Abstract
Whole genome bisulfite sequencing (WGBS) analysis of DNA methylation uses massively parallel next generation sequencing technology to characterize global epigenetic patterns and fluctuations throughout a range of tissue samples. Development of the vertebrate retina is thought to involve extensive epigenetic reprogramming during embryogenesis. The chicken embryo (Gallus gallus) is a classic model system for studying developmental biology and retinogenesis, however, there are currently no publicly available data sets describing the developing chicken retinal methylome. Here we used Illumina WGBS analysis to characterize genome-wide patterns of DNA methylation in the developing chicken retina as well as cornea and brain in an effort to further our understanding of retina-specific epigenetic regulation. These data will be valuable to the vision research community for correlating global changes in DNA methylation to differential gene expression between ocular and neural tissues during critical developmental time points of retinogenesis in the chicken retina.
Highlights
Background & SummaryAdvances in generation sequencing (NGS) technology have substantially increased the number of species with completed high quality genome assemblies
The epigenetics community has benefited greatly from next generation sequencing (NGS) experiments mapping genome-wide profiles of specific histone tail and genomic DNA modifications. Consortium projects such as the ENCODE Project and the Roadmap Epigenomics Project have deepened our understanding of numerous specialized human cell and tissue types and have paved the way for similar experiments in model systems of human development and disease[2,3]
High quality libraries, having a distribution of DNA fragments centered around 300 bps were used for sequencing analysis using the Illumina HiSeq 2,500 sequencing platform yielding 32.8–60.2 million 125 bp paired end sequence reads per sample (Fig. 3b)
Summary
Background & SummaryAdvances in generation sequencing (NGS) technology have substantially increased the number of species with completed high quality genome assemblies. There are no publicly available data sets characterizing epigenetic modifications of the genome in the developing chicken retina. The focus of this project is to characterize global patterns of DNA methylation, an epigenetic modifier of vertebrate genomes, in the developing chicken retina as well as in non-retinal tissues using whole genome bisulfite sequencing (WGBS) NGS technology.
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