Extended Data Fig. 2: Genotoxic pks⁺ E. coli induce SBS-pks and ID-pks mutational signatures after long-term co-culture with wild-type intestinal organoids.

a, Ninety-six-trinucleotide mutational spectra of SBSs in each of the three individual clones sequenced per condition. Top three, dye; middle three, pksΔclbQ E. coli; bottom three, pks⁺ E. coli. b, Total 96-trinucleotide mutational spectra of organoids injected with pks⁺ E. coli or pksΔclbQ E. coli from which SBSs in dye-injected organoids have been subtracted. c, Heatmap depicting cosine similarity between 96-trinucleotide mutational profiles of organoids injected with dye, pks⁺ E. coli or pksΔclbQ E. coli. d, Indel mutational spectra plots from each of the three individual clones sequenced per condition. Top three, dye; middle three, pksΔclbQ E. coli; bottom three, pks⁺ E. coli. e, Total indel mutational spectra of organoids injected with pks⁺ E. coli and pksΔclbQ E. coli from which indels in dye-injected organoids have been subtracted. f, Heatmap depicting cosine similarity between indel mutational profiles of organoids injected with dye, pks⁺ E. coli or pksΔclbQ E. coli.