GSM3901665: WT duplicate ATAC-Seq; Mus musculus; ATAC-seq
Assay for transposase-accessible chromatin (ATAC) was performed as previously described (Bossen et al., 2015; Buenrostro et al., 2013).  Briefly, 200,000 RAG2-deficient pro-B cells with WT or IGCR1-mutated (CBE-/-(1) and CBE-/-(2)) IgH alleles were collected by centrifugation and washed once with 100μl PBS.  Cell pellets were then resuspended in 50μl lysis buffer (10mM Tris-HCl, pH 7.4, 3mM MgCl2, 10mM NaCl, 0.1% NP-40 (Igepal CA-630)) and immediately centrifuged at 500g for 10 min at 4 °C.  Nuclei-containing pellets were resuspended in 50μl transposition buffer (25μl 2 × TD buffer, 22.5μl dH20, 2.5μl Illumina Tn5 transposase) and incubated at 37 °C for 30 min.  Transposed DNA was purified with DNA Clean and Concentrator columns (ZymoResearch).  Library fragments were amplified with 1× NEB Next PCR Master Mix and custom Nextera PCR primers 1–6.  The number of cycles was 11.  Libraries were purified with DNA Clean and Concentrator columns. ATAC-Seq libraries were prepared for sequencing using standard Illumina protocols. Libraries were sequenced on a HiSeq 2500 system as single reads.