GSM6448619: mouse, WT Treg cells, rep2; Mus musculus; ATAC-seq
For the Omni-ATAC-sequencing, samples were isolated as follows: (i) Treg cells (Thy1.1+ CD4+), T conv cells (Thy1.1- CD4+) and CD8+ T cells were prepared from tumors in Foxp3Thy1.1 mice; and (ii) Thy1.1+ CD4+ Treg cells were prepared from the tumors of either Foxp3Thy1.1 or Batf-/- Foxp3Thy1.1mice. The Omni-ATAC-seq protocol was performed as described previously with minor modifications ((PMID: 28846090). In brief, 5000 to 10000 sorted T cells (for clinical samples), 1000 to 10000 sorted T cells (for murine samples), and 50000 cells (for cell lines) were washed with PBS and then lysed. The cell lysates were resuspended in 50 μl once with TD Buffer containing 2.5 μl of Nextera enzyme (Illumina). The transposition reaction was performed at 37°C for 30 min. The products were then purified with a MinElute polymerase chain reaction (PCR) purification kit (Qiagen, Hilden, Germany), and the fragments for the Omni-ATAC-seq library were amplified for five cycles of PCR. The additional number of PCR cycles was determined for each sample after quantification by real-time PCR. The PCR-amplified products were purified with a MinElute PCR purification kit again.