Extended Data Fig. 8: Spatial expression and IPA analysis of ageing associated genes after OxPC mediated neurodegeneration.
From: Single-cell and spatial RNA sequencing identify perturbators of microglial functions with aging
a) Histological demarcation of the OxPC induced lesion to spatially compare gene expression between 6wk and 52wk mice during neurodegeneration. b) Violin plots comparing the spatial expression of Lgals3 (6wk/52wk min = 2.0/3.6, max = 6.4/7.3, mid = 4.5/5.6, mean = 4.5/5.5, q1 = 3.7/4.9, q3 = 5.5/6.3), Lyz2 (6wk/52wk min = 4.9/5.1, max = 9.2/10, mid = 7.0/7.9, mean = 7.0/7.8, q1 = 6.2/7.2, q3 = 7.6/8.7), Cd74 (6wk/52wk min = 0/0, max = 4.2/4.9, mid = 1.0/1.6, mean = 1.0/1.9, q1 = -/1.0, q3 = 1.6/2.6), Wfdc17 (6wk/52wk min = 1.0/2.0, max = 5.9/7.4, mid = 3.8/4.6, mean = 3.7/4.6, q1 = 3.0/4.6, q3 = 4.5/5.6), H2-Aa (6wk/52wk min = -/-, max = 3.4/3.7, mid = 0/0, mean = 0.5/1.0, q1 = -/-, q3 = -/2.0), Ccl2 (6wk/52wk min = -/0, max = 2.3/3.0, mid = 0/1.0, mean = 0.4/0.8, q1 = -/-, q3 = 1.0/1.3), Plin2 (6wk/52wk min = 1.6/1.0, max = 5.4/6.5, mid = 3.9/4.8, mean = 3.8/4.4, q1 = 3.2/3.6, q3 = 4.5/5.4), Gas6 (6wk/52wk min = 1.6/0, max = 5.2/4.9, mid = 4.4/3.3, mean = 4.1/3.2, q1 = 3.8/2.5, q3 = 4.6/4.0), Gnas (6wk/52wk min = 3.8/1.0, max = 7.5/6.5, mid = 6.6/5.5, mean = 6.4/5.1, q1 = 6.1/4.6, q3 = 6.9/6.0), Lgmn (6wk/52wk min = 3.7/2.0, max = 7.1/7.3, mid = 6.5/5.7, mean = 6.3/5.4, q1 = 6.0/4.8, q3 = 6.8/6.2), Lpl (6wk/52wk min = 1.6/1.0, max = 5.1/5.2, mid = 4.2/3.7, mean = 4.0/3.5, q1 = 3.8/3.2, q3 = 4.5/4.2), Apoc1 (6wk/52wk min = 1.0/0, max = 6.1/3.0, mid = 3.8/1.0, mean = 3.7/1.0, q1 = 3.0/-, q3 = 4.5/2.0), Qk (6wk/52wk min = 2.0/0, max = 5.4/5.1, mid = 4.5/3.6, mean = 4.4/3.4, q1 = 4.1/2.8, q3 = 5.0/4.0), and Cd9 (6wk/52wk min = 2.8/1.0, max = 6.7/6.2, mid = 6.0/5.2, mean = 5.7/4.7, q1 = 5.3/4.1, q3 = 6.2/5.8) mRNA in the OxPC lesion of 6wk and 52wk spinal cords. c) Top IPA predicted activated or inhibited causal regulator genes (z-score cut off -2 and 2) identified by scRNAseq in the MPH clusters from the PAzePC injected 52wk spinal cord compared with the PAzePC injected 6wk spinal cord. d) Summary of IPA predicted pathway changes in MPH clusters from differentially expressed ageing associated genes during OxPC mediated neurodegeneration. Clusters without sufficient high z-score connectable features are not shown. e) Day 7 lesions from 6wk and 52wk old mice labeled with CD68 (green) and OPN (red). f-h) Graphs comparing the proportion of CD68+ area that is also OPN+ (f), the fold difference in total lesional OPN MFI (g), and fold difference in OPN MFI from CD68+ area (h) between 6wk and 52wk old lesion spinal cords. i) Representative images and violin plots comparing the spatial expression of Itgb1 (6wk/52wk min = 1.6/0, max = 4.6/4.6, mid = 3.2/2.8, mean = 3.3/2.7, q1 = 2.8/2.2, q3 = 3.8/3.5), Itgav (6wk/52wk min = 1.6/1.0, max = 4.1/4.5, mid = 3.1/2.6, mean = 2.9/2.5, q1 = 2.3/1.8, q3 = 3.3/3.2), and Itgb5 (6wk/52wk min = 3.0/1.0, max = 5.9/5.3, mid = 4.9/4.1, mean = 4.0/3.9, q1 = 4.5/3.2, q3 = 5.4/4.8) mRNA in the lesion area of 6wk and 52wk spinal cords. For ScRNAseq, n = 3 per experimental group (each n represents a pool of 4 spinal cords for a total of 12 mice per group) and data are represented as mean ± SD. For spatial sequencing, n = 2 per experimental group. Microscopy data were acquired from 2 separate experiments, n = 6 per experimental group. Significance indicated as * p < 0.05, ** p < 0.01, two-tailed, unpaired t-test, comparing 6wk and 52wk old mice. Data are represented as mean ± SD.
