Extended Data Fig. 9: Integrated MERFISH and scRNA-seq data to predict neuronal projections. | Nature Neuroscience

Extended Data Fig. 9: Integrated MERFISH and scRNA-seq data to predict neuronal projections.

From: Spatial transcriptomics reveals the distinct organization of mouse prefrontal cortex and neuronal subtypes regulating chronic pain

Extended Data Fig. 9

a, UMAP showing integration of cells from scRNA-seq (left) and MERFISH (right). The colors represent the projection sites in scRNA-seq data and the excitatory subtype in MERFISH data, respectively. b, Spatial location of neurons projecting to six different brain regions. c, Amygdala projection validation: mCherry expressing retrograde AAV was injected in amygdala (injection site shown) (scale = 0.5mm). Brain slice of PFC were stained with DAPI and mCherry to image the labeled neurons. smFISH co-labeling of mCherry with Pou3f1 (L5 ET marker), or Foxp2 (L6 CT marker) reveal partial overlap with both neuron subtypes. (Stains independently repeated 3 times). Arrows in enlarged images indicate dual labeled cells (scale bar = 20µm). d, High resolution images showing smFISH co-labeling of mCherry with Foxp2 and Pou3f1 within individual neurons (scale bar = 20µm).

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