Extended Data Figure 2: Real-time lineage tracing of individual clones.

a, Expression of a Confetti colour was induced in Lgr5⁺ CBC cells, and their progeny was followed over time. Two examples of Confetti-labelled Lgr5⁺ CBC cells expanding over time are shown to illustrate clonal competition at indicated times. The top images show the continuous expansion of a YFP-expressing Lgr5⁺ CBC cell (yellow line) in the central region of the crypt. The bottom images show the size of a clone derived from an RFP-expressing Lgr5⁺ CBC cell in the central region of the crypt, which first increases and then declines (red line). The Confetti-labelled cells are outlined by a white dashed line and the crypts by a grey dashed line. Scale bars, 20 µm. Right, graph shows the increase in the number of YFP- or RFP-expressing Lgr5⁺ CBC cells in the entire stem-cell compartment of the crypts shown in the images on the left (yellow and red line, respectively). b, A total of 80 crypts were imaged in four mice. The total clone size (border and central) of Confetti⁺ cells present in the stem-cell niche independent of Lgr5 expression (row 0 to +4, which translates to z0 to z13 of the z-stack) was analysed at the indicated times (n = 4 mice) for all 80 lineages. The first time point translates to several days after induction. Every graph represents one crypt.