ATAC-seq of dNK Cell Subsets

ATAC-seq of dNK cell subsets was performed as previously described^{45 (link)}, with minor modifications. Briefly, dNK1, dNK2, and dNK3 subsets were sorted using the SH800S sorter (Sony). Samples were obtained from a distinct cohort from those were used for the scRNA-seq. Approximately 50k cells were used per library. Samples were lysed in cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl₂, and 0.1% NP-40 (Roche) for 3 min on ice to prepare the nuclei. Immediately after cell lysis, nuclei were centrifuged at 500× g for 5 min and the supernatant was discarded. Nuclei extracts were then incubated with the generated Tn5 transposomes and 5× Tris-DMF tagmentation buffer (pH 8.0, 50 mM Tris-HCl, 25 mM MgCl₂, 50% DMF) at 37 °C for 30 min. After DNA purification with a MinElute Kit (Qiagen), PCR was performed to amplify the library for 12–15 cycles according to a quantitative PCR reaction for optimum cycles. The PCR thermocycling program was as follows: 98 °C for 30 s; then 98 °C for 10 s, 63 °C for 30 s, and 72 °C for 1 min for the appropriate number of cycles. Following PCR, sample libraries were purified and sequenced using the Illumina HiSeq X Ten platform with the 150-bp paired-end configuration.