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. 2023 Jun 3;14:3212. doi: 10.1038/s41467-023-39043-x

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© The Author(s) 2023

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 6 — a Scheme of the modified Rosa26 with mutant SETBP1 (G870S) cDNA, before and after CRE recombination. b Brains of control (Cre-) and mutant (Cre+) P30 mice. Square side = 1 mm. c Nissl staining of P30 brains. Scale bar = 500 μm. d Western blot for SETBP1, SET, and H3K27ac levels: H3 and Calnexin (CLNX) are used as loading controls. e UMAP plots of scMultiome clusters. RNA (left) and ATAC (right) dataset. f UMAP of RNA velocity, each arrow shows the direction and speed of the velocity flow in both experimental conditions. Heatmaps on the left contains average velocity value for each cluster. g Heatmaps showing accessibility Z-score during AP_RGCs to ExN_DL trajectory. The left heatmap shows Z-score calculated in control condition, the middle heatmap shows Z-score calculated in control peaks using only mutant cells, while the right heatmap shows Z-score calculated in mutant condition. The Venn diagram shows overlap mutant and control peaks used in the analysis. h Scatter plot of Nrxn1 expression along pseudo time trajectory of AP_RGCs to ExN_DL in control (left) and mutant (right). i Differential gene regulation inside the ExN_DL cluster, each point represents a gene. Number of unique peaks associated to each gene, in each genotype, are plotted. Points in blue are downregulated genes, while those in red are upregulated. j Enhancer-promoter regulatory network inside the Nlgn1 gene locus (chr3: 25,425,522-26,444,634), magnifications in 1 and 2 show differential accessibility at two enhancers ExN_DL cluster. k Pseudo time density plot of AP_RGC to ExN trajectory. l Immunostaining in E14.5 developing cortex. SOX2 marks apical radial glia, TBR2 intermediate progenitors and DCX marks early neurons (statistic two-sided t-test, SOX2, Control vs Mutant, ***P < 0.001, n = 9 independent embryos for each group; TBR2, Control vs Mutant, ***P < 0.001, n = 7 embryos for each group; DCX, ***P < 0.001, n = 7 independent embryos for each group. Data are presented as mean values +/− SEM). Bar = 40 μm. m Schematic representation of in utero electroporation (IUE) experiment in E13.5 embryos, created with BioRender.com. RFP immunostaining on IUE brains (P10) with magnification on the right. Left bar = 50 μm; right bar = 10 μm.