title: GSM5582102: TiKD cell line +tet at NMP - expt 2; Homo sapiens; ATAC-seq
library_construction_protocol: Day 3 NMPs (50,000 cells) obtained from TBXT shRNA sOPTiKD hESC in the presence and absence of Tetracycline (three biological replicates) were harvested After centrifugation, the pellet was carefully resuspended 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 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. Library amplification was followed by SPRI (Beckman Coulter) size selection to exclude fragments larger than 1,200 bp. DNA concentration was measured with a Qubit fluorometer (Life Technologies). Library amplification was performed using custom Nextera primers.