Single-read MethylC-Seq and RNA-Seq libraries were sequenced for up to 85 cycles using the Illumina Genome Analyser IIx. Paired-read MethylC-Seq libraries were sequenced for up to 75 cycles for each read using the Illumina HiSeq2000. Image analysis and base calling were performed with the standard Illumina pipeline, performing automated matrix and phasing calculations on a control library that was sequenced in a single lane of each flowcell.
