CD28 region-capture HiC of resting and anti-CD3/CD28-stimuated Jurkat cells

To meticulously explore how local chromatin architecture influences T cell activation, we conducted high-resolution regional capture Hi-C by designing tiling capture probes that span the CD28, CTLA4, and ICOS genes along with their distal regulatory sequences (chr2:204300000-205000000, GRCh37) in both resting and stimulated Jurkat cells. Overall design: We performed CD28 region-capture HiC on both resting and anti-CD3/CD28-stimulated Jurkat cells. Anti-CD28 and anti-CD3 antibodies were utilized to activate T cells as previously described (Simeonov et al. Nature, 2017). Briefly, the culture plate was coated with 10 µg/ml of anti-CD28 (TONBO Biosciences, 40-0289) for 12 hours at 4°C prior to cell inoculation. Jurkat or CD4+ T cells were then seeded with 10 µg/ml of anti-CD3 (40-0038). The cells were harvested 24 hours later for subsequent experimental analysis.