Overview of the experimental procedure of DNA sample preparation for Illumina Sequencing. A population of wild-type Saccharomyces cerevisiae was spheroplasted by zymolase. For nucleosomal DNA sample (left), proteins were cross-linked to their binding sites in vivo with formaldehyde (bold green) and chromatin was extracted and fragmented with MNase. For naked DNA samples (right), proteins and RNA were removed. Naked DNA was extracted and fragmented either by MNase or Bioruptor system (sonication). All the obtained fragments were sequenced on the Illumina/Solexa Genome Analyzer (GA) IIx.