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For each primer set used, MCF-7 total DNA which had been sheared by sonication to a size range of 0.5 1.5 kb was diluted to give 20,000, 4,000, 800, 160, and 32 genomic copies per µl respectively.
DNA was sheared by sonication to a fragment size of 500 - 800bp, and adaptors ligated.
As described by Illumina, cDNA was sheared by sonication to a 200 400 bp fragment size (Covaris Inc., Woburn, MA).
The chromatin was sheared by sonication to a DNA fragment size of 200 600 bp and precipitated by centrifugation at 12 000 × g at 4 °C for 10 min.
Double-stranded DNA was fragmented by sonication to a median size of 200 bp and purified with the Agencourt RNAClean XP system (Beckman Coulter, Brea, CA) using magnetic beads.
Pelleted nuclei were resuspended in nuclei lysis buffer (50 mM Tris HCl, pH 8.0, 10 mM EDTA, and 1% SDS) at an approximate concentration of 10 cells per ml prior to shearing chromatin by sonication to a final size range of ∼100 750 bp.
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The chromatin was sheared by sonication to an average fragment size of 500 to 1000 bp.
Chromatin DNA was fragmented by sonication to an average length of 0.5 kb.
Following lysis, cellular DNA was sheared by sonication to an average size of 150 to 500 bp.
Chromatin was sheared by sonication to an average fragment size between 200 and 300 bp using a Bioruptor sonication instrument (Diagenode).
Following a gentle digestion, cells were cross-linked with 1% formaldehyde (252549, Sigma) and chromatin was sheared by sonication to an average length of 500 bp.
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