Extended Data Fig. 6: Extended transcriptomic analysis of human isogenic APOE3/3 and APOE4/4 iAstrocytes.
From: The Neurolipid Atlas: a lipidomics resource for neurodegenerative diseases
a-b) Volcano plots present log2fold change of differentially expressed genes (DEGs) in ApoE4 vs ApoE3 iAstrocytes from BIONi037 (a) or Kolf2.1J set #1 (b) from transcriptomics experiments. Top ten genes with the highest log2fold change and top ten genes with the most significant P-value are labeled. c-d) Top 10 Reactome pathways upregulated or downregulated (with lowest FDR) in ApoE4 vs ApoE3 iAstrocytes by gene-set enrichment analysis of transcriptomics data. e) Heatmap shows transcriptomic changes of indicated genes (all genes from the Reactome interferon signaling pathway) in ApoE4 vs ApoE3 iAstrocytes from our study and previous studies (as indicated). f) Plin2 gene expression based on the transcriptomic analysis of ApoE4 vs ApoE3 iAstrocytes from BIONi037 or Kolf2.1J set #1. n=3 wells per genotype in each isogenic set. Mean + sd. CPM = normalized counts per million. g) Relative mRNA expression levels of indicated genes in ApoE4 vs ApoE3 iAstrocytes quantified by qPCR. N=3 independent experiments from each isogenic set. Mean + sem. *P<0.05 one sample t-test with Benjamini-Hochberg correction on the p-values. (Kolf2.1J set #1).
