ChIP and FAIRE

Effector T cells were crosslinked with 0.6% formaldehyde for 10 min at RT. Following sonication, immune-precipitation was performed with anti-H3K4me3, H3K27me3 or HK3K27Ac ChIP-grade antibodies and Protein A magnetic beads (Millipore). FAIRE was performed on samples fixed and sonicated as per ChIP, with accessible chromatin extracted twice with phenol:chloroform:isoamyl (25:24:1) (Sigma). FAIRE enrichment was normalized against a total input for which reverse cross-linking had been performed. ChIP and FAIRE enrichment was measured using quantitative real-time PCR, with data normalized against a total input and no-antibody control. Primers used in these assays were reported previously.³