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PCR products for each sample were combined and purified using a PCR cleanup kit (Invitrogen corp., Carlsbad, CA).
Samples were treated with RNaseA, and purified using a PCR cleanup kit (Qiagen).
The products were digested with NheI, purified using a PCR cleanup kit, and ligated together.
Following agarose gel analysis of the PCR product, the relevant band was eluted from the gel by using a PCR Cleanup kit (Qiagen).
PCR products were analyzed by non-denaturing gel electrophoresis and ethidium bromide staining and purified using a PCR cleanup kit (Promega) per the manufacturer's instruction.
This resulted in >80% excess full-length DNA in the chromatin samples used for MNase-seq, which was removed prior to Solexa library preparation using a PCR cleanup kit (Clontech, Mountain View, CA).
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PCR products were purified using a Qiagen PCR Cleanup kit.
PCR products were purified using a GenElute PCR cleanup kit (Sigma-Aldrich, St Louis, MO, USA).
The DNA templates for the PCR products were purified using a QIAquick PCR Cleanup Kit (QIAGEN, CA, USA) as per the manufacturer's instructions and were subjected to DNA sequencing.
DNA was purified using a Wizard PCR cleanup system (Promega, Madison, WI).
The uncoupled dye was removed using a Qiagen PCR cleanup kit according to the the manufacturer's protocol.
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