Fig. 3: DiLiCre2.0 small intestine organoids recombine ex vivo with high efficiency.

a Schematic representation of the design to generate the DiLiCre2.0 mice and the breeding with Rosa26-Confetti mice. Recombination outputs of the Confetti cassette are annotated. The Confetti cassette contains a LoxP-flanked NeoR-cassette serving as transcriptional roadblock (NeoS) which prevents any fluorophore of the array to be expressed unless Cre becomes active. b Graphical scheme of the FACS experiment setup for the evaluation of the genetic recombination in small intestine derived organoids from the DiLiCre2.0;R26-Confetti mice. Quantification of FACS data (left graph) and dynamic range (right graph) derived from the experiments in panel b (see representative flow cytometry plots in Supplementary Fig. 6a). Data represents mean ± SD from n = 3 biologically independent experiments. c The upper image shows the experimental timeline. In brief, organoids were treated with doxycycline (50 nM) and/or exposed to whole field illumination (WFI, 405 nm LED light 0.5 mW/mm² 30 s pulse) or z-plane confocal illumination (imaged with 1.87 mW laser output power for 30 s). The lower panel consist of representative maximum projection images at different time points. Blue, green, yellow, and red color code represents mCFP, nGFP, cYFP, and cRFP, respectively. This experiment was independently repeated n = 3 times with similar results. d Schematic summary of the workflow to quantify the light-mediated recombination in small intestine organoids. Plots represent the CFP/GFP/YFP or RFP total intensities divided by the organoid size. Data represents the mean ± SD from n = 3 biologically independent experiments. Entire curves were compared statistically and the P values were determined by permutation test adapted from Elso et al. (2004). Source data are provided as a Source Data file.