Extended Data Fig. 8: Single-cell ribosome profiling in primary mouse intestinal EEC cells.

a, UMAP (n = 350 cells) generated using the RPF counts per CDS. Corresponding cell types and associated marker genes for each cluster are indicated. b, c, UMAPs illustrating the fluorescence of the mNeonGreen (b) and dTomato (c) markers from the bi-fluorescent Neurog3Chrono reporter²⁴. d, UMAP depicting the intestinal region origin of each cell. As expected, there is no enrichment of the cell types within each region. e, Scatter plots of the Neurog3Chrono fluorescence denoting the position of each cell cluster within the FACS space. As expected, progenitor cells show an increased mNeonGreen fluorescence, that changes through a double-positive population to dTomato-positive as EEC cells develop. f, Heat map showing ribosome-site-specific pausing over CAG and GAA codons. To remove any effects of the uneven distribution of RPFs along highly translated hormone genes, any gene that was more than an average of 2.5% of the RPFs per cell was removed from this analysis. g, h, UMAPs showing the CAG (g) and GAA (h) pausing. i, Heat map showing the distribution of RPF A sites along the Chgb CDS. Cells are grouped based on their CAG and GAA pausing status. The position of CAG (orange) and GAA (purple) codons within the CDS are denoted as ticks at the top, with shared prominent pausing sites for each codon indicated with inverted triangles. j, k, Scatter plots showing the fold change in gene-wise A-site frequency of occurrence between the pausing and non-pausing (normal) cells within each cluster.