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. Author manuscript; available in PMC: 2020 Jan 17.
Published in final edited form as: Nature. 2019 Jul 17;573(7772):75–82. doi: 10.1038/s41586-019-1404-z

Extended Data Fig. 2. Molecular changes in cortical neuron subtypes in MS lesions.

Extended Data Fig. 2

(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 excitatory neurons (EN-L2-3 and EN-L4) in MS lesion tissue versus deep cortical layer excitatory and inhibitory neurons (EN-L5-6 and IN-SST). For all tSNE and violin plots, data are shown from 9 control and 12 MS samples. For tSNE plots, data from 48,919 nuclei are shown. For EN-L2-3, EN-L4 and EN-L5-6 violin plots, data 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 EN-L2-3, EN-L4 and EN-L5-6 cells based on differential gene expression analysis (linear mixed model regression). Binomial test with FDR correction was utilized to calculate FDR-corrected p values using genes differentially expressed in EN-L2-3, EN-L4 and EN-L5-6 nuclei (n= 428, 364 and 327).