GSM5068560: L-Pha low_ATAC-seq [CK-2L_S26]; Mus musculus; ATAC-seq
Tumors were harvested, processed and FACS sorted for TCRB+CD3+ and L-Pha low or high TILs, followed by ATAC-seq Cells were washed once in ice-cold PBS and lysed in ATAC lysis buffer (0.1% Tween-20, 0.1% NP-40, 3mM MgCl2, 10mM NaCl, 10mM Tris HCl pH 7.4). Tagmentation was performed with Tn5 transposase and 2x TD Buffer (Nextera DNA Library Prep Kit, Ilumina) for 30 minutes at 37°C. Tagmented DNA was purified using a MinElute colum (Qiagen, 28004) and amplified for 12 cycles using 2x KAPA HiFi HotStart ReadyMix (Kapa Biosystems, KK2602). The amplified libraries were purified using MinElute columns (Qiagen) and sequenced on an Ilumina NextSeq 500 with 75 bp single-end reads. Library QC and quantification was performed using D1000 high-sensitivity screen tape with 4200 TapeStation Instrument (Agilent Technologies) and size selected for between 200 bp and 700 bp using a Pippin Prep system (Sage Science). Nextera DNA Library Prep Kit, Ilumina