title:    Illumina sequencing of H9 AFP- Methyl-seq library:  HpaII genomic fragments   
design:      H9 alpha-fetoprotein (AFP) negative hESC-derived cells were generated by growing H9 hESCs in suspension to create H9 embryoid bodies, plating the embryoid bodies with FgF, and FACS sorting by using green fluorescent protein (GFP) reporter driven from the AFP promoter.  Genomic DNA was extracted from non-expressing AFP- cells and digested with HpaII.  Fragments were made into Illumina sequencing libraries by addition of Illumina linkers to repaired ends, PCR amplification, gel extration of fragments ~30-260bp (excluding linkers), and a second PCR amplification.  Purified DNA was used for cluster generation and sequencing using the Illumina 1G Genome Analyzer.     