An emergent disease-associated motor neuron state precedes cell death in a mouse model of ALS [multiome]

To uncover molecular determinants of motor neuron degeneration and selective vulnerability in amyotrophic lateral sclerosis (ALS), we performed longitudinal single-nucleus RNA sequencing, paired single-nucleus RNA and ATAC sequencing, and MERFISH spatial transcriptomics from control and SOD1-G93A mouse spinal cords. For the final snRNA-seq analysis, control experiments from Blum et al., Nat Neurosci, 2021 (GEO accession: GSE161621) were also used. Overall design: Nuclei were isolated from the spinal cords of control and SOD1-G93A mice at early-stage (~P65), mid-stage (~P100), and end-stage (~P125). All mice carried ChAT-IRES-Cre and ROSAnT-nG alleles, which labeled nuclei from cholinergic neurons with GFP and nuclei from other cell types with tdTomato. Fluorescence-Activated Nuclei Sorting (FANS) was performed to enrich GFP+ cholinergic nuclei while also collecting tdTomato+ non-cholinergic nuclei. Following nuclei sorting, either snRNA-seq (Chromium Single Cell 3' Reagent Kit v3, 10x Genomics) or multiome ATAC + gene expression profiling (Chromium Single Cell Multiome ATAC + Gene Expression v1, 10x Genomics) was performed according to manufacturer protocols, and libraries were sequenced on an Illumina NextSeq 550 or NovaSeq 6000.