title: GSM5047336: INTACT_ATAC_rep2; Mus musculus; ATAC-seq
library_construction_protocol: 50,000 INTACT or FANS nuclei were collected in 50 μL cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630) and centrifuged at 750 xg for 15 min using a cold centrifuge (4 oC). Immediately after centrifugation, the pellet was resuspended in the transposase reaction mix (25 μL 2× TD buffer, 2.5 μL transposase (Illumina FC-121–1030) and 22.5 μL nuclease-free water). The transposition reaction was carried out for 30 min at 37 °C.  Following transposition, the sample was purified using a Qiagen MinElute kit (Qiagen, 28006) following the manufacturer's instructions. Libraries were amplified using 1× NEBnext PCR master mix (NEB M0541) and 1.25 μM of custom Nextera PCR primers 1 and 2 (See Buenrostro et al. 2013). An optimization qPCR quantification was performed as described in Buenrostro et al. 2013.  After 11–12 cycles of PCR amplification, samples were further purified using Qiagen MinElute kit. Samples were further purified using AMPure beads XP (Beckman Coulter) with a ratio of x0.9 of beads to samples. The purified samples were then analyzed in bioanalyzer (Agilent) prior to sequencing