Single-cell SLAM-seq profiling of normal and tumor organoids

Differentiation trajectories and cellular plasticity in CRC were assessed using single-cell SLAM seq on patient-derived organoids. Organoids were perturbed in MAPK and WNT signalling. Patent-derived organoids derived from 6 CRC tumors and one normal colon were grown under different conditions (control/DMSO, different small molecule inhibitors, medium with EGF and WNT and with EGF), incubated with 4SU for 2h before harvesting, disagregated into single cell suspensions using TrypLE, and fixed with metanol. Samples were then incubated O/N with 10mM iodoacetamide for alkalyation. Samples were subsequently barcoded using BD sample TAG antibodies, and pooled (all perturbation of 2 organoids per library for inhibitor treatment, one perturbation of three organoids for growth condition), and subjected to droplet based scRNA-seq analysis (Chromium controller, 10x genomics) ---------------------------------------------------- Authors state "Unfortunately, we can currently not supply raw data files (sequencing) as these are patient sequences for which the current data access policies in our institution only allow submission of count data. "