Journal: Scientific Reports

Article Title: Reconstructing temporal and spatial dynamics from single-cell pseudotime using prior knowledge of real scale cell densities

doi: 10.1038/s41598-020-60400-z

Figure Lengend Snippet: MAPiT derived Ki-67 distribution in an 11-day-old HCT116 cell spheroid. ( a ) Representative spheroid cross-section stained for Ki-67. Rectangles display cross sectional signal intensities for comparison with MAPiT. ( b ) Transversal quantified Ki-67 intensities in spheroid sections (rectangles in ( a ), \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$n=9$$\end{document} n = 9 ). ( c ) MAPiT employs cell density in radial-symmetric spheroids with radius \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$r$$\end{document} r , of which the derivation is contained in detail in the Materials and Methods. ( d ) Marginal Ki-67 signal density obtained by MAPiT from flow cytometric data (blue) closely match Ki-67 intensity profiles determined microscopically in spheroid cross-sections.

Article Snippet: The human colon carcinoma cell line HCT116 was obtained from the Banca Biologica e Cell Factory of the IRCCS Azienda Ospedaliera Universitaria San Martino in Genoa (ICLC HTL95025).

Techniques: Derivative Assay, Staining, Comparison

Journal: Scientific Reports

Article Title: Reconstructing temporal and spatial dynamics from single-cell pseudotime using prior knowledge of real scale cell densities

doi: 10.1038/s41598-020-60400-z

Figure Lengend Snippet: Studying cellular composition in spheroids of HCT116 cells with MAPiT. ( a ) Marginal signal densities \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$p(y| x)$$\end{document} 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 \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\mu m$$\end{document} μ 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 \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$50 \% $$\end{document} 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 \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$n=23$$\end{document} 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 \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$n=3$$\end{document} 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.

Article Snippet: The human colon carcinoma cell line HCT116 was obtained from the Banca Biologica e Cell Factory of the IRCCS Azienda Ospedaliera Universitaria San Martino in Genoa (ICLC HTL95025).

Techniques: Comparison