Characterization of the DNA methylome in embryonic retina, retinal progenitors, and RGCs

We investigated the dynamics of DNA methylation during differentiation of retinal progenitor cells (RPCs) into retinal neurons using the whole-genome bisulfite sequencing (WGBS) approach Overall design: To study DNA methylation, the WGBS libraries were prepared using DNA from embryonic-day (E) 11.5 and 12.5 retinas, Notch1+ cells (RPCs) isolated from postnatal-day (P) 0 and 3 retinas, and retinal ganglion cells (RGCs) isolated from P14 retinas. The WGBS libraries were sequenced and bisulfite sequence reads were aligned using the Bismark software package. The global methylation level in studied samples was measured and the percentages of methylation of CpG, CHG, and CHH contexts (where H is A, C or T) were identified.