Reduced representation bisulfite sequencing (RRBS) of cultured cells derived from Parkinson's disease patient [RRBS-seq]

High throughput sequencing of MSPI digested, size selected and bisulfite converted genomic DNA from control- and sporadic Parkinson´s disease patient derived fibroblasts (n=15), induced pluripotent stem cells (n=26) and differentiated midbrain neurons (n=10). We were able to sequence more than 400,000 CpGs at ≥5x coverage in all samples. Nonetheless, statistical analysis with RnBeads did not identify major differences on single CpG or promoter methylation level between control- and Parkinson´s disease patient derived cells in any cell type. Two-condition experiment in three cell types: Control- and Parkinson´s disease patient derived fibroblasts, induced pluripotent stem cells and differentiated midbrain neurons were compared. Fibroblast cell cultures were established from skin biopsies from six control patients and nine sporadic Parkinson´s disease patients and reprogrammed with the OSKM cocktail. Reduced representation bisulfite sequencing libraries were prepared with the NEXTflex™ Bisulfite Library Prep Kit (BIOO Scientific) and sequencing was performed on an Illumina HiSeq1000 instrument (1x50 bp). Differential expression analysis was performed comparing control- and Parkinson´s disease patient derived cells within each cell type (fibroblasts, induced pluripotent stem cells or neurons). Please note that Raw data is only available via dbGAP due to privacy concerns