To test more directly whether neurons in brains from patients with RTT have the same phenotype we observed in vitro, we first sorted nuclei using the same strategy as for RNA sequencing, and then stained for pH2AX, an established marker of DNA breaks, known to be elevated in MECP2-null neurons in vitro (Nan et al., 1998b; Young et al., 2005). Here, MECP2 is linked to Rett syndrome.