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SAHA rescues chromatin and transcriptomic changes (A) Outline of the experimental strategy. (B) PCA plot of ATAC-seq data obtained from four WT, five TS mice, and three TS-SAHA (TST). (C) PCA plot <t>of</t> <t>RNA-seq</t> data obtained from four WT and four TS mice and three TS-SAHA (TST). (D) Number of differentially accessible regions (DARs) for each comparison (left), and number of DARs in non-triplicated and triplicated genomic regions (right). (E) Number of differentially expressed genes (DEGs) for each comparison (left) and number of DEGs in non-triplicated and triplicated genomic regions (right). (F) Analysis of differentially accessible regions (DARs) in TS neurons and their rescue upon SAHA treatment, shown as line-plots (left) and Venn diagram (left). Kruskal-Wallis test followed by pairwise Wilcoxon tests with multiple-comparison correction, ∗∗∗ p < 0.001. (G) Analysis of differentially expressed genes (DEGs) in TS neurons and their rescue upon SAHA treatment, shown as line-plots (left) and Venn diagram (right). Kruskal-Wallis test followed by pairwise Wilcoxon tests with multiple-comparison correction, ∗∗∗ p < 0.001. (H) Heatmap of transcription factor motif enrichment among gained peaks in TS and TS-SAHA neurons, with significance and fold enrichment. (I) Gene set enrichment analysis of differentially expressed genes in TS (red) and TS-SAHA neurons (orange). See also .
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SAHA rescues chromatin and transcriptomic changes (A) Outline of the experimental strategy. (B) PCA plot of ATAC-seq data obtained from four WT, five TS mice, and three TS-SAHA (TST). (C) PCA plot of RNA-seq data obtained from four WT and four TS mice and three TS-SAHA (TST). (D) Number of differentially accessible regions (DARs) for each comparison (left), and number of DARs in non-triplicated and triplicated genomic regions (right). (E) Number of differentially expressed genes (DEGs) for each comparison (left) and number of DEGs in non-triplicated and triplicated genomic regions (right). (F) Analysis of differentially accessible regions (DARs) in TS neurons and their rescue upon SAHA treatment, shown as line-plots (left) and Venn diagram (left). Kruskal-Wallis test followed by pairwise Wilcoxon tests with multiple-comparison correction, ∗∗∗ p < 0.001. (G) Analysis of differentially expressed genes (DEGs) in TS neurons and their rescue upon SAHA treatment, shown as line-plots (left) and Venn diagram (right). Kruskal-Wallis test followed by pairwise Wilcoxon tests with multiple-comparison correction, ∗∗∗ p < 0.001. (H) Heatmap of transcription factor motif enrichment among gained peaks in TS and TS-SAHA neurons, with significance and fold enrichment. (I) Gene set enrichment analysis of differentially expressed genes in TS (red) and TS-SAHA neurons (orange). See also .

Journal: iScience

Article Title: HDAC inhibitor treatment restores transcriptome, chromatin accessibility, and memory deficits in a mouse model for Down syndrome

doi: 10.1016/j.isci.2026.117670

Figure Lengend Snippet: SAHA rescues chromatin and transcriptomic changes (A) Outline of the experimental strategy. (B) PCA plot of ATAC-seq data obtained from four WT, five TS mice, and three TS-SAHA (TST). (C) PCA plot of RNA-seq data obtained from four WT and four TS mice and three TS-SAHA (TST). (D) Number of differentially accessible regions (DARs) for each comparison (left), and number of DARs in non-triplicated and triplicated genomic regions (right). (E) Number of differentially expressed genes (DEGs) for each comparison (left) and number of DEGs in non-triplicated and triplicated genomic regions (right). (F) Analysis of differentially accessible regions (DARs) in TS neurons and their rescue upon SAHA treatment, shown as line-plots (left) and Venn diagram (left). Kruskal-Wallis test followed by pairwise Wilcoxon tests with multiple-comparison correction, ∗∗∗ p < 0.001. (G) Analysis of differentially expressed genes (DEGs) in TS neurons and their rescue upon SAHA treatment, shown as line-plots (left) and Venn diagram (right). Kruskal-Wallis test followed by pairwise Wilcoxon tests with multiple-comparison correction, ∗∗∗ p < 0.001. (H) Heatmap of transcription factor motif enrichment among gained peaks in TS and TS-SAHA neurons, with significance and fold enrichment. (I) Gene set enrichment analysis of differentially expressed genes in TS (red) and TS-SAHA neurons (orange). See also .

Article Snippet: SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian , Takara , Cat#634411.

Techniques: RNA Sequencing, Comparison, Analysis

Journal: iScience

Article Title: HDAC inhibitor treatment restores transcriptome, chromatin accessibility, and memory deficits in a mouse model for Down syndrome

doi: 10.1016/j.isci.2026.117670

Figure Lengend Snippet:

Article Snippet: SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian , Takara , Cat#634411.

Techniques: Cell-Signaling, Recombinant, Bicinchoninic Acid Protein Assay, Isolation, DNA Library Preparation, Software, Analysis