This data was generated by Siletti K et al. (2023), re-processed by HPA (see methods) and simplified for global overview
SINGLE CELL TYPE - BRAIN NEURONSi
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
Cerebellar granular cells V...
c-1
Cortical superficial intrat...
c-2
Hippocampal excitatory VGLU...
c-3
Midbrain inhibitory (PCP4+ ...
c-4
Medium spiny neurons GAD1/G...
c-5
Medium spiny neurons GAD1/G...
c-6
Dentate gyrus excitatory VG...
c-7
Cortex/hippocampus CGE Inte...
c-8
Medium spiny neurons GAD1/G...
c-9
Medium spiny neurons GAD1/G...
c-10
Mammillary/tuberal excitato...
c-11
Cerebellar granular cells V...
c-12
Cortex/hippocampus CGE Inte...
c-13
Supraoptic nucleus/POA unas...
c-14
Cortex/hippocampus MGE Inte...
c-15
Cortex/hippocampus MGE Inte...
c-16
Eccentric medium spiny neur...
c-17
Midbrain excitatory VGLUT2 ...
c-18
Hypothalamus unassigned
c-19
Cortical deep projecting ex...
c-20
Cerebellar granular cells V...
c-21
Cerebellar basket/stellate ...
c-22
Cortical intermediate excit...
c-23
Midbrain excitatory
c-24
Cortiex/hippocampus superfi...
c-25
Dentate gyrus excitatory VG...
c-26
Cortical intermediate intra...
c-27
Medium spiny neurons GAD1/G...
c-28
Midbrain inhibitory
c-29
Midbrain inhibitory (CALB2+
c-30
Midbrain/hypothalamic excit...
c-31
Cortical superficial intrat...
c-32
Tectum excitatory VGLUT2
c-33
Septal nuclei inhibitory
c-34
Hypothalamic inhibitory (LH
c-35
Cortex/hippocampus LAMP5-LH...
c-36
Midbrain unassigned
c-37
Midbrain/hypothalamic excit...
c-38
Mammillary body unassigned
c-39
Tectum inhibitory
c-40
Basal ganglia MGE Interneur...
c-41
Hippocampal excitatory VGLU...
c-42
Basal ganglia MGE Interneur...
c-43
Dentate gyrus excitatory VG...
c-44
Cortical superficial intrat...
c-45
Midbrain/hypothalamus unass...
c-46
Hypothalamic inhibitory (RO
c-47
Midbrain excitatory VGLUT2 ...
c-48
Midbrain inhibitory (CALB2+...
c-49
Basal striatal-projecting c...
c-50
Mammillary body excitatory ...
c-51
Midbrain/hippocampus excita...
c-52
Midbrain excitatory VGLUT2 ...
c-53
Midbrain inhibitory
c-54
Cortical deep projecting ex...
c-55
Midbrain/hypothalamus unass...
c-56
Hippocampal excitatory VGLU...
c-57
Midbrain/hypothalamic excit...
c-58
Midbrain/hypothalamic inhib...
c-59
Tuberal hypothalamus excita...
c-60
Midbrain excitatory VGLUT2
c-61
Hypothalamic/SN HIST monoam...
c-62
Cortex/hippocampus MGE Inte...
c-63
Hypothalamic excitatory VGL
c-64
Hypothalamic AVP magnocellu...
c-65
Hippocampal excitatory VGLU...
c-66
Deep cerebellar nuclei inte...
c-67
Cortex/hippocampus MGE Inte...
c-68
Basal cortical-projecting c...
c-69
Deep cerebellar nuclei exci...
c-70
Cortex/hippocampus excitato...
c-71
Cerebellar unipolar brush c...
c-72
Deep cerebellar nuclei proj...
c-73
Tegmentum excitatory VGLUT2...
c-74
Tegmentum inhibitory (BCL11...
c-75
Hippocampal excitatory VGLU...
c-76
Hypothalamic OXT magnocellu...
c-77
Midbrain/hypothalamic dopam...
c-78
Midbrain/Hypothalamic hista...
c-79
Supraoptic nucleus inhibito...
c-80
Hypothalamic parvocellular ...
c-81
Midbrain dopaminergic
c-82
Supraoptic nucleus inhibito...
c-83
Hippocampus unasigned (BHLH...
c-84
Tegmentum excitatory VGLUT1...
c-85
Midbrain serotonergic
c-86
GPi unasigned
c-87
POA/BNST inhibitory (SST+ V...
c-88
Cerebellar golgi cells
c-89
Cortex/hippocampus unassign...
c-90
Septal nuclei excitatory VG...
c-91
Mammillary body excitatory ...
c-92
Superior colliculus choline...
c-93
GPe inhibitory (CUX2+)
c-94
Cerebellar purkinje cells
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This data was generated by Siletti K et al. (2023), re-processed by HPA (see methods) and simplified for global overview
SINGLE CELL TYPE - BRAIN NON-NEURONSi
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
Bergmann glia
c-1
Choroid plexus epithelial c...
c-2
Oligodendrocyte progenitor ...
c-3
Microglia
c-4
Astrocytes
c-5
Oligodendrocytes
c-6
Fibroblasts
c-7
Ependymal cells
c-8
Oligodendrocyte progenitor ...
c-9
Microglia
c-10
Oligodendrocytes
c-11
Astrocytes
c-12
Oligodendrocytes
c-13
Astrocytes
c-14
Capillary endothelial cells
c-15
Immature oligodendrocytes (...
c-16
Immature oligodendrocytes
c-17
Pericytes
c-18
T-cells
c-19
Choroid plexus epithelial c...
c-20
Ependymal cells
c-21
Fibroblasts
c-22
Arterial endothelial cells
c-23
Venous endothelial cells
c-24
NK-cells
c-25
Vascular smooth muscle cell
c-26
Macrophages
c-27
Monocytes
c-28
Microglia
c-29
Astrocytes
c-30
Oligodendrocytes
c-31
B-cells
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This data was generated by Siletti K et al. (2023), re-processed by HPA (see methods) and simplified for global overview
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 - BRAIN NEURONS
SINGLE CELL TYPE - BRAIN NON-NEURONS
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 - BRAINi
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 cerebral cortex of the brain, and includes NeuN (RBFOX3) labeling of neurons.
Cell type
Astrocytes and Neuropil
RNA
Cluster
Cell type
Expression (nCPM)
c-4
Astrocytes
c-13
Astrocytes
Protein
Sample name
Intensity
Astrocytes and Neuropil_01
Astrocytes and Neuropil_02
Astrocytes and Neuropil_03
Astrocytes and Neuropil_04
Astrocytes and Neuropil_05
Immunofluorescence image with DVP segmentation contours, high resolution cropped area with cell type markers (More info). This is cerebral cortex of the brain, and includes GFAP labeling of astrocytes.
Cell type
Microglia and Neuropil
RNA
Cluster
Cell type
Expression (nCPM)
c-3
Microglia
Protein
Sample name
Intensity
Microglia and Neuropil_01
ND
Microglia and Neuropil_02
ND
Microglia and Neuropil_03
ND
Microglia and Neuropil_04
ND
Microglia and Neuropil_05
ND
Immunofluorescence image with DVP segmentation contours, high resolution cropped area with cell type markers (More info). This is cerebral cortex of the brain, and includes TMEM119 labeling of microglia.
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