Extended data figure 7. In vitro mutations of murine small bowel organoids.

a, Mutational spectra of small bowel in vitro mutations. Small bowel organoids were isolated and expanded from a third mouse (mouse 3). After 56 days in culture single Lgr5+ stem cells were isolated from the parental organoid cultures and expanded to obtain sufficient quantities of DNA for sequencing. Both subclones exhibit a different mutational spectrum, compared to parental cultures, characterised by a decrease in C>A and an increase in T>G mutations. b, Mutation burden of in vitro mutations. The absolute number of mutations unique to each organoid is shown. Mutations that were found in more than one organoid were excluded from the count. In vitro the small bowel organoid cells, subclone A and B, acquired 507 and 739 mutations, respectively. c, Non-negative matrix factorisation extracted a distinct mutational signature from the mutations of the subclones termed in vitro signature, which is characterised by an excess of T>X mutations at XpTpT trinucleotides. Vertical axis: contribution of each mutation-type at each context to the overall mutation burden. Horizontal axis: six classes of base substitutions including the bases immediately 5′ and 3′ to the mutation.