ATAC-seq method applied to embryonic germ cells and neural stem cells from mouse: Practical tips and modifications

The chromatin state affects the level of transcription at the initial stage of gene expression. Therefore, it is important to determine chromatin accessibility in regions of the genome that contain regulatory elements. To this end, several methods have been developed. The ATAC-seq method outperforms the other methods in profiling chromatin accessibility for every single cell, and standardized library preparation kits are now commercially available. In this chapter, we describe the ATAC-seq method that we have applied to mouse embryonic germ cells as well as to mouse neural stem cells, which are relatively rare. We also developed new method to examine the changes in global accessibility during their developmental process using spike-in normalization with fly cells.