Strand-specific mRNA-Seq libraries were produced as described previously18. MethylC-Seq libraries were generated by ligation of methylated sequencing adapters to fragmented genomic DNA followed by purification, sodium bisulphite conversion and 4–8 cycles of polymerase chain reaction (PCR) amplification as described previously18 with minor modifications (see Supplementary Materials). ChIP-Seq libraries were prepared following Illumina protocols with minor modifications (see Supplementary Materials). Sequencing was performed using the Illumina Genome Analyser IIx and HiSeq2000 instruments as per the manufacturer's instructions.
