Genomic DNA was purified from RPE samples using the DNeasy Blood & Tissue Kit (QIAGEN #69504). DNA concentration of the samples was measured using the Qubit® dsDNA BR Assay Kit (Thermo Fisher Scientific). DNA quality of the samples was assessed with the Fragment AnalyzerTM and the DNF-487 Standard Sensitivity genomic DNA Analysis Kit (Advanced Analytical).  Genomic DNA was sheared using Bioruptor® Pico sonication device (Diagenode Cat# B01060001). 1μl of this sample was used to assess the size of the DNA fragments obtained by High Sensitivity DNA chip for 2100 Bioanalyzer (Agilent). DNA concentration of the sample was measured after shearing using the Qubit® dsDNA BR Assay Kit (Thermo Fisher Scientific). WGBS libraries were prepared using the Whole Genome Bisulfite Sequencing (RRBS) Kit (Diagenode Cat# C02030034) following the kit manual. 1μg of sheared genomic DNA was used to start library preparation for each sample. Following library preparation, samples were bisulfite converted and amplified by PCR using 9 amplification cycles. Final PCR clean-up was performed twice using a 1.1x beads:sample ratio of Agencourt® AMPure® XP (Beckman Coulter). DNA concentration of the libraries was measured using the Qubit® dsDNA HS Assay Kit (Thermo Fisher Scientific). The library profiles were checked using the High Sensitivity DNA chip for 2100 Bioanalyzer (Agilent). WGBS libraries were sequenced on a HiSeq3000 (Illumina) using 150 bp Paired-end sequencing (PE150).
GEO Accession
GSM3405394