title: ATAC-Seq of mus musculus: polyclonal Effector CD4 T cells from SLO
design: Chromatin accessibility in sorted CD4+ T cell populations was determined using the ATAC-seq method as previously described (Buenrostro et al., 2015; PMCID: PMC4374986). Briefly, 5 x 104 captured cells from each of the indicated groups (n = 2 or 3) were pelleted, washed with PBS, resuspended in cold sterile-filtered lysis buffer (10mM Tris-Cl pH 7.4, 10mM NaCl, 3mM MgCl2, 0.1% Igepal CA-630), and immediately centrifuged for 10 minutes (500 x g, 4oC). Pellets were then resuspended in the transposition reaction mix (Nextera TD buffer, Nextera TDE1 transposase, nuclease-free H2O) and incubated for 30 minutes at 37oC. After transposition, DNA was purified with the MinElute PCR Purification kit (QIAGEN) according to the manufacturers instructions. Library amplification (Nextera dual-indexed), quality control (Agilent sizing and PicoGreen quantification), and sequencing (Illumina NovaSeq SP flow cell 2x50-bp paired-end run) were carried out at the University of Minnesota Genomics Center.