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RNA expression in the single nuclei cluster types identified in this brain region visualized by a UMAP plot (top) and a bar chart (to the right).
- 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 two the right. 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. There are 3 options for cell intensities: 1) Intensity, which color the individual cells according to % of max (log2(read_count+1)/log2(max(read_count)+1)*100) in five different bins (<1%,<25%,<50%,<75%,≥75%) 2) Interval, which color the individual cells according to fixed interval of read count (0,1,2-4,5-9,>10) 3) Hexagon, which color the hexagon on average read count of all cells inside the hexagon
- The BAR CHART shows RNA expression (nTPM) in each cluster type. 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
Cluster type
Expression (nTPM)
c-0
Upper rhombic lip
c-1
Splatter
c-2
Amygdala excitatory
c-3
Eccentric medium spiny neuron
c-4
CGE interneuron
c-5
LAMP5-LHX6 and Chandelier
c-6
MGE interneuron
c-7
Medium spiny neuron
c-8
Deep-layer near-projecting
c-9
Deep-layer corticothalamic and 6b
c-10
Miscellaneous
c-11
Hippocampal CA1-3
c-12
Upper-layer intratelencephalic
c-13
Deep-layer intratelencephalic
c-14
Hippocampal dentate gyrus
c-15
Hippocampal CA4
c-16
Leukocyte
c-17
Oligodendrocyte
c-18
Committed oligodendrocyte precursor
c-19
Astrocyte
c-20
Oligodendrocyte precursor cell
c-21
Ependymal cell
c-22
Choroid plexus epithelial cell
c-23
Fibroblast
c-24
Pericyte
c-25
Vascular associated smooth muscle cell
c-26
Endothelial cell
c-27
Central nervous system macrophage
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.
