Fig. 3

Conserved patterns of RNA destabilization in C9ALS iPSCs. Scatter plot (a), gene ontology (b), and STRING analysis (c) for the 956 transcripts showing changes in stability ≥1.5-fold in C9ALS iPSCs, in comparison to control (Cntl) cells. Higher resolution views for boxed areas in c are shown in d and e. Scatter plot (f) and gene ontology (g) for 865 transcripts with altered stability ≥1.5-fold in sALS iPSCs, in comparison to control cells. h Gene ontology analysis of RNA transcripts showing ≥1.5-fold reduction in C9ALS iPSCs vs. controls, acquired from the NeuroLINCS database. FDR false discovery rate. Cell lines used for these experiments, performed in duplicate, are listed in Supplementary Table 1. i−k Quantitative (q)RT-PCR in patient postmortem tissue, showing reduced abundance of RNAs related to mitochondrial oxidative phosphorylation (COX6B, COX6C-X1, COX5B, NDUFA1, NDUFA13) and the ribosome (RPL28, RPL38, RPS18) in C9ALS spinal cord (i), C9FTD frontal cortex (j), and sALS spinal cord (k). Graphs in i−k depict mean ± standard error. *p < 0.05, #p < 0.01, two-way ANOVA with Sidak’s multiple comparison test. All data in i−k were assembled from ≥3 biological replicates. Supplementary Table 3 lists the number of samples in each condition and clinical characteristics for each patient