Fig. 3

scRNA-seq of Tet-TKO mutant embryos during mouse early organogenesis reveals that TET enzymes are required for the specification of primitive erythrocytes. a Schematic summarising the chimaera assay. Fluorescently labelled Tet-TKO ESCs are injected into wild type blastocysts, transferred into pseudopregnant hosts then collected at E7.5 or E8.5. FACS is used to isolate labelled KO cells (red) and non-labelled WT host cells (blue) which are processed and sequenced using scRNA-seq. b Mapping of the KO cells to the reference atlas using the matching nearest neighbours (MNN) algorithm [26]. UMAP plot of wildtype reference atlas [25] with cells coloured whether they are a nearest neighbour to a WT host (red) or Tet-TKO (blue) cell. c Box plots display the log2 difference in cell type proportions between WT and Tet-TKO E8.5 embryos. Each point represents a comparison of proportions between a Tet-TKO sample and the corresponding proportions in the matching WT host embryo. d Polar bar plots display the number of differentially expressed genes for each KO and cell type. In the right panel bar plots are coloured by cell type identity and in the left panel, they are coloured by whether genes are up or downregulated. e Bar plots display the number of DE genes 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 values in the y-axis are not directly comparable to d. f RNA expression levels of the haemoglobin X alpha-like embryonic chain gene (Hba-x) in WT to Tet-TKO cells. Shown are different cell types grouped from the haematoendothelial trajectory