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                                          • SUMMARY

                                          • TISSUE

                                          • BRAIN

                                          • SINGLE CELL

                                          • SUBCELL

                                          • CANCER

                                          • BLOOD

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                                          • STRUCTURE

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                                          • GET1
                                          SINGLE CELL EYE Show tissue menu
                                          ADIPOSE TISSUE ADRENAL GLAND BLOOD BONE MARROW BRAIN BREAST COLON ENDOMETRIUM EPIDIDYMIS ESOPHAGUS
                                          EYE FALLOPIAN TUBE HEART MUSCLE KIDNEY LIVER LUNG LYMPH NODE OVARY PANCREAS PITUITARY GLAND
                                          PLACENTA PROSTATE RECTUM SALIVARY GLAND SKELETAL MUSCLE SKIN SMALL INTESTINE SPLEEN STOMACH TESTIS
                                          THYMUS THYROID GLAND TONGUE URINARY BLADDER VASCULATURE
                                          Single cell type
                                          Tabula sapiens
                                          Tissue cell type
                                          SINGLE CELL TYPE TABULA SAPIENS CELL TYPE MARKERS
                                          Cell types
                                          Blood and immune cells
                                          Specialized epithelial cells
                                          Endothelial and mural cells
                                          Neuronal cells
                                          Mesenchymal cells
                                          Pigment cells
                                          Glial cells
                                          Glandular epithelial cells
                                          Methods
                                          EYE DETAIL SUMMARY
                                          Retinal amacrine cellsRetinal horizontal cellsRetinal ganglion cellsRetinal bipolar cellsRod photoreceptor cellsCone photoreceptor cellsMüller gliaSchwann cellsMelanocytesRetinal pigment epithelial cellsOcular epithelial cellsLacrimal acinar cellsConjunctival goblet cellsVascular endothelial cellsLymphatic endothelial cellsPericytesVascular smooth muscle cellsFibroblastsMast cellsNeutrophilsMonocytesMacrophagesT-cellsB-cellsPlasma cellsNK-cells0246810nCPMNeuronal cellsGlial cellsPigment cellsSpecialized epithelial cellsGlandular epithelial cellsEndothelial and mural cellsMesenchymal cellsBlood and immune cells
                                          SINGLE CELL TYPE - EYEi

                                          RNA expression in the single cell type clusters identified in this tissue visualized by a UMAP plot (top) and a bar chart (bottom).

                                          - UMAP PLOT visualizes the cells in each cluster; where each dot corresponds to a cell. For each individual cell, mouseover reveals read count and which cluster the cell belongs to. Hovering over a cluster name will highlight the corresponding cluster in the bar chart below. There are 2 options for color schemes: 1) cell type color, which is based on cell type groups used in the Single cell type part of the Single cell resource and 2) cluster color, which assigns a unique color to each cluster. The cells are colored according to % of max (log2(read_count+1)/log2(max(read_count)+1)*100) in five different bins (<1%,<25%,<50%,<75%,≥75%)

                                          - The LEGEND shows RNA expression (nTPM) in each cell type cluster. Hovering over the cluster name reveals nTPM value and number of included cells. Hovering over a bar highlights the corresponding cluster in the UMAP plot above. Color-coding can be toggled on the top of the page, between 2 options: 1) cell type color, which is based on cell type groups used in the Single cell type part of the Single cell resource and 2) cluster color, which assigns a unique color to each cluster.

                                          Cell type color
                                          Cluster color
                                          Colored according to cell type group
                                          Colored according to clusters
                                          Read count filter: 0
                                          Cluster filter:
                                           
                                          Cluster Cell type Expression (nCPM)
                                          0 10
                                          c-0 B-cells
                                          c-1 Corneal apical cells
                                          c-2 T-cells (CD4+)
                                          c-3 Venous ECs
                                          c-4 B-cells
                                          c-5 Rod photoreceptor cells
                                          c-6 Corneal suprabasal epitheli...
                                          c-7 T-cells (CD8+)
                                          c-8 Fibroblasts
                                          c-9 Conjunctival epithelial cel
                                          c-10 B-cells
                                          c-11 Conjunctival epithelial cel
                                          c-12 Conjunctival epithelial cel
                                          c-13 T-cells
                                          c-14 Conjunctival epithelial cel
                                          c-15 Fibroblasts
                                          c-16 Conjunctival epithelial cel
                                          c-17 Plasma cells
                                          c-18 Resident macrophages
                                          c-19 T-cells (CD4+)
                                          c-20 Conjunctival epithelial cel
                                          c-21 Corneal basal epithelial ce
                                          c-22 Vascular smooth muscle cell
                                          c-23 Limbal epithelial cells
                                          c-24 Fibroblasts
                                          c-25 Capillary ECs
                                          c-26 T-cells (CD4+)
                                          c-27 T-cells (CD8+)
                                          c-28 Lymphatic endothelial cells
                                          c-29 Monocytes
                                          c-30 NK-cells
                                          c-31 M2-like macrophages
                                          c-32 Conjunctival Melaonocytes
                                          c-33 Arterial ECs
                                          c-34 NK-T-cells
                                          c-35 Neutrophils
                                          c-36 Transitional M2-like macrop...
                                          c-37 Müller glia
                                          c-38 Mast cells
                                          c-39 B-cells
                                          c-40 Pericytes
                                          c-41 Serous acinar cells
                                          c-42 Uveal Melanocytes
                                          c-43 Mixed cell types
                                          c-44 Corneal Fibroblasts
                                          c-45 Bipolar cells
                                          c-46 Conjunctival goblet cells
                                          c-47 Schwann cells
                                          c-48 Amacrine cells
                                          c-49 Cone photoreceptor cells
                                          c-50 Retinal pigment epithelia
                                          c-51 Oligodendrocytes
                                          c-52 Horizontal cells
                                          SINGLE CELL TYPE - RETINAi

                                          RNA expression in the single cell type clusters identified in this tissue visualized by a UMAP plot (top) and a bar chart (bottom).

                                          - UMAP PLOT visualizes the cells in each cluster; where each dot corresponds to a cell. For each individual cell, mouseover reveals read count and which cluster the cell belongs to. Hovering over a cluster name will highlight the corresponding cluster in the bar chart below. There are 2 options for color schemes: 1) cell type color, which is based on cell type groups used in the Single cell type part of the Single cell resource and 2) cluster color, which assigns a unique color to each cluster. The cells are colored according to % of max (log2(read_count+1)/log2(max(read_count)+1)*100) in five different bins (<1%,<25%,<50%,<75%,≥75%)

                                          - The LEGEND shows RNA expression (nTPM) in each cell type cluster. Hovering over the cluster name reveals nTPM value and number of included cells. Hovering over a bar highlights the corresponding cluster in the UMAP plot above. Color-coding can be toggled on the top of the page, between 2 options: 1) cell type color, which is based on cell type groups used in the Single cell type part of the Single cell resource and 2) cluster color, which assigns a unique color to each cluster.

                                          Cell type color
                                          Cluster color
                                          Colored according to cell type group
                                          Colored according to clusters
                                          Read count filter: 0
                                          Cluster filter:
                                           
                                          Cluster Cell type Expression (nCPM)
                                          0 10
                                          c-0 Rod photoreceptor cells
                                          c-1 Müller glia
                                          c-2 Rod photoreceptor cells
                                          c-3 Rod photoreceptor cells
                                          c-4 Rod photoreceptor cells
                                          c-5 Rod photoreceptor cells
                                          c-6 ON bipolar cells
                                          c-7 Müller glia
                                          c-8 Rod bipolar cells
                                          c-9 OFF bipolar cells
                                          c-10 Müller glia
                                          c-11 Rod photoreceptor cells
                                          c-12 OFF bipolar cells
                                          c-13 Amacrine cells
                                          c-14 Rod bipolar cells
                                          c-15 Horizontal cells
                                          c-16 Glycinergic amacrine cells
                                          c-17 OFF bipolar cells
                                          c-18 Cone photoreceptor cells
                                          c-19 Rod bipolar cells
                                          c-20 OFF bipolar cells
                                          c-21 Rod bipolar cells
                                          c-22 OFF bipolar cells
                                          c-23 ON bipolar cells
                                          c-24 ON bipolar cells
                                          c-25 ON bipolar cells
                                          c-26 Amacrine cells (SLC18A2+)
                                          c-27 Glycinergic horizontal-like...
                                          c-28 Starbust amacrine cells (Ch...
                                          c-29 Retinal ganglion cells
                                          c-30 Astrocytes
                                          c-31 Microglia
                                          c-32 Mural & Epithelial cells
                                          SINGLE CELL TYPE TABULA SAPIENS - EYEi

                                          RNA expression in the single cell type clusters identified in this tissue visualized by a UMAP plot and a bar chart. This window shows single cell expression data generated by the https://tabula-sapiens.sf.czbiohub.org/about#consortium, that also offers UMAP visualization and cell type clusters for each tissue sample: https://tabula-sapiens.sf.czbiohub.org/organs, here integrate offering easy comparison to the HPA cluster method of single cell types.

                                          • UMAP PLOT visualizes the cells in each cluster; where each dot corresponds to a cell. For each individual cell, mouseover reveals read count and which cluster the cell belongs to. Hovering over a cluster name will highlight the corresponding cluster in the bar chart below. There are 2 options for color schemes: 1) cell type color, which is based on cell type groups used in the Single cell type part of the Single cell resource and 2) cluster color, which assigns a unique color to each cluster. The cells are colored according to % of max (log2(read_count+1)/log2(max(read_count)+1)*100) in five different bins (<1%,<25%,<50%,<75%,≥75%)

                                          • The LEGEND shows RNA expression (nTPM) in each cell type cluster. Hovering over the cluster name reveals nTPM value and number of included cells. Hovering over a bar highlights the corresponding cluster in the UMAP plot above. Color-coding can be toggled on the top of the page, between 2 options: 1) cell type color, which is based on cell type groups used in the Single cell type part of the Single cell resource and 2) cluster color, which assigns a unique color to each cluster.

                                          Cell type color
                                          Cluster color
                                          Colored according to cell type group
                                          Colored according to clusters
                                          Read count filter: 0
                                           
                                          Cluster Cell type Expression (nCPM)
                                          0 6540
                                          c-0 Conjunctival epithelial cel
                                          c-1 Monocyte
                                          c-2 Microglial cell
                                          c-3 Eye photoreceptor cell
                                          c-4 Muller cell
                                          c-5 Fibroblast
                                          c-6 T cell
                                          c-7 Limbal stem cell
                                          c-8 Retinal blood vessel endoth...
                                          c-9 Epithelial cell of lacrimal...
                                          c-10 Corneal keratocyte
                                          c-11 B cell
                                          c-12 Retinal pigment epithelial ...
                                          c-13 Corneal epithelial cell
                                          c-14 Limbal stromal cell
                                          c-15 Melanocyte
                                          c-16 Retinal bipolar neuron
                                          c-17 Dendritic cell
                                          c-18 Plasma cell
                                          c-19 Lacrimal gland functional u...
                                          c-20 Macrophage
                                          c-21 Erythroid lineage cell
                                          c-22 Radial glial cell
                                          c-23 Ocular surface cell
                                          c-24 Cd8-positive, alpha-beta t ...
                                          c-25 Endothelial cell
                                          c-26 Retina horizontal cell
                                          c-27 Ciliary body
                                          c-28 Cd4-positive, alpha-beta t ...
                                          c-29 Mast cell
                                          c-30 Adipocyte
                                          c-31 Retinal ganglion cell
                                          CELL TYPE MARKERSi

                                          The heatmap in this section shows expression of the currently selected gene (on top) and well-known cell type markers in the different single cell type clusters of this tissue. The panel on the left shows which cell type each marker is associated with. Color-coding is based on cell type groups, each consisting of cell types with functional features in common.

                                          Hover the mouse-pointer over the individual data points (squares) to see nTPM level and Z-score. Clicking on a gene name redirects to the corresponding gene page.

                                          Z-score is when you normalize a variable such that the standard deviation is 1 and the mean is 0. Thus, all the genes are easier to compare, as they have the same center and distribution.

                                          SINGLE CELL TYPE - EYE
                                          SINGLE CELL TYPE - RETINA
                                          TABULA SAPIENS
                                          Max-norm
                                          Z-score
                                          Fraction of highest expression (≥1 nTPM)
                                          log2(nTPM+1) z-score
                                          GET1C1QL2GAD1GAD2ONECUT1ONECUT2OTX2VSX2CNGA1CNGB1PDE6AGRK7OPN1LWGLULRLBP1MAGMBPMOGS100BMPZCDH19L1CAMDCTMLANAPAX3KITSPP1BEST1RBP1RPE65MMP10KRT13KRT4WFDC2KRT12MOXD1KRT24AQP5LTFLYZPRR4AGR3MUC5ACPECAM1VWFACKR1POSTNHEY1HEY2SEMA3GCA4RGCCLYVE1PROX1PDGFRBRGS5STEAP4ACTA2CNN1MYH11COL1A1DCNFBLN2PDGFRAKERALUMCPA3TPSAB1TPSB2CEACAM8CSF3RCXCR2FCGR3BFCN1IL1BS100A8S100A9VCANCD14FCGR3AC1QBC1QCHLA-DRAHLA-DRB1F13A1CD3DCD3GCD4CD8AIL7RBANK1CD19MS4A1DERL3IGHA1GZMANKG7PRF1B-cells c-0Ocular epithelial cells c-1T-cells c-2Vascular endothelial cells c-3B-cells c-4Rod photoreceptor cells c-5Ocular epithelial cells c-6T-cells c-7Fibroblasts c-8Ocular epithelial cells c-9B-cells c-10Ocular epithelial cells c-11Ocular epithelial cells c-12T-cells c-13Ocular epithelial cells c-14Fibroblasts c-15Ocular epithelial cells c-16Plasma cells c-17Macrophages c-18T-cells c-19Ocular epithelial cells c-20Ocular epithelial cells c-21Vascular smooth muscle cells c-22Ocular epithelial cells c-23Fibroblasts c-24Vascular endothelial cells c-25T-cells c-26T-cells c-27Lymphatic endothelial cells c-28Monocytes c-29NK-cells c-30Macrophages c-31Melanocytes c-32Vascular endothelial cells c-33T-cells c-34Neutrophils c-35Macrophages c-36Müller glia c-37Mast cells c-38B-cells c-39Pericytes c-40Lacrimal acinar cells c-41Melanocytes c-42Mixed cell types c-43Fibroblasts c-44Retinal bipolar cells c-45Conjunctival goblet cells c-46Schwann cells c-47Retinal amacrine cells c-48Cone photoreceptor cells c-49Retinal pigment epithelial cells c-50Oligodendrocytes c-51Retinal horizontal cells c-52Current geneRetinal amacrine cellsRetinal horizontal cellsRetinal bipolar cellsRod photoreceptor cellsCone photoreceptor cellsMüller gliaOligodendrocytesSchwann cellsMelanocytesRetinal pigment epithelial cellsOcular epithelial cellsLacrimal acinar cellsConjunctival goblet cellsVascular endothelial cellsLymphatic endothelial cellsPericytesVascular smooth muscle cellsFibroblastsMast cellsNeutrophilsMonocytesMacrophagesT-cellsB-cellsPlasma cellsNK-cells00.250.50.751-4-2024
                                          Max-norm
                                          Z-score
                                          Fraction of highest expression (≥1 nTPM)
                                          log2(nTPM+1) z-score
                                          GET1C1QL2GAD1GAD2ACHECHATSLC18A3ONECUT1ONECUT2FABP3NEFMOTX2VSX2GRM6ISL1GRIK1PRKCACNGA1CNGB1PDE6AGRK7OPN1LWAQP4GFAPGLULRLBP1P2RY12TMEM119PECAM1VWFPDGFRBRod photoreceptor cells c-0Müller glia c-1Rod photoreceptor cells c-2Rod photoreceptor cells c-3Rod photoreceptor cells c-4Rod photoreceptor cells c-5Retinal bipolar cells c-6Müller glia c-7Retinal bipolar cells c-8Retinal bipolar cells c-9Müller glia c-10Rod photoreceptor cells c-11Retinal bipolar cells c-12Retinal amacrine cells c-13Retinal bipolar cells c-14Retinal horizontal cells c-15Retinal amacrine cells c-16Retinal bipolar cells c-17Cone photoreceptor cells c-18Retinal bipolar cells c-19Retinal bipolar cells c-20Retinal bipolar cells c-21Retinal bipolar cells c-22Retinal bipolar cells c-23Retinal bipolar cells c-24Retinal bipolar cells c-25Retinal amacrine cells c-26Retinal horizontal cells c-27Retinal amacrine cells c-28Retinal ganglion cells c-29Astrocytes c-30Microglia c-31Mural & Epithelial cells c-32Current geneRetinal amacrine cellsRetinal horizontal cellsRetinal ganglion cellsRetinal bipolar cellsRod photoreceptor cellsCone photoreceptor cellsAstrocytesMüller gliaMicrogliaVascular endothelial cellsPericytes00.250.50.751-4-2024
                                          Max-norm
                                          Z-score
                                          Fraction of highest expression (≥1 nTPM)
                                          log2(nTPM+1) z-score
                                          GET1C1QL2GAD1GAD2ACHECHATSLC18A3ONECUT1ONECUT2FABP3NEFMOTX2VSX2GRM6ISL1GRIK1PRKCACNGA1CNGB1PDE6AGRK7OPN1LWAQP4GFAPGLULRLBP1MAGMBPMOGS100BMPZCDH19L1CAMP2RY12TMEM119DCTMLANAPAX3KITSPP1BEST1RBP1RPE65MMP10KRT13KRT4WFDC2KRT12MOXD1KRT24AQP5LTFLYZPRR4AGR3MUC5ACPECAM1VWFACKR1POSTNHEY1HEY2SEMA3GCA4RGCCLYVE1PROX1PDGFRBRGS5STEAP4ACTA2CNN1MYH11COL1A1DCNFBLN2PDGFRAKERALUMCPA3TPSAB1TPSB2CEACAM8CSF3RCXCR2FCGR3BFCN1IL1BS100A8S100A9VCANCD14FCGR3AC1QBC1QCHLA-DRAHLA-DRB1F13A1CD3DCD3GCD4CD8AIL7RBANK1CD19MS4A1DERL3IGHA1GZMANKG7PRF1Conjunctival epithelial cell c-0Monocyte c-1Microglial cell c-2Eye photoreceptor cell c-3Muller cell c-4Fibroblast c-5T cell c-6Limbal stem cell c-7Retinal blood vessel endothelial cell c-8Epithelial cell of lacrimal sac c-9Corneal keratocyte c-10B cell c-11Retinal pigment epithelial cell c-12Corneal epithelial cell c-13Limbal stromal cell c-14Melanocyte c-15Retinal bipolar neuron c-16Dendritic cell c-17Plasma cell c-18Lacrimal gland functional unit cell c-19Macrophage c-20Erythroid lineage cell c-21Radial glial cell c-22Ocular surface cell c-23Cd8-positive, alpha-beta t cell c-24Endothelial cell c-25Retina horizontal cell c-26Ciliary body c-27Cd4-positive, alpha-beta t cell c-28Mast cell c-29Adipocyte c-30Retinal ganglion cell c-31Current geneRetinal amacrine cellsRetinal horizontal cellsRetinal ganglion cellsRetinal bipolar cellsRod photoreceptor cellsCone photoreceptor cellsAstrocytesMüller gliaOligodendrocytesSchwann cellsMicrogliaMelanocytesRetinal pigment epithelial cellsOcular epithelial cellsLacrimal acinar cellsConjunctival goblet cellsVascular endothelial cellsLymphatic endothelial cellsPericytesVascular smooth muscle cellsFibroblastsMast cellsNeutrophilsMonocytesMacrophagesT-cellsB-cellsPlasma cellsNK-cells00.250.50.751-4-2024
                                           

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