Extended Data Fig. 4: Comparison between hTLS and an axioloid dataset.
From: Modelling co-development between the somites and neural tube in human trunk-like structures
(a) UMAP projection of an axioloid dataset1, with clusters annotated according to published labels. (b) Projection of axioloid single cells onto the hTLS UMAP, coloured by label transfer from hTLS cluster identity. Note that the somitic lineages are well populated by axioloid cells, while the neural identies are mostly absent. (c) Projected cell coloured by prediction score as a measure of confidence. (d) Correlation in gene expression between timepoints in the axioloid and hTLS datasets, by cell cluster. (e) Label transfer of axioloid cells onto an embryonic dataset2 showing maximal number of cells at the CS13-14 stage. (f) Comparison between axioloid somitic mesoderm (SM) and hTLS somite clusters. Cells within the overlapping region were taken for downstream processing including differential gene expression analysis. (g) MA plot for differentially expressed genes bewteen the axioloid and hTLS somitic clusters. Some significantly different genes of interest are annotated. (h–m) Analysis of alternative somite- and neural tube-containing in vitro models compared to hTLS data shown here. (h–j) Single cell data from Hamazaki and colleagues3, or (k–m) Yaman and colleagues4, was plotted by UMAP using the original annotations (h, k), and then projected onto the hTLS dataset for label transfer (i, l). Additionally, the data was compared by Spearmans Correlation to the hTLS populations (j, m). IM, Intermediate mesoderm; EC, Endothelial Cells; SM, Somitic mesoderm; PSM, Presomitic mesoderm; aPSM, anterior PSM; DF, Determination Front; NMPs, Neuromesodermal progenitors; NP, neural progenitor; MG, Matrigel; RAL, Retinal; PNT, Posterior Neural Tube; CS, Carnegie Stage.
