Illumina HiSeq 4000 paired end sequencing; In situ promoter capture Hi-C data of differentiated SGBS human preadipocytes (days 0, 2, 8 and 16 of differentiation to adipocytes) and iPSC-derived hypothalamic neurons (days 12, 16 and 27 of differentiation)
In situ promoter capture Hi-C was performed as previously described [Rao et al. 2014 (doi: 10.1016/j.cell.2014.11.021.)]. 5 million SGBS cells per replicate were harvested, counted and crosslinked using 37% formaldehyde for 10 minutes at room temperature while rocking. This reaction was quenched with 0.175M Glycine and cells were frozen in liquid nitrogen and stored at -80C until ready for the next stage of HiC processing.  See Rao et al. 2014 (doi: 10.1016/j.cell.2014.11.021.) Five million cells were crosslinked with 1% formaldehyde for 10 min at room temperature. Nuclei were permeabilized. DNA was digested with 100 units of MboI, and the ends of restriction fragments were labeled using biotinylated nucleotides and ligated in a small volume. After reversal of crosslinks, ligated DNA was purified and sheared to a length of âˆ¼400 bp, at which point ligation junctions were pulled down with streptavidin beads and prepped for Illumina sequencing. For each Hi-C library, we used 5 million cells and the MboI restriction enzyme. Pre-capture Hi-C libraries were amplified with 6 PCR cycles and post-capture Hi-C libraries were amplified with 8 PCR cycles. The capture probes were designed to target the ends of MboI fragments at least 1kb apart surrounding all RefSeq genes, with four baits per gene.