Overview of the targeted chromosome capture (T2C) procedure. Isolated cross-linked chromatin is digested with a restriction enzyme (dark blue lines) and ligated under diluted conditions to favor ligations between restriction fragments that are spatially in proximity. After de-cross-linking and a secondary digestion (orange lines), the overhangs are repaired followed by adapter ligation. Different address sequences can be used in the adapters for different samples to allow multiplexing of different samples (hybridization of different samples to the same set of oligonucleotides). The resulting library is hybridized to a set of unique oligonucleotides on an array or oligonucleotides in solution that are captured on beads. The unique oligonucleotides (green, red, black, and blue lines) are located as close as possible to the first restriction site. The hybridized DNA, which contains the library of all interactions from the selected area of the genome, is eluted and is pair-end sequenced on an Illumina HiSeq2000 followed by bioinformatic analysis and visualization of the chromatin interactions (that is, sequences in close proximity). Each point in the chromatin interaction map, represents an interaction (in restriction fragment resolution, each block represents the size of the restriction fragment) between two fragments in the genome.