ChIP-sequencing datasets were generated with an antibody recognizing the alpha isoforms of p63 (H129, Santa Cruz), an antibody that detects all forms of the large subunit of RNA polymerase II (8WG16, Santa Cruz), and a H3K27ac antibody recognizing the acetylation of the lysine 27 residue of Histone H3 (H3K27ac, Diagenode). RNAPII, p63 and H3K27ac ChIP experiments were performed as previously described (Denissov et al. 2007; Kouwenhoven et al. 2010; Smeenk et al. 2008), with a minor change of using magnetic beads (Novex by Life Technologies, Cat. No. 10008D and 10009D). DNA samples were prepared for sequencing by end repair of 6 ng total DNA (p63 ChIP-seq, and RNAPII ChIP-seq samples) and 10 ng total DNA (H3K27ac ChIP-seq samples) as measured by Qubit (Invitrogen). Adaptors were ligated to the DNA fragments, followed by a pre-PCR of 4 cycles, size selection (∼300 bp) and subsequently 11 cycles of PCR amplification.
GEO Accession
GSM1446918