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Fig. 4 | BMC Biology

Fig. 4

From: Altered neuronal physiology, development, and function associated with a common chromosome 15 duplication involving CHRNA7

Fig. 4

Transcriptomic analysis of differentiated cortical neuroids, defining differential gene expression between the AP and UM. RNA-seq was conducted on cortical neuroids after 15 days of differentiation. a Principal Component Analysis (PCA) of gene expression in differentiated neuroids derived from the UC-M, UC-F, UM, and AP models is displayed as a multidimensional scaling plot derived from four independent biological replicate experiments (n = 4) performed using one clonal line for each subject. Data values are in Additional file 5. b Venn diagram showing differentially expressed genes (DEGs) defined by pairwise comparisons of the AP versus (vs.) UM, AP vs. UC-M, and AP vs. UC-F datasets. AP vs. UM-specific DEGs are shown in blue. c These AP-specific DEGs were further analyzed by hierarchical clustering analysis, with the other samples included for comparison. dh DEGs were assessed by Ingenuity Pathway Analysis (IPA), identifying de AP-enriched pathways, and f disease-related GO terms. d IPA-pathway analysis identified differential enrichment for Wnt signaling-related gene expression, with expression of these genes visualized as a heat map in e; inset at right shows protein levels of two targets in the UM and AP, as assessed by Western blotting, with GAPDH as a loading control. In d and f, the number of genes related to each term is represented on the x-axis, while red and blue color indicates up and downregulated genes, respectively. P values for each term are indicated to the right of each bar. f IPA disease GO terms identified gene networks associated with g behavior and h nervous system development and function. Numbers (#) of upregulated and downregulated genes in each network are indicated. Within each network, red and green symbols indicate upregulated and downregulated genes, respectively, while color intensity indicates the relative degree of differential expression

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