Extended Data Fig. 6: Multimodal quantification of Cluster 8 gene Igtp and Cluster 4 gene Timp1.

a, Representative sagittal section from female P30 mouse 24 h after LPS injection highlighting Igtp (red, top), Slc1a3 (cyan, middle) and co-localization (bottom) using RNAScope based on 4 saline- and 4 LPS-injected animals. Scale bar = 250 μm. b, Magnification of area in (a) indicated by yellow box. Yellow arrows indicate Igtp + astrocytes in Layer1 and surface of the brain. Scale bar = 100 μm. Inset shows a magnification of a single Igtp + astrocyte. Scale bar = 10 μm c, Quantification of Igtp + /Slc1a3 + astrocyte numbers using RNAScope in Layer1 of the cortex. A cell is identified as Igtp + if it expresses ≥20 dots/cell. P-value calculated with Mann-Whitney test, n = 4 saline-treated mice, n = 4 LPS-treated mice, 2-3 sections per mouse. Bar graphs show the mean, error bars SEM. d, Igtp expression in FACS-purified astrocytes 3 h (n = 4 saline, 5 LPS), 24 h (n = 5 saline, 4 LPS) and 72 h (n = 4 saline, 3 LPS) after LPS injection. * = padj<0.05, DESeq2, compared to corresponding saline-injected mice. Exact padj values can be found in Supplementary Table 1. N indicates number of animals, bar graphs show the mean, error bars are SEM. e, Igtp expression as quantified with Visium. Log Igtp levels (left) and percentage of spots with detectable Igtp levels as well as scaled average expression (right), across all spots from 3 saline- and 3 LPS-treated animals. f, Representative sagittal section from female P30 mouse 24 h after LPS injection highlighting Timp1 (red, top), Slc1a3 (cyan, middle) and co-localization (bottom) using RNAScope based on 4 saline- and 4 LPS-injected animals. Scale bar = 250 μm. g, Magnification of area in (f) indicated with a yellow box. White dashed line demarcates transition from white to gray matter. Scale bar = 50 μm. h, Quantification of Timp1 + /Slc1a3 + astrocyte numbers using RNAScope in corpus callosum. A cell is identified as Timp1 + if it expresses ≥20 dots/cell. P-value calculated with Mann-Whitney test, n = 4 saline-treated mice, n = 4 LPS-treated mice, 2-3 sections per mouse. Bar graphs show the mean, error bars SEM. i, Timp1 expression in FACS-purified astrocytes 3 h (n = 4 saline, 5 LPS), 24 h (n = 5 saline, 4 LPS) and 72 h (n = 4 saline, 3 LPS) after LPS injection. * = padj<0.05, DESeq2, compared to corresponding saline-injected mice. Exact padj values can be found in Supplementary Table 1. N indicates number of animals, bar graphs show the mean, error bars are SEM. e, Timp1 expression as quantified with Visium. Log Timp1 levels (left) and percentage of spots with detectable Igtp levels as well as scaled average expression (right), across all spots from 3 saline- and 3 LPS-treated animals.