GSM5597258: ATAC-seq LSK+ XistΔ/Δ Rep2; Mus musculus; ATAC-seq
ATAC experiments were performed as previously described with minor modifications (Buenrostro et al., 2015). Briefly, 10,000 bone marrow LSK+ or LSK- cells were lysed in ice-cold lysis buffer (10mM Tris-HCl, pH 7.4, 10mM NaCl, 3mM MgCl2, 0.1% NP-40) for 5 min and then washed twice with 10mM Tris-HCl, pH 7.4. Following the last wash, 25 ml of extracted nuclei was mixed with 25 ml of 2XTD buffer (66 mM Tris-Ac pH 7.8, 132 mM KAc, 20 mM MgAc, 32% Dimethyl Formamide) containing 1 ml of Tn5 with loaded tagmentation adapters. Transposition reaction mixture was incubated using a thermocycler rotating at 500 rpm for 1 hour at 37°C. Tagmented DNA fragments were purified using MinElute PCR Cleanup Kit (Qiagen, 28206) and amplified for 15 PCR cycles using Q5 polymerase (NEB, M0491). PCR products were run on a gel, and fragments of ~200-800 bp size were isolated and libraries were sequenced on MGI MGISEQ-2000 or Illumina NovaSeq 6000 with paired-end reads. Libraries were constructed by PCR amplificaiton of tagmented DNA fragments.