FAIRE performed in human foreskin fibroblast cells

To perform FAIRE, chromatin is crosslinked with formaldehyde in vivo, sheared by sonication, and phenol-chloroform extracted. The DNA recovered in the aqueous phase is fluorescently labeled and hybridized to a DNA microarray. FAIRE performed in human cells strongly enriches DNA coincident with the location of DNaseI hypersensitive sites, transcriptional start sites, and active promoters. Keywords: Genome wide map of active chromatin Human foreskin fibroblast (ATCC CRL 2091) cells were cultured in 245 x 245 cm plates (90% confluent). Formaldehyde was added directly to the plates at room temperature to a final concentration of 1%; and incubated for 1, 2, 4, or 7 minutes. Cells were glass bead disrupted and sheared using sonication, yielding fragments of DNA 0.5 to 1 kb. Proteins and DNA fragments crosslinked to proteins were removed using a phenol/chloroform extraction.