Fig. 5

Single-cell transcriptomic profiling of mock- and LACV-infected organoids. a t-distributed stochastic neighbor embedding (tSNE) plots of canonical correlation analysis (CCA) aligned cell transcript profiles from 3 dpi mock- and LACV-infected COs clustered according to relatedness. Seven clusters were identified for optimal data resolution according to CCA and each is indicated by a different color. Each dot within each cluster represents the transcript profile from an individual cell. b Neural progenitors, committed neurons or extracellular matrix (ECM) producing mesenchymal cell-related transcript expression are shown for each identified cluster in a. Ribosomal (house-keeping) transcript expression in each cluster is shown as a positive control for sequencing. Increasing expression of each transcript is illustrated according to the deepening shade of gray to purple to blue. The proportion of cells expressing each transcript within the cluster is indicated by the size of the dot (scales at bottom). The tSNE plot in a was split to show cell transcript profiles from the (c) mock- or (d) LACV-infected CO still arranged within the 7 clusters. The two ellipses on each plot represent the boundaries of C1. The proportion of input cell transcript profiles in each cluster (e) is shown for both the mock (red) and LACV (blue) CO. The arrow in e denotes the decrease observed in C1 with LACV infection