GSM2232761: input DNA; Zea mays; MNase-Seq
Nuclei were prepared as described in the ChIP protocol except that EDTA was omitted from buffers.  Nuclei pellet was resuspended in 500 μl Digestion Buffer (50 mM Tris-HCl pH8.0, 5 mM CaCl2, 0.1 mM PMSF, 1 µg/ml cOmplete Protease Inhibitor Cocktail (Roche, Penzberg, Germany)). Samples were sonicated for 5 second and treated with 0.02 U /µl of micrococcal nuclease (NEB, Ipswich, MA, USA) for 10 min at room temperature.  The reaction was stopped with 10 mM EDTA and DNA was prepared as in the ChIP protocol.  The purified DNA was separated in a 2% agarose gel and fragments ~150 bp in size were recovered.  Approximately 100 ng of mononucleosome DNA was used for Illumina library construction.  As a control, randomly fragmented chromatin was prepared by sonication to produce 200 - 500 bp fragments.