Fore- and hindlimb buds, hearts and branchial arches of approximately 150 Hand2-3xFLAG embryos and 150 wild-type control embryos at E10.5 were collected in ice-cold PBS. Single nuclei suspensions were cross-linked for 5min with 1% formaldehyde and processed as described (Visel et al., 2009). The ChIP procedure was performed using established protocols with minor modifications (Kim et al. 2007, Lopez-Rios et al. 2012) Library was constructed using the DNA library Prep Kit (New England Biolabs). Following end repair and adaptor ligation, DNA fragments were size selected (200-250bp) by agarose gel electrophoresis and PCR amplified (18 cycles) using Illumina primers. After purification, samples were loaded on an Illumina flow cell for solid-phase amplification. SR50 sequencing of libraries was carried out on a HiSeq 2000 system (Illumina)