Fig. 1: Multi-transcriptomics depicting SC gene expression in NP.

a Schematic figure illustrating a flow chart of ST combined with snRNA-seq to map mice SC gene expression landscape in the sham and NP states 10 days after surgeries. Created with BioRender. b Hematoxylin-eosin-stained coronal sections of SCs from sham and SNL mice subject to ST analysis (two biological repeats). c Overview of the ST-spot clusters within spinal cord samples, with the left schematic illustrating the anatomical context of the spinal cord and the relative positions of the clusters. The upper right panel displays the spatial distribution across four samples, while the lower right panel provides a UMAP visualization of the clusters. d Heatmap showing each spatial cluster’s correlation according to their gene expression files. e Heatmap shows the top 5 enriched genes in each spacial cluster. f ST showing the top 5 upregulated and downregulated genes in the ipsi DH of the SNL mice compared with the sham mice. g ST showing top 5 upregulated and downregulated genes in the ependyma’s region in the SNL mice compared with the sham mice. h t-SNE plots showing identified cell types within SCDH from mice 10 days after sham and SNI, colored according to identified clusters. The dot plot shows the expression of established marker genes to annotate snRNA-seq-identified subpopulations of the DH. i The top 5 enriched genes in each snRNA-seq identified subpopulation. j, k t-SNE plots and heatmaps showing the top five upregulated and downregulated genes in microglia (j) or excitatory neuron (k) in the SNI mice compared with the sham mice. l t-SNE plots of snRNA-seq and Spatial plot showing the spatial and cellular expression pattern of Slc5a7 in the SC; m Immunofluorescence staining for CHT1 coded by Slc5a7 on SC sections 10 days after surgeries. Scale bar = 200 μm. n t-SNE plots of snRNA-seq and Spatial plot showing the spatial and cellular expression pattern Ly86. o RNA Scope analyses showed Ly86 expression in SC. Scale bar = 200 μm. p Timecourse of Ly86 mRNA expression in SC 10 days after SNL. Values are shown as mean (bar) ± SD (error bar). ****P < 0.0001, N = 5–7, one-way ANOVA followed by Bonferronis test.