Extended Data Fig. 9: Comparative analysis of DNA methylation and RNA expression between E11 and E13 mouse embryos.
From: Spatial joint profiling of DNA methylome and transcriptome in tissues
a, Spatial distribution and UMAP visualization of clusters identified from spatial DNA methylation data (left), spatial RNA transcription data (middle), and integrated DNA and RNA data using WNN analysis (right) for the E13 embryo. Each color represents a different cluster, illustrating the spatial distribution of methylation patterns, gene expression profiles, and the integrated data across different regions such as the forebrain, midbrain, hindbrain or spinal cord, heart, and face, nose and jaw region. Scale bars, 500 µm. b, c, Comparative analysis of RNA expression (b) and DNA methylation levels (c) for upregulated genes in E13 heart region, indicating significant changes in methylation and gene expression patterns during embryonic development with two-sided Wilcoxon test. d, Heatmaps comparing global RNA expression (left) and DNA methylation levels (right) in brain and spinal cord regions between E11 and E13 embryos. e, GO enrichment analysis from one-sided hypergeometric test for biological processes related to demethylated and upregulated genes in the heart region of E13 embryo. The size of the dots indicates the count of genes associated with each term, and the color represents the adjusted p-value (p.adjust).
