The MeDIP-seq approach, i.e. the coupling of MeDIP with next generation, short-read sequencing technologies such as 454 pyrosequencing or Illumina (Solexa), was first described by Down et al. in 2008.  The high-throughput sequencing of the methylated DNA fragments produces a large number of short reads (36-50bp or 400 bp, depending on the technology).  The short reads are aligned to a reference genome using alignment software such as Mapping and Assembly with Quality ([http://maq.sf.net Maq]), which uses a Bayesian approach, along with base and mapping qualities to model error probabilities for the alignments.  The reads can then be extended to represent the ~400 to 700 bp fragments from the sonication step.  The coverage of these extended reads can be used to estimate the methylation level of the region.  A genome browser such as [http://www.ensembl.org Ensembl] can also be used to visualize the data.
Validation of the approach to assess quality and accuracy of the data can be done with quantitative PCR.  This is done by comparing a sequence from the MeDIP sample against an unmethylated control sequence.  The samples are then run on a gel and the band intensities are compared.  The relative intensity serves as the guide for finding enrichment.  The results can also be compared with MeDIP-chip results to help determine coverage needed.