Extended Data Fig. 5. Multiple retinal trajectories are diminished in Ttc21b KO mice.

a, The log2 transformed ratio of the cell proportions of each sub-trajectory, comparing Ttc21b KO and C57BL/6 wildtype embryos, are shown. Although reductions in the retina epithelial and lens trajectories were excluded from the regression analysis due to their low numbers, they were, together with the retinal neuron trajectory, the most extreme in magnitude. b, 3D UMAP visualisation of the hepatocyte major trajectory, highlighting cells from either the Ttc21b KO (left), C57BL/6 wildtype (middle), or other mutants on the C57BL/6 background (right). The three plots were randomly downsampled to the same number of cells (n = 264 cells) c, 3D UMAP visualisation of the epithelial major trajectory, highlighting cells from either the Ttc21b KO (left), C57BL/6 wildtype (middle), or other mutants on the C57BL/6 background (right). The three plots were randomly downsampled to the same number of cells (n = 937 cells). d, UMAP visualisation of co-embedded cells of limb mesenchyme trajectory from the ZRS limb enhancer KO and FVB wildtype. The same UMAP is shown eight times, highlighting cells from either ZRS limb enhancer KO (top row) or FVB wildtype (bottom row), and breaking out the four individual replicates for each strain. e, UMAP visualisation of co-embedded cells of various sub-trajectories from the ZRS limb enhancer KO and FVB wildtype. The same UMAP is shown twice for each, highlighting cells from either FVB wildtype (left) or ZRS limb enhancer KO (right). These are the seven sub-trajectories in which, in addition to limb mesenchyme, we detected nominally significant differences in cell type proportions for the ZRS limb enhancer KO.