Fig. 3: Single-cell transcriptomics of mixed neural cultures reveals time- and cell type- dependent activation of innate immunity pathways. | Nature Communications

Fig. 3: Single-cell transcriptomics of mixed neural cultures reveals time- and cell type- dependent activation of innate immunity pathways.

From: AAV vectors trigger DNA damage response-dependent pro-inflammatory signalling in human iPSC-derived CNS models and mouse brain

Fig. 3

A Scheme illustrating the differentiation process and transduction of hiPSC-derived mixed 2D cultures. Scheme created in BioRender. Costa, H. (2025) https://BioRender.com/u34k332. (B) UMAP plot of single-cell data generated with Seurat showing clustered untreated and treated samples from day 2. Cells are plotted in two dimensions using the UMAP dimensionality reduction technique and annotated by cell type. C Donut plot showing the frequency of each cell type in the UMAP shown in (B). D Quantification of the % of cells positive for GFP mRNA within each cell type for AAV9-treated samples on day 4. E Heat maps visualizing the enriched GSEA terms in total astrocytes, neurons and oligodendrocytes against the Hallmark gene set (Molecular Signatures Database). GSEA was performed on logFC pre-ranked gene lists obtained from gene expression levels of samples transduced with AAV9 compared to untransduced (UT) within each cell type using Kolmogorov-Smirnov test with FDR for multiple test correction (NES, normalized enrichment score; *, adjusted P < 0.05; **, adjusted P < 0.01; ***, adjusted P < 0.001).

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