Extended Data Fig. 10: Marker gene expression and public atlas integration informs snRNA-seq cell typing from the PFC of mice. | Nature Neuroscience

Extended Data Fig. 10: Marker gene expression and public atlas integration informs snRNA-seq cell typing from the PFC of mice.

From: The psychoplastogen tabernanthalog induces neuroplasticity without proximate immediate early gene activation

Extended Data Fig. 10: Marker gene expression and public atlas integration informs snRNA-seq cell typing from the PFC of mice.

(a) Canonical marker genes establish cellular identity and distinguish between layer specific neuronal subtypes. (b) L4/5_IT_Glut_2 and L4/5_IT_Glut_4 cells are distinguished by their expression of certain genes and those with the greatest fold change in both directions are shown. (c) Brain Initiative Cell Census Network (BICCN) snRNA-seq data of cortical regions is shown in a UMAP with subtype labels shown. (d) The nuclei from our data (red) projected onto the dimensionality reduction of the BICCN data (black) map to cortical subsets of the reference which enables label transfer of cell type annotations. Our final cell type annotations are a combination of label transfer approach with manual curation based on published information on marker genes. (e) Feature plots show cluster specific patterning of select marker gene expression. The scales denote the normalized expression level. (f) Feature plots show overlapping distribution of the Camk2a driver with Htr2a-expressing cells. (g) Quantification of the co-expression of Camk2a in Htr2a-expressing cells indicates a high percentage of Htr2a-expressing neuronal cells also express Camk2a.

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