Single cell ATAC-seq of neural crest derivatives in mouse embryos

Neural crest cells are multipotent embryonic progenitors that give rise to a large number of cell types in a vertebrate embryo, thus, sometimes being considered as a 4th germ layer. Neural crest cells originate within the dorsal neural tube at the time of its closure, delaminate and migrate to multiple destinations. The paths of fate selection and differentiation in the neural crest cells are not fully understood. The analysis of open chromatin regions at single cell level will help to clarify the genetic programs behind the development of a vagal neural crest stream. Overall design: Mouse embryos were collected at embryonic day E9.5. Transgenic embryos contained Wnt1-Cre/R26Tomato construct (therefore, Tomato-positive cells had expressed Wnt at some point in their lineage and are expected to be the derivatives of Neural crest cells). After the dissociation of a certain anatomical part of the embryo, Tomato-positive cells (neural crest derivatives) were FACS-sorted and profiled with single-cell ATAC-seq.