Figure 5
Studying cellular composition in spheroids of HCT116 cells with MAPiT. (a) Marginal signal densities \(p(y| x)\) of indicated markers related to the distance from the surface, as obtained by MAPiT. Signal frequencies at the outermost layer and at 150 \(\mu m\) distance from the spheroid surface, as indicated by the dashed rectangles, are shown for an exemplary 11-day-old spheroid. (b) Comparison of single-cell positions in pseudotime, as obtained by Wanderlust or DPT algorithms. (c) MAPiT robustly reconstructs cell positions, irrespective of the pseudotime algorithm used. Ranges show \(50 \% \) confidence intervals of the signal intensities obtained from transforming Wanderlust and DPT pseudotime data. (d) Schematic of spheroid growth. (e) Spheroid growth follows a linear growth model. Microscopically obtained data shows spheroid radius over 15 days after seeding from \(n=23\) spheroids in three independent replicates. (f) Median profiles for Ki-67, RNA and p27, as obtained by MAPiT, were conserved throughout spheroid sizes (median of \(n=3\) spheroids, in three independent replicates). Notable deviations towards the ends of the profiles (dashed) and thus within the centre of the spheroids arise from inaccuracies due to the low number of cells available for analysis at these locations.
