Extended Data Fig. 8: Multiplexed immunohistochemistry on matrix perturbations.
From: Morphodynamics of human early brain organoid development
a) Selected images show protein stainings on day 15 and 21 on organoid slices in Matrigel and no-matrix conditions, n numbers are added to c. b) UMAP embedding of multiplexed immunohistochemistry data (4i) based on cellular expression of proteins (Fig. 4d), with cells colored by treatment (Matrigel, no-matrix) and time (day 7, 15, 21). c) Spatial mapping of cell clusters in each organoid used for the combined analysis. The cell clusters are projected back to the original images from Matrigel and no-matrix conditions over the time course (day 7, 15, 21). Matrigel: day 7 n = 2, day 15 n = 3 and day 21 n = 4. No-matrix: day 7 n = 2, day 15 n = 4 and day 21 n = 3. d) UMAP embedding of multiplexed immunohistochemistry data (4i) based on the protein expression in the extracellular compartment of cells, with cells colored by treatment (Matrigel, no-matrix) and time (day 7, 15, 21). e) Spatial mapping of ECM clusters in each organoid used for the combined analysis. The ECM clusters are projected back to the original images from Matrigel and no-matrix conditions over the timecourse (day 7, 15, 21). f) Dotplot showing average expression and percentage of cells expressing selected regional marker proteins per cluster in b. g) Dotplot showing average expression and percentage of cells expressing ECM proteins per cluster in d. h) Violin plots showing the distance of each cell cluster from the organoid surface. The boxes in the violin plots show the interquartile range, with the line at the center as the median and the whiskers extending to the data range excluding outliers. i) UMAP embedding of multiplexed immunohistochemistry data (4i) based on the protein expression in the extracellular compartment of cells (shown in d, Fig. 4f), showing the distribution of cellular clusters shown in c and Fig. 4d. Right: Dotplot showing average expression and percentage of cells expressing ECM proteins in each cellular cluster. Scale, 100 micrometers in all images.
