Extended Data Fig. 2: Integrated snRNA-seq and spatial transcriptomic profiling of lesion-remote regions of the injured mouse spinal cord.
From: Lesion-remote astrocytes govern microglia-mediated white matter repair
a, UMAP of the final snRNAseq dataset after quality control (230,570 nuclei) colored by timepoint (healthy, 3dpi, 7dpi, 28dpi) and b, spinal region (Rostral vs Caudal). c, Heatmap plotting expression of putative marker genes used to identify different cell types. d, Violin plots showing the distribution of total counts and genes detected, and a stacked bar plot showing the proportions of cell types for each individual snRNAseq sample. All samples showed similar quality control statistics and cell type contribution. e, Aligned Visium data shown for the rostral and caudal regions in space and colored by timepoint (healthy, 3dpi, 7dpi, 28dpi). f, Mean expression for Synaptophysin (Syp) and g, Myelin Basic Protein (Mbp) confirming localization to the grey and white matter respectively. h, Violin plots showing the distribution of total counts and genes detected, and a stacked barplot showing the proportions of spinal region for each individual Visium experimental replicate. All replicates showed similar quality control metrics and tissue region contribution. Exact P values can be found in source data. i, Schematic showing pipeline for intraspinal regional spatial transcriptomics. For iSCI tissue sections, unbiased clustering identifies the lesion ipsilateral spinal cord white matter, which exhibits elevated expression of inflammation and gliosis genes relative to contra-lesional spinal cord regions.
