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                                          • SUMMARY

                                          • TISSUE

                                          • BRAIN

                                          • SINGLE CELL

                                          • SUBCELL

                                          • CANCER

                                          • BLOOD

                                          • CELL LINE

                                          • STRUCTURE

                                          • INTERACTION

                                          • GET1
                                          SINGLE CELL BONE MARROW 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
                                          Stem and proliferating cells
                                          Mesenchymal cells
                                          Methods
                                          BONE MARROW DETAIL SUMMARY
                                          Neutrophil progenitorsNeutrophilsMonocyte progenitorsMonocytesMacrophagesT-cellsB-cellsPlasma cellsNK-cellsMegakaryocyte progenitorsMegakaryocyte-Erythroid progenitorsMegakaryocytesErythrocyte progenitorsErythrocytesHematopoietic stem cells02468101214nCPMBlood and immune cellsStem and proliferating cells
                                          SINGLE CELL TYPE - BONE MARROWi

                                          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 20
                                          c-0 Segmented neutrophils (CXCR
                                          c-1 Band neutrophils (CXCR2-)
                                          c-2 Band neutrophils (CXCR2-)
                                          c-3 Monocytes
                                          c-4 Segmented neutrophils (CXCR
                                          c-5 NK-cells
                                          c-6 T-cells (CD8+)
                                          c-7 T-cells (CD4+)
                                          c-8 Naive B-cells
                                          c-9 Naive T-cells (CD8+)
                                          c-10 Naive T-cells (CD4+)
                                          c-11 Promonocyte
                                          c-12 T-cells (CD8+)
                                          c-13 Memory B-cells
                                          c-14 Macrophages
                                          c-15 Plasma cells
                                          c-16 Late promonocyte
                                          c-17 Intermediate monocytes
                                          c-18 Mixed cells with RBCs
                                          c-19 Intermediate monocytes/Macr...
                                          c-20 T-cells (CD8+)
                                          c-21 Hematopoietic stem cells
                                          c-22 Reticulocytes
                                          c-23 Early myelocytes (DEFA4+)
                                          c-24 Regulatory T-cells (CD4+)
                                          c-25 Late myeloblasts (CD38-)
                                          c-26 Early monoblast (KIT+)
                                          c-27 Late myelocytes (CAMP+)
                                          c-28 Monoblast
                                          c-29 Mid myeloblasts (DEF4A+)
                                          c-30 Monocytes/Megakaryocytes
                                          c-31 Megakaryocyte-Erythroid pro...
                                          c-32 Late erythroblasts
                                          c-33 Megakaryocyte progenitors
                                          c-34 Early myeloblasts (KIT+)
                                          c-35 Megakaryocyte-Erythroid pro...
                                          c-36 Monocytes
                                          c-37 Pre-megakaryocyte progenito
                                          c-38 Megakaryocytes
                                          c-39 Mid erythroblasts
                                          c-40 Mixed cell types
                                          c-41 Early erythroblasts
                                          c-42 Multipotent progenitors
                                          c-43 Mast cells
                                          c-44 Plasmacytoid DCs
                                          c-45 Stromal cells
                                          SINGLE CELL TYPE TABULA SAPIENS - BONE MARROWi

                                          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)
                                          0 300
                                          c-0 Monocyte
                                          c-1 Plasma cell
                                          c-2 Hematopoietic stem cell
                                          c-3 Erythroid progenitor
                                          c-4 Nk cell
                                          c-5 Granulocyte
                                          c-6 Naive b cell
                                          c-7 Macrophage
                                          c-8 Myeloid progenitor
                                          c-9 Memory b cell
                                          c-10 Cd8-positive, alpha-beta t ...
                                          c-11 Cd4-positive, alpha-beta t ...
                                          c-12 Nampt neutrophil
                                          c-13 Cd24 neutrophil
                                          c-14 Neutrophil
                                          c-15 Plasmablast
                                          c-16 Erythrocyte
                                          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
                                          TABULA SAPIENS
                                          Max-norm
                                          Z-score
                                          Fraction of highest expression (≥1 nTPM)
                                          log2(nTPM+1) z-score
                                          GET1COL1A1DCNFBLN2PDGFRACPA3TPSAB1TPSB2CEBPEKITCAMPCEACAM8LTFCSF3RCXCR2FCGR3BCSF1RIRF8CD14VCANFCN1IL1BS100A8S100A9FCGR3AC1QBC1QCHLA-DRAHLA-DRB1F13A1LYVE1CD3DCD3GCD4CD8AIL7RBANK1CD19MS4A1CD27TNFRSF13BDERL3IGHA1CLEC4CIL3RAIRF7GZMANKG7PRF1CD34GP1BAGATA1PROM1GP9PF4GYPATFRCHBA1HBBCD38AVPHLFHOPXPRDM16Neutrophils c-0Neutrophils c-1Neutrophils c-2Monocytes c-3Neutrophils c-4NK-cells c-5T-cells c-6T-cells c-7B-cells c-8T-cells c-9T-cells c-10Monocyte progenitors c-11T-cells c-12B-cells c-13Macrophages c-14Plasma cells c-15Monocyte progenitors c-16Monocytes c-17Erythrocytes c-18Monocytes c-19T-cells c-20Hematopoietic stem cells c-21Erythrocytes c-22Neutrophil progenitors c-23T-cells c-24Neutrophil progenitors c-25Monocyte progenitors c-26Neutrophil progenitors c-27Monocyte progenitors c-28Neutrophil progenitors c-29Mixed cell types c-30Megakaryocyte-Erythroid progenitors c-31Erythrocyte progenitors c-32Megakaryocyte progenitors c-33Neutrophil progenitors c-34Megakaryocyte-Erythroid progenitors c-35Monocytes c-36Megakaryocyte progenitors c-37Megakaryocytes c-38Erythrocyte progenitors c-39Mixed cell types c-40Erythrocyte progenitors c-41Multipotent progenitors c-42Mast cells c-43PDCs c-44Stromal cells c-45Current geneFibroblastsMast cellsNeutrophil progenitorsNeutrophilsMonocyte progenitorsMonocytesMacrophagesT-cellsB-cellsPlasma cellsPDCsNK-cellsMegakaryocyte progenitorsMegakaryocyte-Erythroid progenitorsMegakaryocytesErythrocyte progenitorsErythrocytesMultipotent progenitorsHematopoietic stem cells00.250.50.751-4-2024
                                          Max-norm
                                          Z-score
                                          Fraction of highest expression (≥1 nTPM)
                                          log2(nTPM+1) z-score
                                          GET1COL1A1DCNFBLN2PDGFRACPA3TPSAB1TPSB2CEBPEKITCAMPCEACAM8LTFCSF3RCXCR2FCGR3BCSF1RIRF8CD14VCANFCN1IL1BS100A8S100A9FCGR3AC1QBC1QCHLA-DRAHLA-DRB1F13A1LYVE1CD3DCD3GCD4CD8AIL7RBANK1CD19MS4A1CD27TNFRSF13BDERL3IGHA1CLEC4CIL3RAIRF7GZMANKG7PRF1CD34GP1BAGATA1PROM1GP9PF4GYPATFRCHBA1HBBCD38AVPHLFHOPXPRDM16Monocyte c-0Plasma cell c-1Hematopoietic stem cell c-2Erythroid progenitor c-3Nk cell c-4Granulocyte c-5Naive b cell c-6Macrophage c-7Myeloid progenitor c-8Memory b cell c-9Cd8-positive, alpha-beta t cell c-10Cd4-positive, alpha-beta t cell c-11Nampt neutrophil c-12Cd24 neutrophil c-13Neutrophil c-14Plasmablast c-15Erythrocyte c-16Current geneFibroblastsMast cellsNeutrophil progenitorsNeutrophilsMonocyte progenitorsMonocytesMacrophagesT-cellsB-cellsPlasma cellsPDCsNK-cellsMegakaryocyte progenitorsMegakaryocyte-Erythroid progenitorsMegakaryocytesErythrocyte progenitorsErythrocytesMultipotent progenitorsHematopoietic stem cells00.250.50.751-4-2024
                                           

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