Single-cell sequencing of muose thymic epithelial cell organoids

Mouse thymic epithelial cell organoids, cultured in (1) expansion medium, (2) differentiation medium, or (3) differentiation medium with Rank ligand and retinoic acid (DM+RR), were FACS sorted into plates to follow the SORT-seq protocol (Muraro et al., 2016). Mouse thymic epithelial cell organoids cultured in (1) expansion medium or (2) differentiation medium were collected and DAPI-negative viable cells were FACS-sorted and analyzed using scRNA-seq. Mouse thymic epithelial cell oganoid, which is CRISPR knock-in line to have Aire-P2A-tdTomato and Foxn1-P2A-Clover, cultured in (DM+RR) were analyzed by using scRNA-seq. In brief, DAPI-negative & tdTomato-positive cells or DAPI-negative & Clover-positive cells, or DAPI-negative without Clover and tdTomato werer FACS sorted for analysis.