Extended Data Fig. 7: Ageing associated transcriptomic changes in the homeostatic spinal cord.
From: Single-cell and spatial RNA sequencing identify perturbators of microglial functions with aging
a) Top significantly upregulated (green) and downregulated (blue) genes identified by scRNAseq in the MPH clusters from the PBS injected 52wk versus 6wk spinal cord (clusters without significantly differentially expressed gene are not shown). b) Graph comparing the number of DEGs between the age groups found in each MPH cluster. c) Summary of IPA predicted regulatory effects network in steady-state associated MG3 and MG5 clusters from differentially expressed ageing associated genes. d-e) Top activated (orange) or inactivated (blue) casual network regulators (d) or disease and biological functions (e) in 52wk PBS injected spinal cords compared to 6wk PBS injected spinal cords as predicted by IPA using the differentially expressed ageing associated genes from each MPH cluster. Clusters without significantly differentially expressed gene are not shown. f) Histological demarcation of the NAWM and the NAGM used to spatially compare gene expression from homeostatic spinal cord tissue. g) Violin plots comparing the spatial expression of Fth1 (6wk/52wk NAWM: min = 2.6/2.0, max = 10/10, mid = 7.1/8.4, mean = 7.2/7.9, q1 = 5.9/7.7, q3 = 8.7/8.9; for NAGM: min = 5.0/5.8, max = 9.3/9.3, mid = 8.0/8.3, mean = 7.9/8.2; q1 = 7.6/8.0, q3 = 8.3/8.5), Lyz2 (NAWM: min = 0/0, max = 6.0/6.7, mid = 1.0/2.3, mean = 1.3/2.3, q1 = -/1.6, q3 = 2.0/3.3; for NAGM: min = 0/0, max = 5.0/6.6, mid = 2.6/3.6, mean = 2.5/3.5; q1 = 2.0/3.0, q3 = 3.0/4.1), Apoe (NAWM: min = 1.0/0, max = 9.4/9.4, mid = 5.0/5.2, mean = 4.8/5.1, q1 = 3.5/4.5, q3 = 5.9/5.8; for NAGM: min = 3.9/4.6, max = 8.2/8.0, mid = 6.8/6.6, mean = 6.7/6.6; q1 = 6.4/6.3, q3 = 7.2/7.0), H2-D1 (NAWM: min = 0/0, max = 4.2/4.6, mid = 1.0/1.6, mean = 0.9/1.7, q1 = -/1.0, q3 = 1.6/2.3; for NAGM: min = 0/0, max = 4.6/4.5, mid = 2.3/2.6, mean = 2.2/2.7; q1 = 1.6/2.0, q3 = 2.8/3.3), and Ifi27l2a (NAWM: min = 0/0, max = 3.2/5.0, mid = 0/1.0, mean = 0.5/1.1, q1 = -/-, q3 = 1.0/1.7; for NAGM: min = 0/0, max = 3.2/4.1, mid = 1.0/1.0, mean = 0.7/1.1; q1 = -/-, q3 = 0/1.6) mRNA in the NAWM and NAGM 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). For spatial sequencing, n = 2 per experimental group.
