Extended Data Fig. 7: Analysis of Tal1^−/− chimaeras.

a, Left, representative chimaera embryo obtained at E8.5 (left: brightfield; right: tdTomato fluorescence; scale bar, 0.25 mm). Right, flow cytometry plot with tdTomato fluorescence distribution and sorting gates. b, Histograms showing the UMI counts for the tdTomato construct in both tdTomato⁻ and tdTomato⁺ fractions in the Tal1^−/− into wild-type experiment (see Methods). c, d, Control mapping results of an E8.0 biological replicate that was removed and mapped back to the atlas. c, Heat map showing the fraction of cells of each labelled cell type that mapped to each cell type in the reference atlas. Numbers above columns indicate the number of cells in each category. Of these cells, 89.4% correctly mapped to their annotated cell type. d, Histogram showing the fraction of cells from the E8.0 biological replicate that mapped to each time point in the reference: 29.2% of cells mapped to the correct time point, and 83.1% of cells mapped within one time point (that is, 6 hours) in either direction. e, Scatter plot comparing the percentage of tdTomato⁺ cells against tdTomato⁻ for each cell type in both Tal1^−/− into wild-type (WT; left) and wild-type into wild-type (right) experiments. Black arrowheads indicate extra-embryonic tissues; white arrowheads indicate haematopoietic tissues. f, Force-directed graph of blood-related lineages from the atlas (Fig. 3), coloured by Tal1 expression levels. Darker colouring shows higher expression. g, Flow cytometry analysis of E8.5 Tal1^−/− into wild-type chimaeras, showing the complete depletion of the haematopoietic markers CD41 and CD45 (top panels), as well as of the CD71⁺ Ter119⁺ erythroid fraction (bottom panels) in Tal1^−/− tdTomato⁺ cells (right panels). h, UMAP plots of wild-type into wild-type experiment, showing balanced contributions to all embryonic lineages. i, Flow cytometry analysis of wild-type into wild-type chimaeras, showing balanced contributions to the haematopoietic lineage from both tdTomato⁺ and tdTomato⁻ cells at E9.5 (representative of 2 individual embryos).