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DNA was digested using standard digestion protocols for restriction enzymes.
Chromatin (equivalent to 1 μg DNA) was digested using 0.0020 U MNase in the digestion buffer.
Chromatin (equivalent to 1 μg DNA) was digested using 0.0014 U MNase in the Atlantis MN Digestion buffer.
Briefly, the genomic DNA was digested by restriction enzyme MspI.
Genomic DNA was digested using an RNase-free DNase Set (Qiagen) prior to cDNA synthesis.
Purified DNA was digested with nuclease P1, phosphodiesterase I, and alkaline phosphatase.
For each individual, 125 ng DNA was digested at 37 °C for 2 h with 15 U PstI-HF (NEB).
100 nmol/L Cy5-labeled star DNA was digested by 500 nmol/L DraIII.
The residual genomic DNA was digested using the RNase-Free DNase set (Qiagen Valencia, CA, USA).
Cy5-labeled canonical or star DNA was digested by DraIII as described in Supplementary EXPERIMENTAL.
Genomic DNA was digested with HindIII, resolved by electrophoresis and hybridized with DIG labeled bar probe.
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