pMEF 1 hMeDIP
Hydroxy MeDIP enrichment
Genomic DNA was prepared using the Qiagen AllPrep DNA/RNA mini kit.     After sonication of gDNA the ends of the DNA fragments were repaired     and paired-end sequencing specific adaptors (Illumina) were ligated using either a Paired-     End DNA Sample Preparation Kit (Illumina) or NEBNext DNA Sample Prep Reagent     Set 1 (NEB). Following adaptor ligation, DNA was immunoprecipitated and purified.     Fragments were amplified with 12-18 cycles using adaptor specific primers (Illumina);     fragments ranging between 300-500 bp in size were gel purified prior to cluster     generation and sequencing. Sequencing was done on an Illumina Genome Analyzer     GAIIX using Cluster Generation v2 and 4 chemistries as well as Sequencing by Synthesis     Kits v3 and v4. Data collection was performed using Sequencing Control Software v2.5     and 2.6. Real-time Analysis (RTA) 1.5-1.8 were used for base calling. Genomic mapping     of short reads was performed using the sequence_pair mode of ELAND in the Illumina     CASSAVA pipeline v1.5-1.8.