GSM6293849: Tgtumor_602170.2R; Mus musculus; ATAC-seq
gDNA of 94 untreated tumors and 51 resistant tumors (from a total of 53 mice) was isolated with a DNeasy Blood and Tissue Kit (Qiagen #69504) and fragmented by sonication (Covaris sonicator) to a size of 250 bp. DNA fragments were end repaired, A-tailed, purified and then ligated to the splikerette adaptor (annealed 5'-gttcccatggtactactcatataatacgactcactataggtgacagcgagcgct-3' with 5'-gcgctcgctgtcacctatagtgagtcgtattataatttttttttcaaaaaaa-3'). Transposon containing DNA fragments were enriched by PCR using a primer specific for the 5'-transposon arm (5'-gacggattcgcgctatttagaaagagag-3') and the common splinkerette primer (5'-gttcccatggtactactcata-3'). An additional PCR was performed for barcoding the individual samples by using a primer specific for the 5' arm of the transposon (5'- aatgatacggcgaccaccgagatctacacatgcgtcaattttacgcagactatc-3') and another primer specific tor the splinkerette side (5'-caagcagaagacggcatacgagatcggtXXXXXXXXtaatacgactcactatagg-3'; Xs standing for the eight-base barcode). Purified libraries were assembled in four pools and sequenced on Illumina HiSeq 2500 (Paired-End, 2 × 100 bp, rapid run, 200 cycles).