Extended Data Fig. 2: Molecular changes in cortical neuron subtypes in MS lesions.
From: Neuronal vulnerability and multilineage diversity in multiple sclerosis
a, NORAD and PPIA expression patterns in cortical neurons and selected glial subtypes. Note baseline expression of NORAD and PPIA in neuronal versus glial subtypes and preferential upregulation of both NORAD and PPIA in upper-cortical-layer ENs (L2–L3 EN (EN-L2-3) and L4 EN (EN-L4)) in MS lesion tissue versus deep-cortical-layer excitatory and inhibitory neurons (L5–L6 EN (EN-L5-6) and IN-SST). For all t-SNE and violin plots, data are shown from 9 control and 12 MS samples. For t-SNE plots, data from 48,919 nuclei are shown. For L2–L3 EN, L4 EN and L5–L6 EN violin plots, data are shown from 6,120, 3,125 and 3,058 nuclei. Box plots inside violin plots represent median and standard deviation of gene expression. b, Visualization of enriched GO terms in L2–L3 EN, L4 EN and L5–L6 EN cells based on DGE analysis (linear mixed model regression). Binomial test with FDR correction was used to calculate FDR-corrected P values using genes differentially expressed in L2–L3 EN, L4 EN and L5–L6 EN nuclei (n = 428, 364 and 327, respectively).
