Fig. 1
scRNA-seq of Dnmt3a-/-, Dnmt3b-/- and Dnmt1-/- mutant embryos during mouse early organogenesis. a Table with the numbers of E8.5 embryos and cells of each genotype analysed in this study. KO refers to the mouse models used in this study, CRISPR indicates published data which was generated using zygotic CRISPR-Cas9 injections [23]. b Dimensionality reduction (UMAP) of the wildtype reference dataset used for assigning cell types in this study. Cells are coloured by cell type as in the original publication [25]. c RNA expression of Dnmt1, Dnmt3a and Dnmt3b for each cell type in the reference atlas (quantified at the pseudobulk level). d Mapping of the KO cells to the reference atlas using the matching nearest neighbours (MNN) algorithm [26]. Each plot shows the UMAP of the reference atlas as in b, but cells are coloured by whether they are a nearest neighbour to a cell in our wildtype (blue) or mutant (red) embryos. e Box plots display the log2 difference in cell type proportions between WT and KO E8.5 embryos. Each point represents a comparison of cell type proportions between a KO embryo and the average proportions in WT embryos. f Polar bar plots display the number of differentially expressed genes for each KO and cell type. In the top panel bar plots are coloured by cell type identity and in the bottom panel, they are coloured by whether genes are up or downregulated. g Bar plots display the number of downregulated (top) or upregulated (bottom) genes in the Dnmt1-/- mutants. Shown are only genes which are markers for embryonic versus extra-embryonic (ExE) tissues. h Bar plots display the number of DE genes in the Dnmt1-/- mutants for each cell type. Genes are grouped and coloured by the cell type that they mark in the reference atlas. Note that a gene might be a marker of multiple cell types, thus the y-axis is not directly comparable to f