Extended Data Fig. 1: Technical parameters of snRNAseq and cell-type distribution across individuals.

a. Schematic diagram of workflow for isolation of nuclei from cortices of ALS patients and age-matched controls followed by single-cell RNA sequencing by DropSeq, library generation and Quality Controls for analysis with Seurat 3.0.2 b. Frozen tissue from one of the individuals. c. Staining for TDP-43 in one of the patient sample, note neuron with skein-like inclusions and faint nuclear staining (scale bar 25μm, n = 3 patients analysed). d. Quality controls post-filtering (FC – Frontal Cortex): number of total nuclei detected (barcodes), average number of genes per nucleus (nFeatures), and average number of UMIs (Unique Molecular Identifiers) per nucleus (nCounts). e. t-SNE projections of the whole cohort with expression of broad cell type markers. f. Dotplot representing percentage of cells expressing additional cell type specific markers. g. t-SNE distribution of whole cohort with annotated cell types split by diagnosis (ALS patients n = 5, age-matched Controls n = 3, n = 79,169 total nuclei). h. Quality controls post-filtering (FC – Frontal Cortex): number of total nuclei detected (barcodes), average number of genes per nucleus (nFeatures), and average number of UMIs (Unique Molecular Identifiers) per nucleus (nCounts). i. Fraction of each cell types identified in whole cohort split by diagnosis (mean ± SEM, ALS patients n = 5, age-matched Controls n = 3).