Extended Data Fig. 1. Co-culture with genotoxic pks⁺ E. coli induces DNA interstrand crosslinks in healthy human intestinal organoids.

a, Representative images (out of n = 5 organoids per group) of DNA interstrand crosslink formation after 1d of co-culture, measured by FANCD2 immunofluorescence (green). Nuclei were stained with DAPI (blue). Yellow boxes represent inset area. Scale bars represent 50 μm (large image) and 10 μm (inset). Experiment was repeated independently twice with similar results. b, Gating strategy to select epithelial cells (left) and to quantify viable cells (right). c, Viability of intestinal organoid cells after 1, 3 and 5 days of co-culture (n = 3 technical replicates) (bacteria eliminated after 3 days of co-culture). Points are independent replicates, center line indicates mean, error bars represent SD.