Additional file 1.

Figure S1 - schematic view of the analysis workflow. (a) Methylated DNA immunoprecipitation (MeDIP) was conducted to isolate methylated DNA fragments across four end-stage cardiomyopathic (EsCM 1 to 4) and four normal healthy control (CTRL A to D) hearts as listed in Additional file 2 and as published [10]. (b) MeDIP samples were sequenced using an Illumina genome analyzer (GIIx). (a) Short single-end reads from high-throughput sequencing were aligned against the human reference genome assembly (Hg18) and repeats database (Repbase). (d) Number of unique reads was normalized with reference to the respective total number of reads generated for each sample, and used as a proxy for the level of methylation for all repeat sequences. (e) Differential methylation between each of EsCM and CTRL samples was compared using Fisher's exact test statistic as well as unpaired Welch's t-test. (f) Differentially methylated repeat elements (DMReps) were selected for downstream analysis.

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Haider et al. Genome Biology 2012 13:R90   doi:10.1186/gb-2012-13-10-r90