Extended Data Fig. 4: Classes of L5-ETNs express higher levels of stress pathways.

a. DGE-based PCA plots showing separation of individuals by diagnosis in Exc1. b. Violin plots of z-scores for genes upregulated in each class of L5-ETNs (DGE1, DGE5, DGE6) in the three groups split by diagnosis (bars denote median – symbols: average score per individual). c, Comparison of DGEs signature (>10% cells, >2-FC, adj.p < 0.05) and redoDGE signatures identified in each subgroup with random seeding of equal cell numbers per diagnosis (>10% cells, >2-FC, adj.p < 0.05, max.cells.per.ident=lowest.number.per.group). d. Violin plots of z-scores for redoDGE signatures (median and interquantile ranges – symbols: average score per individual). e. Correlation plot of Log Fold Changes in ALLminus1 comparisons. f. Venn diagram comparing genes shared between ALLminus1 analyses. g. Venn diagram comparing genes in common between ALLminus1 analysis and ExcAll. h. Violin plots of z-scores for genes globally downregulated in Excall (geometric boxplots represent median and interquantile ranges – symbols: average score per individual). i. Comparison of genes globally upregulated in ALS (DGEall) with genes upregulated in CUX2-exc0 (>10% of cells, >2-FC, adj.p < 0.05) j. Gene Ontology analysis of terms for DGE0 highlighted terms involved in synaptic biology (CC=Cellular Components). k. Gene Ontology analysis of terms for DGEall highlighted terms involved in synaptic biology (CC=Cellular Components). l,m. Selected GO terms for DGE0, DGE1 and DGEall. n. Venn Diagram for shared upregulated genes between other excitatory neurons and global signature. o,p. Venn Diagrams for shared upregulated genes between treated MS excitatory neurons from Schirmer et al. and AD excitatory neurons from Mathys et al. with changes found in this study.