cell of epithelium of ... 41 trachea epithelial serous cell of epithelium of trachea
   
trachea smooth muscle cell 96 trachea stromal smooth muscle cell
   
trachea T cell 131 trachea immune T cell
   
trachea tracheal goblet cell 77 trachea epithelial tracheal goblet cell
   
uterus B cell 10 uterus immune B cell
   
uterus ciliated epithelial cell 31 uterus epithelial ciliated epithelial cell
   
uterus endothelial cell of lymphatic ... 86 uterus endothelial endothelial cell of lymphatic vessel
   
uterus endothelial cell 2077 uterus endothelial endothelial cell
   
uterus epithelial cell of uterus 194 uterus epithelial epithelial cell of uterus
   
uterus epithelial cell 68 uterus epithelial epithelial cell
   
uterus fibroblast 3014 uterus stromal fibroblast
   
uterus leukocyte 17 uterus immune leukocyte
   
uterus macrophage 344 uterus immune macrophage
   
uterus mature NK T cell 53 uterus immune mature NK T cell
   
uterus myometrial cell 199 uterus stromal myometrial cell
   
uterus pericyte cell 95 uterus stromal pericyte cell
   
uterus T cell 546 uterus immune T cell
   
uterus vascular associated smooth mus... 390 uterus stromal vascular associated smooth muscle cell
   
vasculature B cell 21 vasculature immune B cell
   
vasculature capillary endothelial cell 1034 vasculature endothelial capillary endothelial cell
   
vasculature endothelial cell of artery 138 vasculature endothelial endothelial cell of artery
   
vasculature endothelial cell of lymph... 44 vasculature endothelial endothelial cell of lymphatic vessel
   
vasculature endothelial cell 1564 vasculature endothelial endothelial cell
   
vasculature epithelial cell 26 vasculature epithelial epithelial cell
   
vasculature erythrocyte 64 vasculature immune erythrocyte
   
vasculature fibroblast 5867 vasculature stromal fibroblast
   
vasculature macrophage 3301 vasculature immune macrophage
   
vasculature mast cell 105 vasculature immune mast cell
   
vasculature mature NK T cell 121 vasculature immune mature NK T cell
   
vasculature pericyte cell 1193 vasculature stromal pericyte cell
   
vasculature plasma cell 42 vasculature immune plasma cell
   
vasculature smooth muscle cell 3075 vasculature stromal smooth muscle cell
   
vasculature T cell 476 vasculature immune T cell
View table schema
Data last updated at UCSC: 2022-05-12 04:58:31

Description

This track shows data from The Tabula Sapiens: a multiple organ single cell transcriptomic atlas of humans. The dataset covers ~500,000 cells from a total of 24 human tissues and organs from all regions of the body using both droplet-based and plate-based single-cell RNA-sequencing (scRNA-seq). Samples were taken from the human bladder, blood, bone marrow, eye, fat, heart, kidney, large intestine, liver, lung, lymph node, mammary, muscle, pancreas, prostate, salivary gland, skin, small intestine, spleen, thymus, tongue, trachea, uterus, and vasculature. The dataset includes 264,009 immune cells, 102,580 epithelial cells, 32,701 endothelial cells, and 81,529 stromal cells. A total of 475 distinct cell types were identified.

This track collection contains two bar chart tracks of RNA expression. The first track, Tabula Tissue Cell allows cells to be grouped together and faceted on up to 3 categories: tissue, cell class, and cell type. The second track, Tabula Details allows cells to be grouped together and faceted on up to 7 categories: tissue, cell class, cell type, subtissue, sex, donor, and assay.

Please see tabula-sapiens-portal.ds.czbiohub.org for further interactive displays and additional data.

Display Conventions and Configuration

The cell types are colored by which compartment they belong to according to the following table. In addition, cells found in the Tabula Details track with less than 100 transcripts will be a lighter shade and less concentrated in color to represent a low number of transcripts.

Color Cell Compartment
epithelial
endothelial
germline
immune
stromal

Methods

All tissues

36 tissue specimens comprising 24 unique tissues and organs were collected from 15 human donors (TSP1-15) with a mean age of 51 years. Tissue specimens were collected at various hospital locations in the Northern California region and transported on ice in less than one hour to preserve cell viability. Single cell suspensions from each organ were prepared in tissue expert laboratories at Stanford and UCSF. For each tissue, the dissociated cells were sorted using MACS and FACS to balance immune, stromal, epithelial, and endothelial cell types.

Sequencing libraries for all tissues were prepared using 10x 3' v3.1, 10x 5' v2, and Smart-seq2 (SS2) protocols for Illumina sequencing. Two 10x reactions per organ were loaded with 7,000 cells each with the goal to yield 10,000 QC-passed cells. Four 384-well Smartseq2 plates were run per organ. In most organs, one plate was used for each compartment (epithelial, endothelial, immune, and stromal), however, to capture rare cells, some organ experts allocated cells across the four plates differently. Sequencing runs for droplet libraries were loaded onto the NovaSeq S4 flow cell in sets of 16 to 20 libraries of approximately 5,000 cells per library with the goal of generating 50,000 to 75,000 reads per cell. Plate libraries were run in sets of 20 plates on Novaseq S4 flow cells to allow generating 1M reads per cell, depending on library quality. 152 10x reactions were performed, yielding 454,069 cells passing QC, and 161 smartseq2 plates were processed, yielding 27,051 cells passing QC.

Tissues collected from the same donor were used to study the clonal distribution of T cells between tissues, to understand the tissue specific mutation rate in B cells, and to analyze the cell cycle state and proliferative potential of shared cell types across tissues. RNA splicing analysis was also used to characterize cell type specific splicing and its variation across individuals.

For detailed methods and information on donors for each organ or tissue please refer to Quake et al, 2021 or the Tabula Sapiens website.

Errata

Some cell types, particularly in the intestines, are duplicated due to the use of multiple ontologies for the same cell type. In a future version, we plan to pool the data from these duplicates.

Data Access

The raw bar chart data can be explored interactively with the Table Browser, or the Data Integrator. For automated analysis, the data may be queried from our REST API. Please refer to our mailing list archives for questions, or our Data Access FAQ for more information.

The cell/gene matrix and cell-level metadata was downloaded from the UCSC Cell Browser. The UCSC command line utility matrixClusterColumns, matrixToBarChart, and bedToBigBed were used to transform these into a bar chart format bigBed file that can be visualized. The UCSC utilities can be found on our download server.

Credits

Thanks to the Tabula Sapiens Consortium who worked on producing and publishing this data set. The data were integrated into the UCSC Genome Browser by Jim Kent, Brittney Wick, and Rachel Schwartz.

References

The Tabula Sapiens Consortium, Quake SR., The Tabula Sapiens: A Multiple Organ Single Cell Transcriptomic Atlas of Humans. bioRxiv. 2021 March 4.; doi: https://doi.org/10.1101/2021.07.19.452956.