Formaldehyde-Assisted Isolation of Regulatory Elements (FAIRE)

FAIRE samples were prepared as outlined in Simon et al. (23). Briefly, cells were cross-linked with 1% formaldehyde and lysed. The cell lysates were sonicated to yield an average DNA fragment distribution of ~200–500 bp. A 50 μl aliquot of fragmented DNA (total input control DNA) was reverse cross-linked at 65°C followed by phenol-chloroform extraction. The remaining sonicated DNA (FAIRE DNA) was directly isolated by phenol-chloroform extraction and purified using the Zymo-SpinTM I kit (Zymo Research, Irvine, CA).