GSM5552533: ATAC_seq_IpmkKD_rep1; Mus musculus; ATAC-seq
ATAC-seq : ATAC-seq libraries were prepared as previously described (Buenrostro et al., 2013; Buenrostro et al., 2015), with minor modification. Briefly, 50,000 mESCs were harvested, washed with cold PBS, lysed with cold lysis buffer, and immediately centrifuged. The nuclear pellets were resuspended in 25 μl of 2X tagmentation reaction buffer (10 mM Tris, pH 8.0, 5 mM MgCl2, 10% dimethylformamide), 23 μl of nuclease-free water, and 2 μl of Tn5 transposase (in-house generated), and incubated at 37°C for 30 min. The samples were then immediately purified using a QIAquick PCR purification kit (28106, Qiagen). The libraries were pre-enriched for five cycles using the KAPA HiFi Hotstart ready mix (KK2601, Kapa Biosystems), and the threshold cycle (Ct) was monitored using qPCR to determine the additional enrichment cycles, which were then applied. The final libraries were purified again with a QIAquick PCR purification kit, and sequenced using an Illumina HiSeq 2500 platform. The libraries were generated from two sets of biological replicates.