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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)
c-0
Alveolar macrophages
c-1
AT2
c-2
Capillary endothelial cells
c-3
Capillary endothelial cells
c-4
Monocyte derived macrophage
c-5
AT1
c-6
Monocytes
c-7
Alveolar macrophages
c-8
Interstitial perivascular m...
c-9
T-cells (CD8+)
c-10
NK-cells
c-11
Mast cells
c-12
AT2
c-13
AT0
c-14
Venous endothelial cells
c-15
Cytotoxic T-cells (CD8+)
c-16
T-cells (CD4+)
c-17
Cytotoxic T-cells (CD8+)
c-18
Arterial endothelial cells
c-19
Basal cells
c-20
AT2 (proliferating)
c-21
Club/Goblet cells
c-22
Suprabasal cells
c-23
Pericytes (STEAP4- LAMC3+)
c-24
Neutrophils
c-25
Alveolar fibroblasts
c-26
Non classical monocyte
c-27
Vascular smooth muscle cell
c-28
Ciliated cells (proximal, B...
c-29
Adventitial fibroblasts
c-30
B-cells
c-31
Ciliated cells (distal, GPC
c-32
Regulatory T-cells (CD4+)
c-33
Lymphatic endothelial cells
c-34
Naive T-cells (CD4+)
c-35
Peribroncheal fibroblasts
c-36
Fibroblasts
c-37
Submucosal gland mucous cel
c-38
Suprabasal cells (Cycling)
c-39
Plasma cells
c-40
ILCs
c-41
Pericytes (STEAP4+ LAMC3-)
c-42
Deuterosomal cells
c-43
Ionocytes
c-44
Submucosal serous mucous ce
c-45
CDC1 & Lymphoid DCs
c-46
Mesothelial cells
c-47
Plasmacytoid DCs
c-48
Schwann cells
SINGLE CELL TYPE TABULA SAPIENS - LUNGi
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)
c-0
Type ii pneumocyte
c-1
Neutrophil
c-2
Cd4-positive alpha-beta t c
c-3
Cd8-positive alpha-beta t c
c-4
Nk cell
c-5
Bronchial vessel endothelia...
c-6
Smooth muscle cell
c-7
Adventitial cell
c-8
Macrophage
c-9
Respiratory mucous cell
c-10
Basophil
c-11
Classical monocyte
c-12
Endothelial cell of artery
c-13
Lung ciliated cell
c-14
Dendritic cell
c-15
Cd4-positive, alpha-beta t ...
c-16
Respiratory goblet cell
c-17
Basal cell
c-18
Plasma cell
c-19
B cell
c-20
Cd8-positive, alpha-beta t ...
c-21
Serous cell of epithelium o...
c-22
Non-classical monocyte
c-23
Capillary endothelial cell
c-24
Capillary aerocyte
c-25
Type i pneumocyte
c-26
Vein endothelial cell
c-27
Alveolar fibroblast
c-28
Endothelial cell of lymphat...
c-29
Bronchial smooth muscle cel
c-30
Plasmacytoid dendritic cell
c-31
Club cell
c-32
Lung microvascular endothel...
c-33
Vascular associated smooth ...
c-34
Myofibroblast cell
c-35
Pericyte cell
c-36
Mesothelial cell
c-37
Fibroblast
c-38
Intermediate monocyte
c-39
Pulmonary ionocyte
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
Max-norm
Z-score
Fraction of highest expression (≥1 nTPM)
log2(nTPM+1) z-score
DVP - LUNGi
Relative protein amount measured using Deep Visual Proteomics. Here, on the detail page, all the biological replicates are shown, compared to the median value displayed on the gene summary page. The matched, selected single cell type clusters for the RNA-Protein comparison is also shown. The selected Cell Type clusters have the same name and ID as in the original dataset, above.
Below, we show a thumbnail overview of the tissue section used for the DVP, as well as smaller cropped area, that is clickable for a high-resolution zoomable image, where you can switch on and off the segmentation mask that was used for sample collection.
Learn more about the DVP method and different markers used the cell types here
Immunofluorescence image with DVP segmentation contours, high resolution cropped area with cell type markers (More info). This is lung, and includes AGER labeling of alveolar cell type 1.
Cell type
Alveolar cells type 2
RNA
Cluster
Cell type
Expression (nCPM)
c-1
AT2
c-12
AT2
Protein
Sample name
Intensity
Immunofluorescence image with DVP segmentation contours, high resolution cropped area with cell type markers (More info). This is lung, and includes SFTPC labeling of alveolar cell type 2.
The Human Protein Atlas project is funded
