Fig. 5

Transcriptome in LPS- and IFNγ-stimulated WT and Nlrx1^−/− primary astrocytes. (A) Schematic of the experimental design. Primary astrocyte cultures were derived from WT and Nlrx1^−/− mice and were then subsequently stimulated with IFNγ and lipopolysaccharide (LPS) or vehicle (phosphate buffered saline) for 24 h at which point RNA was isolated and analyzed by bulk RNA sequencing. (B) Multidimensional scaling (MDS) plot of the top 1000 highly variable genes from normalized RNA-seq libraries from Nlrx1^+/+ and Nlrx1^−/− astrocyte cultures treated with or without LPS + IFNγ (C) Barcode plot showing genes associated with TNFα Signaling Via NF-κB (top, red) or genes associated with Oxidative Phosphorylation (bottom. blue). Genes associated with the pathway in question are represented by solid vertical line and are ranked from left to right using the moderated t statistic based on the difference in how Nlrx1^−/− cells responded to LPS + IFNγ vs. Nlrx1^+/+. Genes toward the left had a higher induction in the WT than in Nlrx1^−/− while genes on the right had a higher induction in the Nlrx1^−/− mice. Dotted lines represent neutral enrichment, and solid lines represent local enrichment in that area of the ranked list generated by a weighted tricube average in a sliding window, so that a value of 1 represents enrichment if distribution of genes were uniform, and a value of 1.5 would mean a 50% increased enrichment within the window. FDR are false discovery rate values calculated by the competitive gene set test CAMERA. (D and E) Heatmap showing scaled log 2-fold change values (LPS + IFNγ  stimulated vs. unstimulated) where row represents a gene, and column represents an independent biological replicate for a selection of genes associated with (D) TNFα Signaling via NF-κB and (E) Oxidative Phosphorylation. Each column’s genotype is indicated below the heatmap. for each gene and each biological replicate