Extended Data Fig. 4: Neurons remain differentiated after SCI.

a, Volcano plots showing differential expression for all level 4 neuron subtypes simultaneously across timepoints. Enlarged points represent the key marker genes for each neuron subtype shown in Supplementary Fig. 11a. Marker genes shown in grey show no evidence of differential expression after SCI in their respective neuron subtype. b, Differential expression of key marker genes for level 4 neuron subtypes across timepoints and injury severities (log₂-fold change, y-axis, and false discovery rate, point color). Timepoints or severities for which key marker genes show evidence of statistically significant differential expression, compared to uninjured neurons, are plotted with light grey backgrounds. Genes without statistical evidence of differential expression (i.e., FDR greater than 5%) are shown as white points. n.d., genes that were not detectably expressed and could not be subjected to DE analysis. c, Volcano plot showing differential expression for averaged gene expression modules comprising the top 5, top 10, or top 50 marker genes identified for each level 4 neuron subtype by unbiased comparisons with all other neurons, simultaneously across all timepoints. The vast majority of marker gene modules show no evidence of downregulation after SCI in their respective neuron subtype. d, As in c, but showing differential expression for averaged gene expression modules comprising the top 50 marker genes for each level 4 neuron subtype, shown separately for each condition in the timecourse experiment.