Fig. 2: Single-cell analysis of intestinal organoids and gastruloids.
a, Intestinal organoid expressing hGem-mVenus and hCdt1-mCherry (left) stained for Lysozyme (Lys) and DLL1 (middle). If not indicated differently. b, MIPs of stills of an intestinal organoid expressing hCdt1-mCherry. Overlaid are the tracks of back-tracked cells color coded over time. The dashed line corresponds to the z projections shown in c. c, The z projections of the intestinal organoid shown in b of detection 1, detection 2 and the fused data. Overlaid are tracks from back-tracked cells showing temporal progression. d, Zoom-ins of intestinal crypts shown in a. Asterisks indicate triple positive cells for hCdt1+/Dll1+/Lysozyme+. e–g, Quantification of hCdt1, Lysozyme and Dll1 intensities over time for individual cells at indicated final positions: hCdt1, Lys, Dll1 positive crypt cells (e); hCdt1-positive villus cells (f) and hCdt1-positive crypt cells (g). h, The z planes of gastruloids expressing Lck-GFP at three time points (42 h pre-Wnt, 66 h peri-Wnt and 90 h post-Wnt). i, Individual cells partly highlighted in h from gastruloids 42, 66 and 90 h after cell seeding. Arrows indicate cell protrusions. j, Representative 3D segmentation (Cellpose) of Lck-GFP positive cells of gastruloid 42 h after cells seeding. k, Comparison of the major/minor axis ratio 42, 66 and 90 h after seeding, showing the median (values depicted in figure) and the first and third quartile. l, MIPs of a gastruloid overlaid with the tracked cells over time. m, Violin plots of cell velocity (µm h−1) grouped by observation windows, showing the median (values depicted in figure) and the first and third quartile. n, Cell tracks of individual cells of gastruloids imaged for 5.5 h mounted at 42, 66 and 90 h postseeding centered at the origin of the coordinate system, color coded for the temporal progression. o, Track length per cell for the individual imaging windows of Lck-GFP gastruloids. Violin plots of cell velocity (µm h−1) grouped by observation windows, showing the median (values shown in figure) and the first and third quartile. p, The m.s.d. averaged over all cells for the individual imaging windows of Lck-GFP chimera gastruloids. Scale bars, 50 µm, a–d,h,j,l; 20 µm (i).
