Fig. 4: Four-dimensional metabolic atlas of zebrafish development.
From: Unified mass imaging maps the lipidome of vertebrate development
a, Overview of developmental stages used for bulk LC–MS/MS and MALDI-MSI acquisitions with selected developmental stages indicated. DG, diacylglycerol; LPE, lysophosphatidylethanolamine; LPI, lysophosphatidylinositol; PI, phosphatidylinositol. b, Low-dimensional representation (UMAP) of bulk LC–MS/MS data. Points represent lipids and are color coded by stage at which concentration peaks (left) or relative changes in concentration over time (right). c, Dot plot indicating overall lipid concentration changes and absolute quantities averaged over classes (left) and specific SM species (right) for each developmental stage. Cers, ceramides; HexCers, hexosylceramides. d, Four-dimensional distributions for selected lipids for analyzed time points (sagittal and dorsal projections, schematic of orientation shown in top row with yolk outlined in yellow). Note that the precise orientation of the embryo at 8 hpf is unknown. Min, minimum. e, Quantification of spatially localized lipids across the sampled time points. Upset plot depicting total molecule counts for each time point (left, n = 1). The time points that are considered within each set are indicated by solid black circles. Stacked bar plot depicting lipid class breakdown for different sets shown in the upset plot (right). f, Stacked bar plots representing the total number (left) and proportions (right) of spatially informative molecules detected at specified time points (n = 1) stratified by lipid class. g, Visualization of the first three principal components (P.C.) over each developmental stage, sagittal (S) and dorsal views. h, Tissue clusters (left) and pseudolineages (right) across sampled time points split generally into anterior and posterior metabolic regions. AR, anterior region; PR, posterior region. i, Correlation matrices between PC species for each developmental stage sorted according to optimal sorting at 72 hpf with SPIN69. Color bar indicates the number of unsaturations for each lipid species. j, Lipid intensity trends for PC species along the anteroposterior (AP) axis for each developmental stage (left). Shaded area indicates standard deviation between biological replicates (n = 2). Varying degrees of unsaturation are indicated by colors. Heatmap of mean-centered average lipid intensity for three species over developmental time (right).
