Reddot1 far red nuclear stain

After time-lapse imaging, organoids were fixed with 4% formaldehyde (Sigma) at room temperature for 30 min. Next, they were permeabilized with 0.2% Triton-X-100 (Sigma) for 1 hr at 4°C and blocked with 5% skim milk in Tris-Buffered Saline (TBS) at room temperature for 1 hr. Subsequently, organoids were incubated in blocking buffer containing primary antibody (rabbit anti-lysozyme 1:800, Dako #A0099) overnight at 4°C and then incubated with secondary antibody (anti-rabbit conjugated to Alexa Fluor405 1:1,000, Abcam #ab175649) at room temperature for 1 hr. Afterward, they were incubated with wheat germ agglutinin (WGA) conjugated to CF488 A (5 μg/ml Biotium) at room temperature for 2 hr, followed by incubation with RedDot1 Far-Red Nuclear Stain (1:200, Biotium) at room temperature for 20 min. Finally, organoids were overlaid with mounting medium (Electron Microscopy Sciences). The procedure was performed in the same imaging chambers used for time-lapse imaging in order to maintain organoids in the same position. Imaging was performed with the same microscope as previously described. Note that WGA stains both Paneth and Goblet cells, but the lysozyme staining allowed the unequivocal distinction between them.

The primary antibodies used in this study are as follows: rabbit anti-Lyz (1:800; Dako, #A0099), rabbit anti-Olfm4 (1:500; Cell Signaling Technology, #39141), recombinant rabbit anti-aldolase B + aldolase C (1:300; Abcam, #ab75751), mouse anti-human KRT20 (1:500; Dako, #M701929-2), mouse anti–Chr-A (1:50; Santa Cruz Biotechnology, #sc-393941), rat anti–E-cadherin (1:400; Santa Cruz Biotechnology, #sc-59778), CD24 Monoclonal Antibody (1:200; Thermo Fisher Scientific, #17-0242-80), and mouse anti-Ki67 (1:200; BD Biosciences, 550609). The secondary antibodies used in this study are as follows: Goat Anti-Rabbit IgG H&L (Alexa Fluor 405) preadsorbed (1:1000; Abcam, #ab175654), Goat Anti-Rat IgG H&L (Alexa Fluor 555) preadsorbed (1:1000; Abcam, #ab150166), Donkey Anti-Mouse IgG H&L (Alexa Fluor 647) (1:500; Thermo Fisher Scientific, #A31571), and Donkey Anti-Rabbit IgG H&L (Alexa Fluor 405) preadsorbed (1:1000; Abcam, #ab175649). The dyes used in this study are as follows: WGA conjugated to CF488A (5 μg/ml; Biotium), RedDot1 Far-Red Nuclear stain (1:200; Biotium), and SYTOX Orange Nucleic Acid Stain (1:5000; Thermo Fisher Scientific, #S11368). The order of staining, optimized to ensure good staining quality for all cell types, was based on the staining quality and stripping difficulty of each antibody (fig. S1G).