Extended Data Fig. 1: Gene expression profile from the frontal grey matter correlates with nCounter bulk tissue direct gene expression.
From: Brain-wide alterations revealed by spatial transcriptomics and proteomics in COVID-19 infection
a) Bar plots showing the number of differentially expressed molecules in different assays (BH-adjusted p < 0.1, MSstatsTMT31 for proteomics; DESeq232 for nCounter direct gene expression; lme433 for spatial transcriptomics). b) Venn diagrams and Pearson’s correlation of overlapped differentially expressed genes from nCounter direct gene expression of the frontal lobe and spatial transcriptomics of frontal grey matter (p = 1.60E-11, GeneOverlap34, Pearson’s correlation, two-sided, r = 0.77, p = 1.62E-33) and frontal white matter (p = 0.60, GeneOverlap34, Pearson’s correlation, two-sided, r = -0.42, p = 0.72). c) 3 SARS-CoV2 transcripts in nCounter direct gene expression (basal ganglia) indicated there was no increased expression of viral mRNA (N = 6 for controls, N = 6 for COVID-19 patients, two-tailed unpaired t test). d) Bar plots showing the results of cell type enrichment analysis (EWCE38) of NRGN neuron from Yang, et al, 202125 and its celltype markers’ enrichment when comparing to the major cell types (level 1) and subclass cell types (level 2) in Wamsley, et al, 202439 and Bakken, et al, 202140. The red dashed line represents a threshold of 2.5 for the sd_from_mean. Cell types with a sd_from_mean value > 2.5 and a BH-adjusted p < 0.05 are considered statistically significant.
