To map chimera cells onto their appropriate positions on the atlas manifold, they were mapped onto it using a strategy similar to that used in Batch correction (above). Individual samples (i.e. one 10X channel) of the E8.5 chimera datasets were mapped onto the corrected atlas using fastMNN, using coordinates from the PC subspace. This operation was repeated for each chimera sample, retaining the mapped coordinate values for each cell. Performing this operation in parallel across samples prevents any mapped chimera cells affecting the future mapping of other samples. For the spinal cord to head mesoderm ordering, mapping was performed only using cells from the relevant cell types. DPT values (i.e., ordering positions) were inferred for chimera cells by considering the mean DPT value for the 5 nearest atlas cells in the PC space, after performing the per-sample mapping. This value of DPT is, effectively, the position of a chimera cell along the atlas backbone. For mapping chimera cells to somite trajectories through the atlas, chimera cells were mapped to the whole atlas (excluding cells from the “mixed gastrulation” atlas time-point, and with the subsampling described above), as above for cell type labelling. As for the previous approach, chimera cells were considered a part of a trajectory if the most common trajectory state of their 10 nearest neighbours was one of the somite trajectories. For differential gene expression analyses, see “quantification and statistical analysis” section below.

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