title: GSM7527912: Focused-HiC_Th1_D3_F_WT1; Mus musculus; Hi-C
library_construction_protocol: cell isolation protocol: Cells from spleen were obtained by mechanical disruption. Peritoneal cells were obtained by washing of the peritoneal cavity with cold PBS. Isolated cells were further sorted as based on their surface markers. 3-5 million cells were aliquoted from pooled naïve T cells or Th1 cells differentiated in vitro for each genotype, then pelleted and fixed with formaldehyde (1% v/v) for 5 minutes with mixing, before the reaction was quenched with glycine (0.2M). Cells were washed, pelleted, and flash frozen on dry ice for storage in -80°C before the Hi-C protocol was initiated. Global Hi-C was performed according to previously published protocols (Rao, 2014). After global Hi-C was completed, 500 ng of Hi-C libraries were used as the pond for the hybrid selection reaction. A 1,550,000 bp region surrounding the Ifng locus was hybridized using a collection of 2367 RNA probes. Local in situ Hi-C was performed according to previously published protocols. DNA libraries were constructed according to to previously published protocols. DNA libraries were sequenced at 100 million reads with 50bp paired-end reads using NovaSeq (Illumina).