This online viewer shows a spatial atlas of neuron types in the mouse hippocampus,
based on their combinatorial expression of 99 genes.
The brain contains hundreds of types of cells, and understanding their organization is an essential
step toward understanding how the brain operates. Each type of cell transcribes a unique combination
of genes from DNA to RNA.
If you know which RNA molecules a cell contains, you can find out what cell type it is.
We used in situ RNA sequencing to map the expression of 99 genes in 28 different sections of mouse
hippocampus – a part of the brain involved in memory, where the subtypes of neurons are understood well.
The Gene Map on the left shows where the RNA molecules were detected.
Each colored symbol represents an RNA detection – hover over a symbol to see what gene it represents.
The white blobs show cell nuclei, and the gray dotted lines show their estimated borders.
Hover over a cell to see what genes were assigned to it (they will connect by lines),
and what cell classes it might belong to (in the bottom left corner).
Click on a cell to show even more information, in the lower right panels.
Use the Section Overview (top right panel) to zoom around – click any cell and it will take you straight there.
To show data from a different experiment, click “Select Data”, in the top left of the window.
A full explanation of this data and algorithms that produced the atlas is in
this paper, where you
can also find details on how to contact us. An explanation of what the different cell types are,
and how we know which RNAs they express,