RNA-Seq comparative analysis of human neuroblastoma cells before and after their confrontation to the embryonic microenvironment

We set up an innovative model for neuroblastoma that consists in using the chick embryo to place human neuroblastoma cells back to their original environment: the trunk neural crest. In this context, human neuroblastoma cells migrate towards sympathetic derivatives and form proliferative tumor masses. To assess the impact of the embryonic microenvironment on neuroblastoma cells gene program, we performed an RNASeq comparative analysis of neuroblastoma naïve cells and tumor masses settled in sympathetic derivatives. Overall design: We performed independent graft experiments and for each, we collected neuroblastoma naïve cells (before the graft) and tumor masses formed in sympathetic ganglia (50 hours after the graft). 12-13 tumor masses formed in independent chick embryos were microdissected and pooled for each experiment to achieve enough RNA material.