GSM3780748: JLAC003F; Mus musculus; ATAC-seq
ATACseq was performed as described in(Buenrostro, et al., 2015).  Briefly, cultures of 50,000 BMDM were washed once in ice cold 1xPBS and then resuspended gently in 100ul ATACseq lysis buffer (1 mM Tris·Cl, pH 7.4, 1 mM NaCl= 500ul 1M NaCl, 0.3 mM MgCl2, and 0.01% (v/v) Triton-X 100) to release nuclei. Nuclei were then pelleted (1,000xg, 10min, 4C) and transposed in 2.5ul Tn5 (Nextera Tn5 transposase, Illumina), 12.5ul TD reaction buffer and 10.5ul water for 40min at 37C with rotation. Following transposition, DNA was purified (MinElute PCR Purification Kit, Qiagen) and stored at -80C. Samples were then thawed on ice and unique barcodes(Buenrostro, et al., 2015) were added to each sample using 5 cycles of PCR(Buenrostro, et al., 2015).  A side PCR reaction was then taken and used as input for qPCR for an additional 20 cycles to assess determine the optimal number of additional PCR cycles for each library (the cycle number that corresponds to one-third of the maximum fluorescent intensity). Each sample was then amplified by the determined number of PCR cycles and then purified (MinElute PCR Purification Kit, Qiagen).  Final libraries were then size selected for fragments between 100-1000bp using AMPure XP beds (Beckman Coulter) and quality was checked by DNA High Sensitivity bioanalyzer. Libraries were pooled (6 per pool) and sequenced across four lanes of the HiSeq2500 to generate 50bp paired end reads.
GEO Accession
GSM3780748