title: GSM9107635: Ly108+CD39- SM cells, PBS group, tumor, Rep1; Mus musculus; ATAC-seq
library_construction_protocol: To obtain SM CD4 T cells in tumor, tumors were mechanically minced and digested using with 1 mg/mL collagenase I (Sigma, c0130) and mashed through filters. Then, lymphocytes were enriched using Percoll (GE Healthcare, 17-0891-09) density gradient. To obtain SM CD4 T cells in spleen, cells were harvested by mashing the spleens through cell strainer (BD Falcon). Next, lymphocytes were stained with flow cytometry antibodies specicifc for CD4, Va2, CD45.1, CD45.2, Ly108 and CD39, SM cells were FACS-sorted. ATAC-seq library was prepared using Hyperactive ATAC-seq Library Prep Kit for Illumina (Vazyme, TD711). Briefly, sorted cells were lysed on ice and fragment DNA in waterbath at 37℃ for 30 min. ATAC DNA Extract Beads were used for DNA extraction of fragmented products and extracted DNA fragments were amplified in a PCR instrument. Finally, ATAC DNA Clean Beads were used for two-step fragment size selection of amplified products and quality and quantity assessments are conducted using methods such as bioanalyzer or Qubit. Finally, the libraries were sequenced using paired-end sequencing, with 150 nucleotides on each end, conducted in a single lane of a NovaSeq 6000 for each sample.