GSM1874069: #16_120; Mus musculus; ChIP-Seq
ChIP-seq was performed as described (Deshpande et al 2014 Cancer Cell).  1-2×106 MEF cells were crosslinked using 1% formaldehyde, washed in 1 mL of wash buffer (20 mM Tris pH8.0, 167mM NaCl, 5mM EDTA, 1% SDS) and lysed in lysis buffer (20 mM Tris pH8.0, 167mM NaCl, 5mM EDTA, 0.66% SDS, 1% Triton X-100).  Chromatin was sheared to 200-400 bp using Covaris E220 sonicator and used for chromatin immunoprecipitation (ChIP) with Dnmt3a-specific antibodies ab13888 mouse mAbs and ab2850 rabbit pAbs  (Abcam) and Protein-A (Life Technologies) magnetic beads.  After washing, the immune complexes were eluted and DNA fragments recovered after de-crosslinking at 65°C for 4 hours and used for TruSeq libraries generated using NEBNext kit (New England BioLabs).  Libraries were sequenced using HiSeq2500 (Illumina) to generate approximately 4×107 single end (SE)50 reads per sample.
GEO Accession
GSM1874069