Extended Data Fig. 2: Interferon related alterations (PCR, snRNA Seq).
Interferon score determined by qPCR of six ISGs (IFIT1, IFI27, IFI44L, ISG15, RSAD2, SIGLEC1) as previously described38,105 in biologically independent brainstem samples from n = 9 acute, n = 9 late, and n = 6 control cases. There were no statistically significant differences between group means as determined by one-way ANOVA (p = 0.34) (a). Gene expression of homeostatic microglia marker. Expression levels are color coded; the percentage of cells expressing the respective gene is size coded (b).Violin plot comparing the expression of IFN score in acute and late COVID-19 and in controls across all cell populations within the brainstem (c) and olfactory mucosa (d). Significance was calculated for IFN scores with a Mann-Whitney U test (two-sided) with the p-values adjustment with the Benjamini-Hochberg method. This is followed by a Wilcoxon effect size (two-sided) calculation for significant differences only. Significance was calculated using the Mann-Whitney U test, the p-values were corrected with FDR. Asterisks indicate level of statistical significance: ***p < 0.001, **p < 0.01, and *p < 0.05 (for the Wilcoxon effect size and the exact p-values, please refer to Supplementary Table 9) (e). Interferons and their receptor expression in all analyzed snRNA sequencing samples from the brainstem (n = 4 acute, n = 4 late, and n = 4 control cases) (c).
