Extended Data Fig. 4: Spatial transcriptomics integration reveals region-specific interactions between LRAs and neighboring cell types after SCI.
From: Lesion-remote astrocytes govern microglia-mediated white matter repair
a, Spatial profiles of additional NMF factors. b, UMAP of spinal cord neuron subtypes identified by snRNA-Seq for healthy and all post-injury time points, rostral and caudal. c, Neuron subtype proportions across healthy and iSCI reveals little injury-reactive alterations in neuron subtype representation after iSCI. d, UMAP of spinal cord neurons colored by expression of established subtype markers. e-h, Spatial and cell identity loading profiles of NMF3 revealed that dorsal horn astrocytes (dGM1,dGM2) intermingle with multiple subtypes of sensory neurons of the superficial laminae (Neuron 8, 9). i, j, Volcano plots of DEGs in Neuron 8 Gal+-expressing inhibitory interneurons or Neuron 9 Tac2+ excitatory interneurons, relative to other neuron subtypes (FDR P ≤ 0.05, LogFC>0.25). k, l, NicheNet analysis of dGM2 LRAs (senders) and cluster 8 or 9 neurons (receivers) identified several putative dorsal grey matter LRA-secreted ligands. m, UMAP of spinal cord endothelial cell subtypes identified by snRNA-Seq for all time points, rostral and caudal. n, Endothelia subtype proportions across healthy and iSCI groups reveals multiple injury-reactive alterations in endothelia subtype representation after iSCI. o-q Spatial and cell identity loading profiles of NMF6 revealed that ventral grey matter reactive LRAs (vGM2) intermingle with local endothelia 14. r, Volcano plot of Endothelia 14 DEGs, relative to other endothelia subtypes (FDR P ≤ 0.05, LogFC>0.25). s, NicheNet analysis of vGM2 LRAs (senders) and cluster 14 endothelia (receivers) identified several putative ventral grey matter LRA-secreted ligands.
