GSM4981489: 412: Capture Hi-C, Primary FLS, unstimulated; Homo sapiens; OTHER
Cultured human FLS from RA patients were treated with 10 ng/ml TNF for 24 h or were left untreated. Cells (1e7 to 3e7 per condition), were scratched in 10ml DMEM, spun down, suspended in 35ml DMEM and fixed (2% formaldehyde in DMEM, 10min, RT, with mixing on a rocker). The reaction was quenched with cold 0.125M glycine. Cells were incubated at RT for 5 min, followed by 15 min incubation on ice and centrifugation (1500 rpm, 10 min, 4 ⁰C). Pellets were suspended and washed in cold PBS (1500 rpm, 10 min, 4 ⁰C). Washed pellets were snap frozen and stored at -80 ⁰C. The regions targeted by the capture HiC (CHiC) were generated based on the LD regions of the lead disease associated SNPs for RA, Juvenile Idiopathic Arthritis (JIA), Psoriatic arthritis (PsA) and Psoriasis (Ps).  This resulted in a total of 242 distinct risk variants.120bp capture baits were designed for all HindIII digestion fragments overlapping these regions as previously described in Martin et al.