Unlike other methods to assess methylation, whole-genome shotgun bisulfite sequencing is used to generate quantitative genome-wide methylation profiles at single-nucleotide resolution. As described in this unit, this method allows for the quantitative measurement of methylation at each cytosine base by treatment of genomic DNA with sodium bisulfite followed by sequencing and alignment of the reads to a reference genome. Curr. Protoc. Mol. Biol. 99:21.23.1-21.23.28. © 2012 by John Wiley & Sons, Inc.