GSM6774640: 17q1qMYCN_D9_2 [ATAC-Seq]; Homo sapiens; ATAC-seq
20,000 to 50,000 cells were lysed in the transposase reaction mix (12.5 μl 2xTD buffer, 2 μl TDE1 [Illumina], 10.25 μl nuclease-free water, and 0.25 μl 1% digitonin [Promega]) for 30 min at 37 °C. Following DNA purification with the MinElute kit (Qiagen) eluting in 12 μl, 1 μl of eluted DNA was used in a quantitative PCR (qPCR) reaction to estimate the optimum number of amplification cycles. The remaining 11 μl of each library were amplified for the number of cycles corresponding to the Cq value (i.e., the cycle number at which fluorescence has increased above background levels) from the qPCR using custom Nextera primers. Library amplification was followed by SPRI (Beckman Coulter) size selection to exclude fragments larger than 1,200 bp. Libraries concentration was measured with a Qubit fluorometer (Life Technologies), and libraries were quality checked using a 2100 Bioanalyzer (Agilent Technologies). Libraries were sequenced by the Biomedical Sequencing Facility at CeMM using the Illumina HiSeq 4000 platform in 1x50bp single-end mode.