Extended Data Fig. 7: Single-cell analysis and validations of control and SHH-induced organoids.
From: Spatiotemporal, optogenetic control of gene expression in organoids
a. Alluvial plot showing the relative composition of the progenitor cells clusters in control (grey) and SHH-induced organoids (blue), before and after data integration (see Methods). b. Sample identity (left), annotated cell types (middle) and SHH module score (right) from 2 replicates of control and SHH-induced organoids scRNA-seq data (UMAP). Same as Fig. 4a, but after data integration (see Methods). c. Dotplot showing % of cells expressing and log-normalized, scaled gene expression for known marker genes of pericytes. d. Representative (n = 3) immunofluorescence images for DAPI, NeonGreen (SHH tag) and PDGFRB (pericyte marker) in control and SHH-induced organoids at 12 days post-photo-stimulation. Experiment was performed in 4 replicates, 3 representative FOVs are shown. Scale bar: 10 μm. e. Representative (n = 3) immunofluorescence of DAPI, NeonGreen (SHH tag) and HB9, ISL1/2 and CHX10 in control (left) and SHH-induced organoids at 30 days post-photo-stimulation. Signal is shown separately in grey scale for each target and merged for SHH and the protein of interest in green and magenta (right). Scale bar: 100 μm.
