title: GSM8596627: HDAC1fl/fl Cd4 Cre Th2 cells, after 48h in culture, sample 2; Mus musculus; ATAC-seq
library_construction_protocol: Cells were harvested, counted and 50000 cells centrifuged at 500 g for 5 min at 4°C. Cell pellets were resuspended in a tagmentation-mix containing Tagment DNA buffer, Tagment DNA Enzyme (Illumina), Digitonin (Promega) and Proteinase K (Roche). The lysate was incubated for 30min at 37°C with shaking (300rpm). The reaction was stopped by incubating the samples on ice. DNA was isolated using the MinElute PCR Purification Kit (Qiagen) according to the manufacturer's instructions and eluted into 12 μl of elution buffer. 1 µl eluate was used in a quantitative PCR (qPCR) reaction to estimate the optimal number of cycles for library amplification. The remaining 10 µl of each tagmented sample was then amplified corresponding to the Cqvalue (i.e., the cycle number at which fluorescence has increased above background levels) in the presence of custom Nextera primers. PCR amplification was followed by SPRI (Beckman Coulter, Brea, CA, USA) size selection to exclude fragments larger than 1,200 bp. The DNA concentration of each library was assessed with a Qubit 2.0 Fluorometric Quantitation system (Life Technologies, Carlsbad, CA, USA), before pooling in equimolar amounts.