GSM7815566: iFoxL2, mES+24hrs, ATAC-seq, rep2; Mus musculus; ATAC-seq
ATAC-seq experiments followed the Omni-ATAC-seq protocol [PMID: 28846090].  For each experiment, 50,000 cells were harvested. Cells were dissociated in 50 μl ATAC-Resuspension Buffer (10 mM Tris (pH 7.4), 10 mM NaCl, 3 mM MgCl2) with 0.1% NP-40, 0.1% Tween-20, and 0.01% Digitonin, incubated on ice for 3 mins, and then suspended in 1 mL ATAC-Resuspension Buffer with 0.1% Tween-20 and centrifuged for 10 min at 4°C and 500g. The pellet was resuspended in transposition mixture (25 μl 2x TD buffer, 2.5 μl transposome (Tn5 + oligo DNA), 16.5 μl PBS, 0.5 μl 1% digitonin, 0.5 μl 10% Tween-20, 5 μl H2O), followed by incubation at 37°C for 30mins. The reaction was cleaned up with AMPure XP beads. Transposed fragments were PCR amplified for a number of PCR cycles determined from one-third of the maximum fluorescence measured by quantitative PCR reaction with 1 × SYBR Green (Invitrogen), custom-designed primers [PMID: 30194434], and 2 × NEB MasterMix (New England Labs, M0541). The library was cleaned up with AMPure XP beads and the fragment length distribution of the library was determined using a Bioanalyzer High Sensitivity chip. The libraries were sequenced on an Illumina NextSeq 2000.