GSM7058786: CD4+CD8+_WT_HiC_rep2; Mus musculus; Hi-C
Hi-C was performed as per Rao (Rao et al., 2014), with the following adjustments: Step 2 - cells were fixed with 1.5% formaldehyde for 10 min at RT. Step 7 - the nuclei extraction buffer contained 0.4% Igepal. Step 12 - restriction digestion was performed overnight with 400U Mbo1 (NEB) in NEB buffer 2.1. Steps 28-35 were skipped. Step 54 - 2.5ul NEBNext Adapter for Illumina (cat # E7370) was used in place of Illumina indexed adapter, with ligation at 20C for 15 min, followed by addition of 3U USER enzyme and further incubation at 37C for 15min. Step 60 - samples were incubated at 95C for 10 min in a thermocycler, and beads were removed before final library amplification with NEBNext Multiplex Oligos for Illumina (cat # E7335S).