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

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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
   
blood//immune/alpha-beta T cell/10x 3... 31 blood immune alpha-beta T cell female TSP7 10x 3' v3
   
blood//immune/basophil/10x 3' v3/fema... 7 blood immune basophil female TSP7 10x 3' v3
   
blood//immune/CD4-positive, alpha-bet... 576 blood immune CD4-positive, alpha-beta memory T cell female TSP7 10x 3' v3
   
blood//immune/CD4-positive, alpha-bet... 92 blood immune CD4-positive, alpha-beta memory T cell female TSP7 Smart-seq2
   
blood//immune/CD8-positive, alpha-bet... 1361 blood immune CD8-positive, alpha-beta cytokine sec... female TSP7 10x 3' v3
   
blood//immune/CD8-positive, alpha-bet... 16 blood immune CD8-positive, alpha-beta cytokine sec... female TSP7 Smart-seq2
   
blood//immune/CD8-positive, alpha-bet... 174 blood immune CD8-positive, alpha-beta T cell female TSP7 10x 3' v3
   
blood//immune/CD8-positive, alpha-bet... 24 blood immune CD8-positive, alpha-beta T cell female TSP7 Smart-seq2
   
blood//immune/CD141-positive myeloid ... 7 blood immune CD141-positive myeloid dendritic cell female TSP7 10x 3' v3
   
blood//immune/classical monocyte/10x ... 2846 blood immune classical monocyte female TSP7 10x 3' v3
   
blood//immune/classical monocyte/Smar... 212 blood immune classical monocyte female TSP7 Smart-seq2
   
blood//immune/erythrocyte/10x 3' v3/f... 7527 blood immune erythrocyte female TSP7 10x 3' v3
   
blood//immune/erythrocyte/Smart-seq2/... 72 blood immune erythrocyte female TSP7 Smart-seq2
   
blood//immune/hematopoietic stem cell... 23 blood immune hematopoietic stem cell female TSP7 10x 3' v3
   
blood//immune/mature NK T cell/10x 3'... 1681 blood immune mature NK T cell female TSP7 10x 3' v3
   
blood//immune/mature NK T cell/Smart-... 28 blood immune mature NK T cell female TSP7 Smart-seq2
   
blood//immune/memory B cell/10x 3' v3... 239 blood immune memory B cell female TSP7 10x 3' v3
   
blood//immune/memory B cell/Smart-seq... 28 blood immune memory B cell female TSP7 Smart-seq2
   
blood//immune/naive B cell/10x 3' v3/... 716 blood immune naive B cell female TSP7 10x 3' v3
   
blood//immune/naive B cell/Smart-seq2... 13 blood immune naive B cell female TSP7 Smart-seq2
   
blood//immune/naive thymus-derived CD... 280 blood immune naive thymus-derived CD4-positive, al... female TSP7 10x 3' v3
   
blood//immune/naive thymus-derived CD... 9 blood immune naive thymus-derived CD4-positive, al... female TSP7 Smart-seq2
   
blood//immune/neutrophil/10x 3' v3/fe... 969 blood immune neutrophil female TSP7 10x 3' v3
   
blood//immune/neutrophil/Smart-seq2/f... 62 blood immune neutrophil female TSP7 Smart-seq2
   
blood//immune/non-classical monocyte/... 5 blood immune non-classical monocyte female TSP7 10x 3' v3
   
blood//immune/plasma cell/10x 3' v3/f... 235 blood immune plasma cell female TSP7 10x 3' v3
   
blood//immune/plasma cell/Smart-seq2/... 3 blood immune plasma cell female TSP7 Smart-seq2
   
blood//immune/plasmacytoid dendritic ... 9 blood immune plasmacytoid dendritic cell female TSP7 10x 3' v3
   
blood//immune/platelet/10x 3' v3/fema... 100 blood immune platelet female TSP7 10x 3' v3
   
blood//immune/platelet/Smart-seq2/fem... 35 blood immune platelet female TSP7 Smart-seq2
   
blood//immune/type I NK T cell/10x 3'... 432 blood immune type I NK T cell female TSP7 10x 3' v3
   
blood//immune/type I NK T cell/Smart-... 19 blood immune type I NK T cell female TSP7 Smart-seq2
   
lymph node/inguinal/immune/B cell/10x... 5673 lymph node inguinal immune B cell female TSP7 10x 3' v3
   
lymph node/inguinal/immune/B cell/Sma... 262 lymph node inguinal immune B cell female TSP7 Smart-seq2
   
lymph node/inguinal/immune/CD1c-posit... 10 lymph node inguinal immune CD1c-positive myeloid dendritic cell female TSP7 10x 3' v3
   
lymph node/inguinal/immune/CD141-posi... 1 lymph node inguinal immune CD141-positive myeloid dendritic cell female TSP7 10x 3' v3
   
lymph node/inguinal/immune/classical ... 28 lymph node inguinal immune classical monocyte female TSP7 10x 3' v3
   
lymph node/inguinal/immune/classical ... 2 lymph node inguinal immune classical monocyte female TSP7 Smart-seq2
   
lymph node/inguinal/immune/effector C... 673 lymph node inguinal immune effector CD4-positive, alpha-beta T cell female TSP7 10x 3' v3
   
lymph node/inguinal/immune/effector C... 38 lymph node inguinal immune effector CD4-positive, alpha-beta T cell female TSP7 Smart-seq2
   
lymph node/inguinal/immune/effector C... 329 lymph node inguinal immune effector CD8-positive, alpha-beta T cell female TSP7 10x 3' v3
   
lymph node/inguinal/immune/effector C... 17 lymph node inguinal immune effector CD8-positive, alpha-beta T cell female TSP7 Smart-seq2
   
lymph node/inguinal/endothelial/endot... 2 lymph node inguinal endothelial endothelial cell female TSP7 10x 3' v3
   
lymph node/inguinal/endothelial/endot... 1 lymph node inguinal endothelial endothelial cell female TSP7 Smart-seq2
   
lymph node/inguinal/immune/erythrocyt... 2 lymph node inguinal immune erythrocyte female TSP7 Smart-seq2
   
lymph node/inguinal/immune/hematopoie... 5 lymph node inguinal immune hematopoietic stem cell female TSP7 10x 3' v3
   
lymph node/inguinal/immune/innate lym... 199 lymph node inguinal immune innate lymphoid cell female TSP7 10x 3' v3
   
lymph node/inguinal/immune/innate lym... 236 lymph node inguinal immune innate lymphoid cell female TSP7 Smart-seq2
   
lymph node/inguinal/immune/intermedia... 18 lymph node inguinal immune intermediate monocyte female TSP7 10x 3' v3
   
lymph node/inguinal/immune/macrophage... 4 lymph node inguinal immune macrophage female TSP7 10x 3' v3
   
lymph node/inguinal/immune/mast cell/... 4 lymph node inguinal immune mast cell female TSP7 10x 3' v3
   
lymph node/inguinal/immune/mast cell/... 4 lymph node inguinal immune mast cell female TSP7 Smart-seq2
   
lymph node/inguinal/immune/mature con... 1 lymph node inguinal immune mature conventional dendritic cell female TSP7 Smart-seq2
   
lymph node/inguinal/immune/mature NK ... 43 lymph node inguinal immune mature NK T cell female TSP7 10x 3' v3
   
lymph node/inguinal/immune/mature NK ... 7 lymph node inguinal immune mature NK T cell female TSP7 Smart-seq2
   
lymph node/inguinal/immune/neutrophil... 8 lymph node inguinal immune neutrophil female TSP7 10x 3' v3
   
lymph node/inguinal/immune/non-classi... 2 lymph node inguinal immune non-classical monocyte female TSP7 10x 3' v3
   
lymph node/inguinal/immune/non-classi... 1 lymph node inguinal immune non-classical monocyte female TSP7 Smart-seq2
   
lymph node/inguinal/immune/plasma cel... 107 lymph node inguinal immune plasma cell female TSP7 10x 3' v3
   
lymph node/inguinal/immune/plasma cel... 20 lymph node inguinal immune plasma cell female TSP7 Smart-seq2
   
lymph node/inguinal/immune/regulatory... 46 lymph node inguinal immune regulatory T cell female TSP7 10x 3' v3
   
lymph node/inguinal/immune/regulatory... 4 lymph node inguinal immune regulatory T cell female TSP7 Smart-seq2
   
lymph node/inguinal/immune/T cell/10x... 293 lymph node inguinal immune T cell female TSP7 10x 3' v3
   
lymph node/inguinal/immune/T cell/Sma... 46 lymph node inguinal immune T cell female TSP7 Smart-seq2
   
lymph node/inguinal/immune/type I NK ... 293 lymph node inguinal immune type I NK T cell female TSP7 10x 3' v3
   
lymph node/inguinal/immune/type I NK ... 2 lymph node inguinal immune type I NK T cell female TSP7 Smart-seq2
   
lymph node/supradiaphragmatic/immune/... 1287 lymph node supradiaphragmatic immune B cell female TSP7 10x 3' v3
   
lymph node/supradiaphragmatic/immune/... 179 lymph node supradiaphragmatic immune B cell female TSP7 Smart-seq2
   
lymph node/supradiaphragmatic/immune/... 46 lymph node supradiaphragmatic immune CD1c-positive myeloid dendritic cell female TSP7 10x 3' v3
   
lymph node/supradiaphragmatic/immune/... 1 lymph node supradiaphragmatic immune CD1c-positive myeloid dendritic cell female TSP7 Smart-seq2
   
lymph node/supradiaphragmatic/immune/... 14 lymph node supradiaphragmatic immune CD141-positive myeloid dendritic cell female TSP7 10x 3' v3
   
lymph node/supradiaphragmatic/immune/... 74 lymph node supradiaphragmatic immune classical monocyte female TSP7 10x 3' v3
   
lymph node/supradiaphragmatic/immune/... 1 lymph node supradiaphragmatic immune classical monocyte female TSP7 Smart-seq2
   
lymph node/supradiaphragmatic/immune/... 776 lymph node supradiaphragmatic immune effector CD4-positive, alpha-beta T cell female TSP7 10x 3' v3
   
lymph node/supradiaphragmatic/immune/... 79 lymph node supradiaphragmatic immune effector CD4-positive, alpha-beta T cell female TSP7 Smart-seq2
   
lymph node/supradiaphragmatic/immune/... 407 lymph node supradiaphragmatic immune effector CD8-positive, alpha-beta T cell female TSP7 10x 3' v3
   
lymph node/supradiaphragmatic/immune/... 37 lymph node supradiaphragmatic immune effector CD8-positive, alpha-beta T cell female TSP7 Smart-seq2
   
lymph node/supradiaphragmatic/endothe... 2 lymph node supradiaphragmatic endothelial endothelial cell female TSP7 10x 3' v3
   
lymph node/supradiaphragmatic/endothe... 1 lymph node supradiaphragmatic endothelial endothelial cell female TSP7 Smart-seq2
   
lymph node/supradiaphragmatic/immune/... 1 lymph node supradiaphragmatic immune erythrocyte female TSP7 10x 3' v3
   
lymph node/supradiaphragmatic/immune/... 25 lymph node supradiaphragmatic immune hematopoietic stem cell female TSP7 10x 3' v3
   
lymph node/supradiaphragmatic/immune/... 133 lymph node supradiaphragmatic immune innate lymphoid cell female TSP7 10x 3' v3
   
lymph node/supradiaphragmatic/immune/... 145 lymph node supradiaphragmatic immune innate lymphoid cell female TSP7 Smart-seq2
   
lymph node/supradiaphragmatic/immune/... 57 lymph node supradiaphragmatic immune intermediate monocyte female TSP7 10x 3' v3
   
lymph node/supradiaphragmatic/immune/... 109 lymph node supradiaphragmatic immune macrophage female TSP7 10x 3' v3
   
lymph node/supradiaphragmatic/immune/... 1 lymph node supradiaphragmatic immune macrophage female TSP7 Smart-seq2
   
lymph node/supradiaphragmatic/immune/... 95 lymph node supradiaphragmatic immune mast cell female TSP7 10x 3' v3
   
lymph node/supradiaphragmatic/immune/... 1 lymph node supradiaphragmatic immune mast cell female TSP7 Smart-seq2
   
lymph node/supradiaphragmatic/immune/... 1 lymph node supradiaphragmatic immune mature conventional dendritic cell female TSP7 10x 3' v3
   
lymph node/supradiaphragmatic/immune/... 130 lymph node supradiaphragmatic immune mature NK T cell female TSP7 10x 3' v3
   
lymph node/supradiaphragmatic/immune/... 1 lymph node supradiaphragmatic immune mature NK T cell female TSP7 Smart-seq2
   
lymph node/supradiaphragmatic/immune/... 16 lymph node supradiaphragmatic immune neutrophil female TSP7 10x 3' v3
   
lymph node/supradiaphragmatic/immune/... 8 lymph node supradiaphragmatic immune non-classical monocyte female TSP7 10x 3' v3
   
lymph node/supradiaphragmatic/immune/... 2 lymph node supradiaphragmatic immune non-classical monocyte female TSP7 Smart-seq2
   
lymph node/supradiaphragmatic/immune/... 190 lymph node supradiaphragmatic immune plasma cell female TSP7 10x 3' v3
   
lymph node/supradiaphragmatic/immune/... 17 lymph node supradiaphragmatic immune plasma cell female TSP7 Smart-seq2
   
lymph node/supradiaphragmatic/immune/... 6 lymph node supradiaphragmatic immune plasmacytoid dendritic cell female TSP7 10x 3' v3
   
lymph node/supradiaphragmatic/immune/... 132 lymph node supradiaphragmatic immune regulatory T cell female TSP7 10x 3' v3
   
lymph node/supradiaphragmatic/immune/... 7 lymph node supradiaphragmatic immune regulatory T cell female TSP7 Smart-seq2
   
lymph node/supradiaphragmatic/stromal... 5 lymph node supradiaphragmatic stromal stromal cell female TSP7 10x 3' v3
   
lymph node/supradiaphragmatic/immune/... 234 lymph node supradiaphragmatic immune T cell female TSP7 10x 3' v3
   
lymph node/supradiaphragmatic/immune/... 47 lymph node supradiaphragmatic immune T cell female TSP7 Smart-seq2
   
lymph node/supradiaphragmatic/immune/... 433 lymph node supradiaphragmatic immune type I NK T cell female TSP7 10x 3' v3
   
saliva-secreting gland/parotid/epithe... 1801 saliva-secreting gland parotid epithelial acinar cell of salivary gland female TSP7 10x 3' v3
   
saliva-secreting gland/parotid/stroma... 210 saliva-secreting gland parotid stromal adventitial cell female TSP7 10x 3' v3
   
saliva-secreting gland/parotid/stroma... 119 saliva-secreting gland parotid stromal adventitial cell female TSP7 Smart-seq2
   
saliva-secreting gland/parotid/immune... 73 saliva-secreting gland parotid immune B cell female TSP7 10x 3' v3
   
saliva-secreting gland/parotid/immune... 56 saliva-secreting gland parotid immune B cell female TSP7 Smart-seq2
   
saliva-secreting gland/parotid/epithe... 31 saliva-secreting gland parotid epithelial basal cell female TSP7 10x 3' v3
   
saliva-secreting gland/parotid/immune... 1097 saliva-secreting gland parotid immune CD4-positive helper T cell female TSP7 10x 3' v3
   
saliva-secreting gland/parotid/immune... 120 saliva-secreting gland parotid immune CD4-positive helper T cell female TSP7 Smart-seq2
   
saliva-secreting gland/parotid/immune... 182 saliva-secreting gland parotid immune CD4-positive, alpha-beta T cell female TSP7 Smart-seq2
   
saliva-secreting gland/parotid/immune... 9 saliva-secreting gland parotid immune CD8-positive, alpha-beta T cell female TSP7 10x 3' v3
   
saliva-secreting gland/parotid/immune... 92 saliva-secreting gland parotid immune CD8-positive, alpha-beta T cell female TSP7 Smart-seq2
   
saliva-secreting gland/parotid/epithe... 121 saliva-secreting gland parotid epithelial duct epithelial cell female TSP7 10x 3' v3
   
saliva-secreting gland/parotid/endoth... 88 saliva-secreting gland parotid endothelial endothelial cell female TSP7 10x 3' v3
   
saliva-secreting gland/parotid/endoth... 57 saliva-secreting gland parotid endothelial endothelial cell of lymphatic vessel female TSP7 10x 3' v3
   
saliva-secreting gland/parotid/stroma... 788 saliva-secreting gland parotid stromal fibroblast female TSP7 10x 3' v3
   
saliva-secreting gland/parotid/stroma... 123 saliva-secreting gland parotid stromal fibroblast female TSP7 Smart-seq2
   
saliva-secreting gland/parotid/immune... 239 saliva-secreting gland parotid immune mature NK T cell female TSP7 10x 3' v3
   
saliva-secreting gland/parotid/immune... 2812 saliva-secreting gland parotid immune memory B cell female TSP7 10x 3' v3
   
saliva-secreting gland/parotid/immune... 63 saliva-secreting gland parotid immune memory B cell female TSP7 Smart-seq2
   
saliva-secreting gland/parotid/immune... 100 saliva-secreting gland parotid immune monocyte female TSP7 10x 3' v3
   
saliva-secreting gland/parotid/epithe... 4 saliva-secreting gland parotid epithelial myoepithelial cell female TSP7 10x 3' v3
   
saliva-secreting gland/parotid/immune... 1120 saliva-secreting gland parotid immune naive B cell female TSP7 10x 3' v3
   
saliva-secreting gland/parotid/immune... 12 saliva-secreting gland parotid immune neutrophil female TSP7 10x 3' v3
   
saliva-secreting gland/parotid/stroma... 30 saliva-secreting gland parotid stromal pericyte cell female TSP7 10x 3' v3
   
saliva-secreting gland/parotid/immune... 7 saliva-secreting gland parotid immune plasma cell female TSP7 10x 3' v3
   
saliva-secreting gland/parotid/immune... 6 saliva-secreting gland parotid immune T cell female TSP7 10x 3' v3
   
saliva-secreting gland/parotid/immune... 77 saliva-secreting gland parotid immune T cell female TSP7 Smart-seq2
   
spleen//immune/CD1c-positive myeloid ... 2 spleen immune CD1c-positive myeloid dendritic cell female TSP7 10x 3' v3
   
spleen//immune/CD4-positive, alpha-be... 342 spleen immune CD4-positive, alpha-beta memory T cell female TSP7 10x 3' v3
   
spleen//immune/CD4-positive, alpha-be... 79 spleen immune CD4-positive, alpha-beta memory T cell female TSP7 Smart-seq2
   
spleen//immune/CD8-positive, alpha-be... 577 spleen immune CD8-positive, alpha-beta memory T cell female TSP7 10x 3' v3
   
spleen//immune/CD8-positive, alpha-be... 146 spleen immune CD8-positive, alpha-beta memory T cell female TSP7 Smart-seq2
   
spleen//immune/CD141-positive myeloid... 14 spleen immune CD141-positive myeloid dendritic cell female TSP7 10x 3' v3
   
spleen//immune/CD141-positive myeloid... 3 spleen immune CD141-positive myeloid dendritic cell female TSP7 Smart-seq2
   
spleen//immune/classical monocyte/10x... 327 spleen immune classical monocyte female TSP7 10x 3' v3
   
spleen//immune/classical monocyte/Sma... 164 spleen immune classical monocyte female TSP7 Smart-seq2
   
spleen//endothelial/endothelial cell/... 287 spleen endothelial endothelial cell female TSP7 10x 3' v3
   
spleen//endothelial/endothelial cell/... 23 spleen endothelial endothelial cell female TSP7 Smart-seq2
   
spleen//immune/erythrocyte/10x 3' v3/... 16 spleen immune erythrocyte female TSP7 10x 3' v3
   
spleen//immune/hematopoietic stem cel... 28 spleen immune hematopoietic stem cell female TSP7 10x 3' v3
   
spleen//immune/innate lymphoid cell/1... 21 spleen immune innate lymphoid cell female TSP7 10x 3' v3
   
spleen//immune/innate lymphoid cell/S... 3 spleen immune innate lymphoid cell female TSP7 Smart-seq2
   
spleen//immune/intermediate monocyte/... 95 spleen immune intermediate monocyte female TSP7 10x 3' v3
   
spleen//immune/intermediate monocyte/... 6 spleen immune intermediate monocyte female TSP7 Smart-seq2
   
spleen//immune/macrophage/10x 3' v3/f... 360 spleen immune macrophage female TSP7 10x 3' v3
   
spleen//immune/macrophage/Smart-seq2/... 10 spleen immune macrophage female TSP7 Smart-seq2
   
spleen//immune/mature NK T cell/10x 3... 525 spleen immune mature NK T cell female TSP7 10x 3' v3
   
spleen//immune/mature NK T cell/Smart... 56 spleen immune mature NK T cell female TSP7 Smart-seq2
   
spleen//immune/memory B cell/10x 3' v... 1362 spleen immune memory B cell female TSP7 10x 3' v3
   
spleen//immune/memory B cell/Smart-se... 254 spleen immune memory B cell female TSP7 Smart-seq2
   
spleen//immune/naive B cell/10x 3' v3... 350 spleen immune naive B cell female TSP7 10x 3' v3
   
spleen//immune/naive B cell/Smart-seq... 50 spleen immune naive B cell female TSP7 Smart-seq2
   
spleen//immune/naive thymus-derived C... 310 spleen immune naive thymus-derived CD4-positive, al... female TSP7 10x 3' v3
   
spleen//immune/naive thymus-derived C... 54 spleen immune naive thymus-derived CD4-positive, al... female TSP7 Smart-seq2
   
spleen//immune/naive thymus-derived C... 126 spleen immune naive thymus-derived CD8-positive, al... female TSP7 10x 3' v3
   
spleen//immune/naive thymus-derived C... 18 spleen immune naive thymus-derived CD8-positive, al... female TSP7 Smart-seq2
   
spleen//immune/neutrophil/10x 3' v3/f... 570 spleen immune neutrophil female TSP7 10x 3' v3
   
spleen//immune/neutrophil/Smart-seq2/... 102 spleen immune neutrophil female TSP7 Smart-seq2
   
spleen//immune/plasma cell/10x 3' v3/... 408 spleen immune plasma cell female TSP7 10x 3' v3
   
spleen//immune/plasma cell/Smart-seq2... 129 spleen immune plasma cell female TSP7 Smart-seq2
   
spleen//immune/platelet/10x 3' v3/fem... 8 spleen immune platelet female TSP7 10x 3' v3
   
spleen//immune/regulatory T cell/10x ... 75 spleen immune regulatory T cell female TSP7 10x 3' v3
   
spleen//immune/regulatory T cell/Smar... 12 spleen immune regulatory T cell female TSP7 Smart-seq2
   
spleen//immune/type I NK T cell/10x 3... 391 spleen immune type I NK T cell female TSP7 10x 3' v3
   
spleen//immune/type I NK T cell/Smart... 58 spleen immune type I NK T cell female TSP7 Smart-seq2
   
tongue/anterior/epithelial/basal cell... 282 tongue anterior epithelial basal cell female TSP7 Smart-seq2
   
tongue/anterior/endothelial/capillary... 1 tongue anterior endothelial capillary endothelial cell female TSP7 Smart-seq2
   
tongue/anterior/endothelial/endotheli... 1 tongue anterior endothelial endothelial cell of artery female TSP7 Smart-seq2
   
tongue/anterior/endothelial/endotheli... 1 tongue anterior endothelial endothelial cell of lymphatic vessel female TSP7 Smart-seq2
   
tongue/anterior/epithelial/epithelial... 2114 tongue anterior epithelial epithelial cell female TSP7 10x 3' v3
   
tongue/anterior/stromal/fibroblast/Sm... 15 tongue anterior stromal fibroblast female TSP7 Smart-seq2
   
tongue/anterior/epithelial/keratinocy... 13 tongue anterior epithelial keratinocyte female TSP7 Smart-seq2
   
tongue/anterior/immune/leukocyte/Smar... 233 tongue anterior immune leukocyte female TSP7 Smart-seq2
   
tongue/anterior/stromal/pericyte cell... 9 tongue anterior stromal pericyte cell female TSP7 Smart-seq2
   
tongue/anterior/stromal/tongue muscle... 2 tongue anterior stromal tongue muscle cell female TSP7 Smart-seq2
   
tongue/anterior/endothelial/vein endo... 5 tongue anterior endothelial vein endothelial cell female TSP7 Smart-seq2
   
tongue/posterior/epithelial/basal cel... 4715 tongue posterior epithelial basal cell female TSP7 10x 3' v3
   
tongue/posterior/epithelial/basal cel... 358 tongue posterior epithelial basal cell female TSP7 Smart-seq2
   
tongue/posterior/endothelial/capillar... 22 tongue posterior endothelial capillary endothelial cell female TSP7 10x 3' v3
   
tongue/posterior/endothelial/endothel... 7 tongue posterior endothelial endothelial cell of artery female TSP7 10x 3' v3
   
tongue/posterior/endothelial/endothel... 20 tongue posterior endothelial endothelial cell of lymphatic vessel female TSP7 10x 3' v3
   
tongue/posterior/stromal/fibroblast/1... 88 tongue posterior stromal fibroblast female TSP7 10x 3' v3
   
tongue/posterior/stromal/fibroblast/S... 12 tongue posterior stromal fibroblast female TSP7 Smart-seq2
   
tongue/posterior/epithelial/keratinoc... 1 tongue posterior epithelial keratinocyte female TSP7 10x 3' v3
   
tongue/posterior/immune/leukocyte/10x... 1120 tongue posterior immune leukocyte female TSP7 10x 3' v3
   
tongue/posterior/immune/leukocyte/Sma... 256 tongue posterior immune leukocyte female TSP7 Smart-seq2
   
tongue/posterior/stromal/pericyte cel... 60 tongue posterior stromal pericyte cell female TSP7 10x 3' v3
   
tongue/posterior/stromal/pericyte cel... 12 tongue posterior stromal pericyte cell female TSP7 Smart-seq2
   
tongue/posterior/stromal/tongue muscl... 4 tongue posterior stromal tongue muscle cell female TSP7 10x 3' v3
   
tongue/posterior/stromal/tongue muscl... 1 tongue posterior stromal tongue muscle cell female TSP7 Smart-seq2
   
tongue/posterior/endothelial/vein end... 61 tongue posterior endothelial vein endothelial cell female TSP7 10x 3' v3
   
tongue/posterior/endothelial/vein end... 4 tongue posterior endothelial vein endothelial cell female TSP7 Smart-seq2
Data schema/format description and download
Assembly: Human Dec. 2013 (GRCh38/hg38)
Data last updated at UCSC: 2022-05-11 19:59:08

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.