ATAC-seq

We used an ATAC-seq protocol adapted from.⁶³ Nuclei were extracted from 50,000 naive, effector or memory, sort-purified OT-1 cells and immediately resuspended in transposition reaction mix (Illumina Nextera DNA Sample Preparation Kit - Cat #FC121–1030) for 30 min at 37C. Transposed DNA was purified using a QIAGEN MinElute PCR Purification kit (Cat #28004), and amplified for 5 PCR cycles using PCR primer 1 (Ad1_noMX) and an indexed PCR primer. Aliquots of each amplicon were used as template in a real-time quantitative PCR for 20 cycles to determine the optimal cycle number for library amplification, with amplicons purified as previously. Library quality was determined using a Bioanalyzer (Agilent) to ensure that amplicons ranged between 50 and 200bp, and samples were subjected to paired-end sequencing on an Illumina Hiseq2500 instrument. Sequence data were mapped to UCSC mm10, then filtered for PCR duplicates and blacklisted regions, then shifted using Alignment Sieve (deepTools;⁶⁴) and lastly peaks were called with MACS2 (https://github.com/macs3-project/MACS).