Additional file 3: of Harnessing single-cell genomics to improve the physiological fidelity of organoid-derived cell types

Figure S1. Image analysis of cell clusters and flow cytometry. A Bright-field microscopy after 6 days of ENR + CD culture shows annular morphology and darkened lumen of cell clusters consistent with presence of granule-rich cells. B Percentage of total cells that are LYZ+ and DEFA+ following 6 days of ENR, ENR + CV, and ENR + CD culture (from cell counting of whole clusters) (n = 3 minimum biological replicates, one-way ANOVA with multiple comparison test versus ENR, **** adj. p < 0.0001). C Collapsed z-stack of whole cluster with individual cells highlighted (1–3) following 6 days of ENR + CD, stained for LYZ and DEFA and counterstained with DAPI and for actin (phalloidin). (1–3) Normalized mean-area intensity versus z-axis depth profiles of representative individual LYZ+/DEFA+ co-staining cells. D Representative flow cytometry of ENR and ENR + CD at 6 days with distinct populations of CD24+ and LYZ+ cells indicative of phenotypic PCs. E Representative gating for flow cytometry, including removal of doublets and non-viable cells in final gating. F Percentage of viable cells (membrane impermeable) over time of ENR versus ENR + CD culture. (PDF 3217 kb