Fig. 3: Transcriptional and epigenetic analysis reveal differences in the differentiation potential of hiPSC-NSC and hfNSC. | Nature Communications

Fig. 3: Transcriptional and epigenetic analysis reveal differences in the differentiation potential of hiPSC-NSC and hfNSC.

From: Human iPSC-derived neural stem cells displaying radial glia signature exhibit long-term safety in mice

Fig. 3

A Gene ontology enrichment analysis of RNA-seq data comparing hiPSC-NSCs vs. hfNSCs (log2 fold change ± 1, adjusted p-value < 0.05, Benjamini–Hochberg correction). Bar plots represent the biological processes (BP, left plots) and pathways (right plots) upregulated (red bars) or downregulated (blue bars) in hiPSC-NSCs as compared to hfNSC (probability density function with Bonferroni correction). B Gene ontology enrichment analysis resulting from integrating ChIP-seq and RNA-seq datasets of hiPSC-NSCs vs hfNSCs (log2 fold change ± 1,5, adjusted p-value < 0.05, Benjamini–Hochberg correction). Bar plots show BP (upper plots) and pathways (bottom plots) of genes close to cell-specific enhancers (100 kb window) upregulated in hiPSC-NSCs (red bars) or hfNSCs (blue bars) (probability density function with Bonferroni correction). C Heatmap showing the expression levels of neurogenic and gliogenic genes in hiPSC-NSCs vs hfNSCs. The colour scale indicates the average expression levels in each cluster (blue, low; red, high). A–C Analyses were performed in hiPSC-NSC clones HD 1.1 (p3), HD 1.3 (p5), HD 2.2 (p3), and HD 2.3 (p4); hfNSCs: three biological replicates at different passages (p19, p23, p25). Source data are provided as a Source Data file.

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