Fig. 3: Spatial analysis of cell types identified in SC. | Communications Biology

Fig. 3: Spatial analysis of cell types identified in SC.

From: An atlas of neuropathic pain-associated molecular pathological characteristics in the mouse spinal cord

Fig. 3

a “CellTrek” imputed near single-cell level information by integrating ST data with snRNA-seq information. b “CellTrek” was used to map single cells onto the spatial coordinates of tissue sections of SC. c The spatial colocalization of cell types in the SC is displayed, where the edge width represents the probability of colocalization. d The spatial location of each identified cell type separately in the snRNA-seq dataset. The translucent blue rectangles indicate SCVH, representing results derived from model-based analysis. e The spacial and cellular expression of marker genes (Plp1, Dcn, Cldn5, Vcan, Trem2, Aldh1l1) displayed by spacial and snRNA-seq t-SNE plot. f Immunofluorescence displays the expression of PKCγ in normal SC. Scale bar: 200 μm (top left), 100 μm (others). g The distribution of Prkcg positive cells (Count > 2) in SC was visualized through the t-SNE diagram. h The spatial location of Prkcg positive cells in SC mapped by CellTrek. i The spatial expression of Prkcg mRNA. j Microglia deconvolution back alone to SC. k The immunofluorescence displays the expression of IBA-1 in SC 10 days after sham and SNL. Scale bar = 200 μm.

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