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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 subtissue cell_class cell_type sex donor assay
   
bladder organ//endothelial/capillary ... 1 bladder organ endothelial capillary endothelial cell female TSP1 Smart-seq2
   
bladder organ//immune/plasmacytoid de... 1 bladder organ immune plasmacytoid dendritic cell female TSP1 Smart-seq2
   
bladder organ//immune/T cell/Smart-se... 1 bladder organ immune T cell female TSP1 Smart-seq2
   
blood//immune/common myeloid progenit... 1 blood immune common myeloid progenitor female TSP1 10x 3' v3
   
blood//immune/erythrocyte/Smart-seq2/... 1 blood immune erythrocyte female TSP1 Smart-seq2
   
blood//immune/neutrophil/Smart-seq2/f... 1 blood immune neutrophil female TSP1 Smart-seq2
   
lung/medial-distal/immune/B cell/Smar... 1 lung medial-distal immune B cell female TSP1 Smart-seq2
   
lung/medial-distal/endothelial/lung m... 1 lung medial-distal endothelial lung microvascular endothelial cell female TSP1 Smart-seq2
   
lung/proximal/endothelial/lung microv... 1 lung proximal endothelial lung microvascular endothelial cell female TSP1 Smart-seq2
   
lung/proximal/immune/plasma cell/Smar... 1 lung proximal immune plasma cell female TSP1 Smart-seq2
   
lung/proximal/immune/plasmacytoid den... 1 lung proximal immune plasmacytoid dendritic cell female TSP1 Smart-seq2
   
lung/proximal/epithelial/type I pneum... 1 lung proximal epithelial type I pneumocyte female TSP1 Smart-seq2
   
muscle tissue//immune/erythrocyte/10x... 1 muscle tissue immune erythrocyte female TSP1 10x 3' v3
   
pancreas/endocrine/immune/mast cell/1... 1 pancreas endocrine immune mast cell female TSP1 10x 3' v3
   
pancreas/endocrine/stromal/pancreatic... 1 pancreas endocrine stromal pancreatic stellate cell female TSP1 10x 3' v3
   
pancreas/exocrine/epithelial/pancreat... 1 pancreas exocrine epithelial pancreatic PP cell female TSP1 10x 3' v3
   
pancreas/exocrine/immune/T cell/10x 3... 1 pancreas exocrine immune T cell female TSP1 10x 3' v3
   
blood//immune/hematopoietic stem cell... 2 blood immune hematopoietic stem cell female TSP1 10x 3' v3
   
blood//immune/neutrophil/10x 3' v3/fe... 2 blood immune neutrophil female TSP1 10x 3' v3
   
lung/medial-distal/endothelial/endoth... 2 lung medial-distal endothelial endothelial cell of lymphatic vessel female TSP1 Smart-seq2
   
lung/medial-distal/stromal/vascular a... 2 lung medial-distal stromal vascular associated smooth muscle cell female TSP1 Smart-seq2
   
lung//stromal/myofibroblast cell/10x ... 2 lung stromal myofibroblast cell female TSP1 10x 3' v3
   
lung/proximal/immune/B cell/Smart-seq... 2 lung proximal immune B cell female TSP1 Smart-seq2
   
lung/proximal/immune/neutrophil/Smart... 2 lung proximal immune neutrophil female TSP1 Smart-seq2
   
muscle tissue//immune/CD8-positive, a... 2 muscle tissue immune CD8-positive, alpha-beta T cell female TSP1 10x 3' v3
   
pancreas/endocrine/epithelial/pancrea... 2 pancreas endocrine epithelial pancreatic PP cell female TSP1 10x 3' v3
   
pancreas/endocrine/epithelial/type B ... 2 pancreas endocrine epithelial type B pancreatic cell female TSP1 10x 3' v3
   
pancreas/exocrine/immune/B cell/10x 3... 2 pancreas exocrine immune B cell female TSP1 10x 3' v3
   
lung/medial-distal/immune/mature NK T... 3 lung medial-distal immune mature NK T cell female TSP1 Smart-seq2
   
lung/medial-distal/immune/non-classic... 3 lung medial-distal immune non-classical monocyte female TSP1 Smart-seq2
   
lung//stromal/pericyte cell/10x 3' v3... 3 lung stromal pericyte cell female TSP1 10x 3' v3
   
lung/proximal/immune/mature NK T cell... 3 lung proximal immune mature NK T cell female TSP1 Smart-seq2
   
lung/proximal/immune/non-classical mo... 3 lung proximal immune non-classical monocyte female TSP1 Smart-seq2
   
pancreas/endocrine/epithelial/pancrea... 3 pancreas endocrine epithelial pancreatic A cell female TSP1 10x 3' v3
   
pancreas/exocrine/epithelial/pancreat... 3 pancreas exocrine epithelial pancreatic A cell female TSP1 Smart-seq2
   
bladder organ//stromal/smooth muscle ... 4 bladder organ stromal smooth muscle cell female TSP1 Smart-seq2
   
lung/medial-distal/immune/basophil/Sm... 4 lung medial-distal immune basophil female TSP1 Smart-seq2
   
lung/medial-distal/stromal/bronchial ... 4 lung medial-distal stromal bronchial smooth muscle cell female TSP1 Smart-seq2
   
lung/medial-distal/epithelial/club ce... 4 lung medial-distal epithelial club cell female TSP1 Smart-seq2
   
lung/medial-distal/epithelial/type I ... 4 lung medial-distal epithelial type I pneumocyte female TSP1 Smart-seq2
   
lung/proximal/immune/basophil/Smart-s... 4 lung proximal immune basophil female TSP1 Smart-seq2
   
lung/proximal/stromal/bronchial smoot... 4 lung proximal stromal bronchial smooth muscle cell female TSP1 Smart-seq2
   
lung/medial-distal/endothelial/vein e... 5 lung medial-distal endothelial vein endothelial cell female TSP1 Smart-seq2
   
lung/proximal/epithelial/basal cell/S... 5 lung proximal epithelial basal cell female TSP1 Smart-seq2
   
lung/proximal/epithelial/club cell/Sm... 5 lung proximal epithelial club cell female TSP1 Smart-seq2
   
pancreas/endocrine/immune/myeloid cel... 5 pancreas endocrine immune myeloid cell female TSP1 10x 3' v3
   
lung//immune/mature NK T cell/10x 3' ... 6 lung immune mature NK T cell female TSP1 10x 3' v3
   
lung/proximal/stromal/vascular associ... 6 lung proximal stromal vascular associated smooth muscle cell female TSP1 Smart-seq2
   
lung//epithelial/serous cell of epith... 6 lung epithelial serous cell of epithelium of bronchus female TSP1 10x 3' v3
   
muscle tissue//endothelial/endothelia... 6 muscle tissue endothelial endothelial cell of lymphatic vessel female TSP1 Smart-seq2
   
muscle tissue//stromal/fast muscle ce... 6 muscle tissue stromal fast muscle cell female TSP1 Smart-seq2
   
muscle tissue//immune/mast cell/10x 3... 6 muscle tissue immune mast cell female TSP1 10x 3' v3
   
pancreas/endocrine/stromal/pancreatic... 6 pancreas endocrine stromal pancreatic stellate cell female TSP1 Smart-seq2
   
pancreas/endocrine/immune/T cell/Smar... 6 pancreas endocrine immune T cell female TSP1 Smart-seq2
   
blood//immune/plasmablast/10x 3' v3/f... 7 blood immune plasmablast female TSP1 10x 3' v3
   
lung/medial-distal/immune/CD8-positiv... 7 lung medial-distal immune CD8-positive, alpha-beta T cell female TSP1 Smart-seq2
   
lung/proximal/immune/CD4-positive, al... 7 lung proximal immune CD4-positive, alpha-beta T cell female TSP1 Smart-seq2
   
lung/proximal/endothelial/vein endoth... 7 lung proximal endothelial vein endothelial cell female TSP1 Smart-seq2
   
lung/medial-distal/epithelial/basal c... 8 lung medial-distal epithelial basal cell female TSP1 Smart-seq2
   
lung/medial-distal/stromal/pericyte c... 8 lung medial-distal stromal pericyte cell female TSP1 Smart-seq2
   
lung/medial-distal/epithelial/respira... 8 lung medial-distal epithelial respiratory goblet cell female TSP1 Smart-seq2
   
lung/proximal/endothelial/endothelial... 8 lung proximal endothelial endothelial cell of artery female TSP1 Smart-seq2
   
muscle tissue//stromal/slow muscle ce... 8 muscle tissue stromal slow muscle cell female TSP1 Smart-seq2
   
muscle tissue//immune/T cell/10x 3' v... 8 muscle tissue immune T cell female TSP1 10x 3' v3
   
lung/medial-distal/immune/CD4-positiv... 9 lung medial-distal immune CD4-positive, alpha-beta T cell female TSP1 Smart-seq2
   
lung/medial-distal/endothelial/endoth... 9 lung medial-distal endothelial endothelial cell of artery female TSP1 Smart-seq2
   
lung/proximal/endothelial/endothelial... 9 lung proximal endothelial endothelial cell of lymphatic vessel female TSP1 Smart-seq2
   
muscle tissue//endothelial/endothelia... 9 muscle tissue endothelial endothelial cell of lymphatic vessel female TSP1 10x 3' v3
   
muscle tissue//immune/mast cell/Smart... 9 muscle tissue immune mast cell female TSP1 Smart-seq2
   
pancreas/endocrine/epithelial/type B ... 9 pancreas endocrine epithelial type B pancreatic cell female TSP1 Smart-seq2
   
pancreas/exocrine/epithelial/pancreat... 9 pancreas exocrine epithelial pancreatic D cell female TSP1 10x 3' v3
   
lung//epithelial/mesothelial cell/10x... 10 lung epithelial mesothelial cell female TSP1 10x 3' v3
   
lung/proximal/stromal/pericyte cell/S... 10 lung proximal stromal pericyte cell female TSP1 Smart-seq2
   
muscle tissue//immune/T cell/Smart-se... 10 muscle tissue immune T cell female TSP1 Smart-seq2
   
bladder organ//immune/B cell/Smart-se... 11 bladder organ immune B cell female TSP1 Smart-seq2
   
blood//immune/mature NK T cell/Smart-... 11 blood immune mature NK T cell female TSP1 Smart-seq2
   
bladder organ//immune/mature NK T cel... 14 bladder organ immune mature NK T cell female TSP1 10x 3' v3
   
lung/medial-distal/epithelial/lung ci... 15 lung medial-distal epithelial lung ciliated cell female TSP1 Smart-seq2
   
lung/proximal/epithelial/respiratory ... 15 lung proximal epithelial respiratory goblet cell female TSP1 Smart-seq2
   
muscle tissue//immune/CD4-positive, a... 16 muscle tissue immune CD4-positive, alpha-beta T cell female TSP1 10x 3' v3
   
bladder organ//stromal/myofibroblast ... 17 bladder organ stromal myofibroblast cell female TSP1 Smart-seq2
   
bladder organ//immune/plasmacytoid de... 17 bladder organ immune plasmacytoid dendritic cell female TSP1 10x 3' v3
   
lung//immune/plasmacytoid dendritic c... 17 lung immune plasmacytoid dendritic cell female TSP1 10x 3' v3
   
lung/proximal/immune/dendritic cell/S... 17 lung proximal immune dendritic cell female TSP1 Smart-seq2
   
lung/proximal/epithelial/lung ciliate... 17 lung proximal epithelial lung ciliated cell female TSP1 Smart-seq2
   
blood//immune/monocyte/Smart-seq2/fem... 18 blood immune monocyte female TSP1 Smart-seq2
   
lung//endothelial/endothelial cell of... 18 lung endothelial endothelial cell of lymphatic vessel female TSP1 10x 3' v3
   
lung/proximal/stromal/adventitial cel... 18 lung proximal stromal adventitial cell female TSP1 Smart-seq2
   
lung//endothelial/lung microvascular ... 20 lung endothelial lung microvascular endothelial cell female TSP1 10x 3' v3
   
lung/medial-distal/immune/macrophage/... 20 lung medial-distal immune macrophage female TSP1 Smart-seq2
   
lung/medial-distal/immune/dendritic c... 21 lung medial-distal immune dendritic cell female TSP1 Smart-seq2
   
lung/proximal/immune/macrophage/Smart... 21 lung proximal immune macrophage female TSP1 Smart-seq2
   
bladder organ//endothelial/endothelia... 22 bladder organ endothelial endothelial cell of lymphatic vessel female TSP1 Smart-seq2
   
lung/medial-distal/stromal/adventitia... 22 lung medial-distal stromal adventitial cell female TSP1 Smart-seq2
   
lung/proximal/immune/CD8-positive, al... 22 lung proximal immune CD8-positive, alpha-beta T cell female TSP1 Smart-seq2
   
pancreas/endocrine/epithelial/pancrea... 22 pancreas endocrine epithelial pancreatic A cell female TSP1 Smart-seq2
   
pancreas/endocrine/immune/T cell/10x ... 22 pancreas endocrine immune T cell female TSP1 10x 3' v3
   
blood//immune/memory B cell/Smart-seq... 24 blood immune memory B cell female TSP1 Smart-seq2
   
lung//stromal/bronchial smooth muscle... 25 lung stromal bronchial smooth muscle cell female TSP1 10x 3' v3
   
blood//immune/CD8-positive, alpha-bet... 26 blood immune CD8-positive, alpha-beta T cell female TSP1 Smart-seq2
   
pancreas/endocrine/endothelial/endoth... 27 pancreas endocrine endothelial endothelial cell female TSP1 Smart-seq2
   
pancreas/endocrine/immune/B cell/10x ... 28 pancreas endocrine immune B cell female TSP1 10x 3' v3
   
pancreas/exocrine/immune/myeloid cell... 28 pancreas exocrine immune myeloid cell female TSP1 10x 3' v3
   
bladder organ//stromal/pericyte cell/... 30 bladder organ stromal pericyte cell female TSP1 Smart-seq2
   
muscle tissue//immune/mature NK T cel... 31 muscle tissue immune mature NK T cell female TSP1 10x 3' v3
   
lung/medial-distal/endothelial/capill... 32 lung medial-distal endothelial capillary endothelial cell female TSP1 Smart-seq2
   
pancreas/exocrine/stromal/pancreatic ... 32 pancreas exocrine stromal pancreatic stellate cell female TSP1 10x 3' v3
   
lung/medial-distal/stromal/fibroblast... 34 lung medial-distal stromal fibroblast female TSP1 Smart-seq2
   
lung//immune/plasma cell/10x 3' v3/fe... 34 lung immune plasma cell female TSP1 10x 3' v3
   
pancreas/endocrine/epithelial/pancrea... 34 pancreas endocrine epithelial pancreatic ductal cell female TSP1 Smart-seq2
   
pancreas/exocrine/epithelial/pancreat... 34 pancreas exocrine epithelial pancreatic ductal cell female TSP1 Smart-seq2
   
blood//immune/naive B cell/Smart-seq2... 35 blood immune naive B cell female TSP1 Smart-seq2
   
lung/medial-distal/immune/classical m... 35 lung medial-distal immune classical monocyte female TSP1 Smart-seq2
   
lung/proximal/epithelial/type II pneu... 35 lung proximal epithelial type II pneumocyte female TSP1 Smart-seq2
   
lung//stromal/vascular associated smo... 35 lung stromal vascular associated smooth muscle cell female TSP1 10x 3' v3
   
muscle tissue//immune/CD8-positive, a... 35 muscle tissue immune CD8-positive, alpha-beta T cell female TSP1 Smart-seq2
   
lung//stromal/adventitial cell/10x 3'... 37 lung stromal adventitial cell female TSP1 10x 3' v3
   
lung//epithelial/basal cell/10x 3' v3... 39 lung epithelial basal cell female TSP1 10x 3' v3
   
muscle tissue//endothelial/endothelia... 43 muscle tissue endothelial endothelial cell of artery female TSP1 10x 3' v3
   
pancreas/exocrine/epithelial/pancreat... 43 pancreas exocrine epithelial pancreatic A cell female TSP1 10x 3' v3
   
lung/proximal/stromal/fibroblast/Smar... 44 lung proximal stromal fibroblast female TSP1 Smart-seq2
   
bladder organ//endothelial/endothelia... 45 bladder organ endothelial endothelial cell of lymphatic vessel female TSP1 10x 3' v3
   
lung//epithelial/club cell/10x 3' v3/... 46 lung epithelial club cell female TSP1 10x 3' v3
   
lung/medial-distal/epithelial/type II... 46 lung medial-distal epithelial type II pneumocyte female TSP1 Smart-seq2
   
muscle tissue//stromal/tendon cell/Sm... 47 muscle tissue stromal tendon cell female TSP1 Smart-seq2
   
pancreas/endocrine/immune/mast cell/S... 50 pancreas endocrine immune mast cell female TSP1 Smart-seq2
   
pancreas/endocrine/immune/myeloid cel... 52 pancreas endocrine immune myeloid cell female TSP1 Smart-seq2
   
bladder organ//endothelial/capillary ... 55 bladder organ endothelial capillary endothelial cell female TSP1 10x 3' v3
   
lung/proximal/immune/classical monocy... 55 lung proximal immune classical monocyte female TSP1 Smart-seq2
   
muscle tissue//stromal/slow muscle ce... 57 muscle tissue stromal slow muscle cell female TSP1 10x 3' v3
   
lung/proximal/endothelial/capillary e... 59 lung proximal endothelial capillary endothelial cell female TSP1 Smart-seq2
   
lung//immune/B cell/10x 3' v3/female/... 62 lung immune B cell female TSP1 10x 3' v3
   
muscle tissue//immune/CD4-positive, a... 62 muscle tissue immune CD4-positive, alpha-beta T cell female TSP1 Smart-seq2
   
bladder organ//endothelial/vein endot... 64 bladder organ endothelial vein endothelial cell female TSP1 Smart-seq2
   
lung//endothelial/endothelial cell of... 67 lung endothelial endothelial cell of artery female TSP1 10x 3' v3
   
muscle tissue//immune/macrophage/10x ... 68 muscle tissue immune macrophage female TSP1 10x 3' v3
   
pancreas/endocrine/epithelial/pancrea... 68 pancreas endocrine epithelial pancreatic PP cell female TSP1 Smart-seq2
   
pancreas/exocrine/epithelial/type B p... 71 pancreas exocrine epithelial type B pancreatic cell female TSP1 10x 3' v3
   
muscle tissue//immune/mature NK T cel... 75 muscle tissue immune mature NK T cell female TSP1 Smart-seq2
   
bladder organ//immune/mast cell/Smart... 76 bladder organ immune mast cell female TSP1 Smart-seq2
   
bladder organ//stromal/smooth muscle ... 77 bladder organ stromal smooth muscle cell female TSP1 10x 3' v3
   
bladder organ//immune/plasma cell/Sma... 84 bladder organ immune plasma cell female TSP1 Smart-seq2
   
bladder organ//immune/macrophage/Smar... 89 bladder organ immune macrophage female TSP1 Smart-seq2
   
blood//immune/erythrocyte/10x 3' v3/f... 89 blood immune erythrocyte female TSP1 10x 3' v3
   
pancreas/endocrine/immune/B cell/Smar... 89 pancreas endocrine immune B cell female TSP1 Smart-seq2
   
pancreas/exocrine/endothelial/endothe... 92 pancreas exocrine endothelial endothelial cell female TSP1 10x 3' v3
   
bladder organ//endothelial/vein endot... 94 bladder organ endothelial vein endothelial cell female TSP1 10x 3' v3
   
lung//stromal/fibroblast/10x 3' v3/fe... 95 lung stromal fibroblast female TSP1 10x 3' v3
   
muscle tissue//immune/macrophage/Smar... 106 muscle tissue immune macrophage female TSP1 Smart-seq2
   
muscle tissue//stromal/tendon cell/10... 106 muscle tissue stromal tendon cell female TSP1 10x 3' v3
   
muscle tissue//stromal/skeletal muscl... 112 muscle tissue stromal skeletal muscle satellite stem cell female TSP1 Smart-seq2
   
blood//immune/mature NK T cell/10x 3'... 115 blood immune mature NK T cell female TSP1 10x 3' v3
   
lung//endothelial/vein endothelial ce... 124 lung endothelial vein endothelial cell female TSP1 10x 3' v3
   
lung//immune/CD8-positive, alpha-beta... 130 lung immune CD8-positive, alpha-beta T cell female TSP1 10x 3' v3
   
bladder organ//epithelial/bladder uro... 133 bladder organ epithelial bladder urothelial cell female TSP1 Smart-seq2
   
lung//endothelial/capillary endotheli... 133 lung endothelial capillary endothelial cell female TSP1 10x 3' v3
   
muscle tissue//endothelial/endothelia... 134 muscle tissue endothelial endothelial cell of vascular tree female TSP1 Smart-seq2
   
muscle tissue//stromal/pericyte cell/... 136 muscle tissue stromal pericyte cell female TSP1 Smart-seq2
   
lung//epithelial/type I pneumocyte/10... 142 lung epithelial type I pneumocyte female TSP1 10x 3' v3
   
muscle tissue//stromal/fast muscle ce... 143 muscle tissue stromal fast muscle cell female TSP1 10x 3' v3
   
blood//immune/memory B cell/10x 3' v3... 144 blood immune memory B cell female TSP1 10x 3' v3
   
lung//immune/CD4-positive, alpha-beta... 144 lung immune CD4-positive, alpha-beta T cell female TSP1 10x 3' v3
   
pancreas/endocrine/endothelial/endoth... 146 pancreas endocrine endothelial endothelial cell female TSP1 10x 3' v3
   
lung//immune/non-classical monocyte/1... 151 lung immune non-classical monocyte female TSP1 10x 3' v3
   
blood//immune/CD4-positive, alpha-bet... 158 blood immune CD4-positive, alpha-beta T cell female TSP1 Smart-seq2
   
muscle tissue//endothelial/capillary ... 174 muscle tissue endothelial capillary endothelial cell female TSP1 Smart-seq2
   
bladder organ//stromal/fibroblast/Sma... 181 bladder organ stromal fibroblast female TSP1 Smart-seq2
   
pancreas/endocrine/epithelial/pancrea... 196 pancreas endocrine epithelial pancreatic acinar cell female TSP1 Smart-seq2
   
blood//immune/naive B cell/10x 3' v3/... 228 blood immune naive B cell female TSP1 10x 3' v3
   
muscle tissue//stromal/skeletal muscl... 234 muscle tissue stromal skeletal muscle satellite stem cell female TSP1 10x 3' v3
   
lung//immune/dendritic cell/10x 3' v3... 240 lung immune dendritic cell female TSP1 10x 3' v3
   
pancreas/endocrine/epithelial/pancrea... 246 pancreas endocrine epithelial pancreatic acinar cell female TSP1 10x 3' v3
   
lung//epithelial/respiratory goblet c... 252 lung epithelial respiratory goblet cell female TSP1 10x 3' v3
   
lung//epithelial/lung ciliated cell/1... 255 lung epithelial lung ciliated cell female TSP1 10x 3' v3
   
lung//immune/classical monocyte/10x 3... 291 lung immune classical monocyte female TSP1 10x 3' v3
   
muscle tissue//endothelial/endothelia... 302 muscle tissue endothelial endothelial cell of vascular tree female TSP1 10x 3' v3
   
pancreas/exocrine/epithelial/pancreat... 317 pancreas exocrine epithelial pancreatic acinar cell female TSP1 Smart-seq2
   
muscle tissue//stromal/mesenchymal st... 328 muscle tissue stromal mesenchymal stem cell female TSP1 Smart-seq2
   
blood//immune/CD8-positive, alpha-bet... 329 blood immune CD8-positive, alpha-beta T cell female TSP1 10x 3' v3
   
muscle tissue//stromal/pericyte cell/... 374 muscle tissue stromal pericyte cell female TSP1 10x 3' v3
   
muscle tissue//endothelial/capillary ... 375 muscle tissue endothelial capillary endothelial cell female TSP1 10x 3' v3
   
bladder organ//stromal/pericyte cell/... 481 bladder organ stromal pericyte cell female TSP1 10x 3' v3
   
lung//immune/basophil/10x 3' v3/femal... 486 lung immune basophil female TSP1 10x 3' v3
   
pancreas/endocrine/epithelial/pancrea... 505 pancreas endocrine epithelial pancreatic ductal cell female TSP1 10x 3' v3
   
bladder organ//immune/mast cell/10x 3... 573 bladder organ immune mast cell female TSP1 10x 3' v3
   
bladder organ//immune/plasma cell/10x... 589 bladder organ immune plasma cell female TSP1 10x 3' v3
   
muscle tissue//stromal/mesenchymal st... 737 muscle tissue stromal mesenchymal stem cell female TSP1 10x 3' v3
   
bladder organ//stromal/myofibroblast ... 988 bladder organ stromal myofibroblast cell female TSP1 10x 3' v3
   
pancreas/exocrine/epithelial/pancreat... 1040 pancreas exocrine epithelial pancreatic ductal cell female TSP1 10x 3' v3
   
lung//epithelial/type II pneumocyte/1... 1109 lung epithelial type II pneumocyte female TSP1 10x 3' v3
   
blood//immune/CD4-positive, alpha-bet... 1132 blood immune CD4-positive, alpha-beta T cell female TSP1 10x 3' v3
   
bladder organ//immune/T cell/10x 3' v... 1220 bladder organ immune T cell female TSP1 10x 3' v3
   
blood//immune/monocyte/10x 3' v3/fema... 1616 blood immune monocyte female TSP1 10x 3' v3
   
bladder organ//epithelial/bladder uro... 1784 bladder organ epithelial bladder urothelial cell female TSP1 10x 3' v3
   
bladder organ//immune/macrophage/10x ... 2004 bladder organ immune macrophage female TSP1 10x 3' v3
   
bladder organ//stromal/fibroblast/10x... 3081 bladder organ stromal fibroblast female TSP1 10x 3' v3
   
pancreas/exocrine/epithelial/pancreat... 3605 pancreas exocrine epithelial pancreatic acinar cell female TSP1 10x 3' v3
   
lung//immune/macrophage/10x 3' v3/fem... 8530 lung immune macrophage female TSP1 10x 3' v3
View table schema
Data last updated at UCSC: 2022-05-12 04:59:08

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.