title: Genome-wide analysis of the interactions of Abcg1, Tgm2 and Vegfa loci (3C-seq) in primary mouse bone marrow-derived macrophages
design: 3C-Seq libraries were prepared as described (Stadhouders et al., 2013), using HindIII (Fermentas). After the first digestion and ligation the 3C DNA pool was purified with phenol/chloroform/isoamyl alcohol (25:24:1) (Sigma). Second restriction digestion was performed by using DpnII (NEB) for 16 hours per manufacturer’s instruction. Second ligation was performed at 16C for 6 hours with 200U of T4 DNA ligase. DNA was then purified again with phenol/chloroform/isoamyl alcohol (25:24:1) followed by QIAquick gel purification column (Qiagen) purification. Bait specific inverse PCRs were performed using primers coupled to Universal Illumina adapters and Barcode sequences. Reactions were purified by QIAquick gel purification columns. Amplicon libraries were quantified and qualified by Agilent using DNA 7500 chip cartridge. Amplicon libraries were sequenced on Illumina HiSeq 2000 sequencer