Extended Data Fig. 7: Additional validation of Single Nuc Seq DEGs and motifs.

a,b, Dotplots showing log₂ fold expression change in alpha prime vs. alpha clusters (alpha DEGs) or type 3 prime vs. type 3 clusters on x-axis and log2 fold expression change in the same genes in treated bulk RNAseq data vs. control bulk RNAseq data. There is an overall positive correlation in these gene expression changes despite differences in the methodology and sensitivity of snRNAseq vs. bulk RNAseq. The positive correlation with bulk RNAseq is stronger for alpha (R2 = 0.40, p < 0.0001) than type 3 (R2 = 0.21, p < 0.0001) DEGs. c, Representative immunostaining for RFP in the AAV-mCherry-treated animal included in Fig. 2b showing extensive transgene expression in CHAT⁺ motor neurons. Scale bar represents 20 µm. d, Enlarged regions of images from Fig. 2b showing MNX1 expression in a subset of ISL1⁺ cells that show strong nuclear CADPS2 staining (arrowheads). No MNX1 signal was detected in animals injected with control mCherry virus. Scale bar represents 20 µm. e, UMAP from Fig. 1h showing distribution and prevalence of Lhx3 motifs among differentially accessible peaks in each cluster.