Mouse embryonic cortex RNA metacell viewer

This interface allows interactive viewing and analysis of RNA metacells analyzed in the paper “Neural stem cell epigenomes and fate bias are temporally coordinated during corticogenesis” (Shapira et al., 2025). In this paper, the temporal evolution of neural stem cells is analyzed across multiple modalities, and it is shown that neural stem cells evolve gradually from a general neural progenitor state towards an astrocytic state. This interface can be used to view expression of specific genes across all or specific metacells, on the manifold 2d projection, and across time.

Where to start

On the left sidebar you will find a list of tabs, click on the tab to open it. See below a short description of each tab.

Additional tabs can be added from the right sidebar which can be opened by clicking on the “Gears” icon at the top right of the screen. Select the tabs you want and then click on “Update Tabs”.

Tabs

Main tabs:

• QC: View QC metrics of the metacell model.
• Manifold: View the 2d projection of the manifold
• Genes: Compare gene expression and metadata over the metacells.
• Diff expression: Compare metacells / cell types.
• Markers: View a heatmap of ‘marker genes’ over the metacell model.
• Cell types: View gene expression and metadata over cell types.
• Annotate: Assign cell types and colors to metacells.
• Gene modules: Create gene modules to be used in other tabs.

QC tabs:

• Inner-fold
• Outliers

Atlas projection tabs:

• Query: Examine the results of a projection of the metacell model over an atlas.
• Atlas: View the 2d projection of the atlas.
• Projected-fold

Additional tabs:

• Samples