Drosophila melanogaster - Ovary stage 12 follicle cell nuclei - OR_s12 - Wild type - MNase-Seq
Follicle cell nuclei were resuspended in 100 μl digestion buffer (50 mM Tris-HCl, 5 mM CaCl2, pH 7.9) and digested with 50 U micrococcal nuclease (New England Biolabs, cat# M0247S) at 37  ̊C for 20 minutes, quenched with 50 mM EGTA, followed by 2 μg RNaseA (Roche) treatment at 37  ̊C for 1 hr. to remove RNA and 40 μg proteinase K treatment at 55  ̊C for 1 hr. NaCl was then added to a final concentration of 250 mM to solubilize undigested DNA (i.e. nucleosome protected). The undigested DNA was purified by phenol / chloroform / isoamyl alchohol extraction, ethanol precipitated, and resuspended in 1x TE buffer. DNA fragments in the 100 – 200 bp size range were purified on a 1.6% agarose gel and recovered with Qiaquick gel purification kit (Qiagen). A bar-coded, paired-end library was constructed using the standard Illumina protocol and 51 bp paired-end sequences obtained at the Tufts University Core Facility Genomics (TUCF genomics, http://tucf-genomics.tufts.edu)