The oligonucleotides (2 pmol each) were labeled at their 3′-end with [P]α-dATP (>2500 Ci/mmol; Perkin-Elmer, Boston, MA) using terminal deoxynucleotidyltransferase (Roche Diagnostics GmbH, Mannheim, Germany), and then purified by centrifugation using QIAquick Nucleotide Removal Kit (Qiagen GmbH, Hilden, Germany).
The cDNA samples were purified using QIAQuick Nucleotide Removal Kit (Qiagen), and fluorescently labeled using LabelIT uArray Cy5 Kit (Mirus Bio, Madison WI) as described by the manufacturer.
For end-repair and phosphorylation, sheared DNA was purified using QIAquick Nucleotide Removal Kit (Qiagen, Hilden, Germany).
Unincorporated nucleotides and random primers were removed using QIAquick Nucleotide Removal columns (QIAGEN) according to the manufacturer's instructions.
For end-repair and phosphorylation, sheared DNA was purified using QIAquick Nucleotide Removal Kit (Quiagen, Crawley, UK).
Primers and free nucleotides from the PCR products were then removed by using QIAquick PCR purification kit (250) (Qiagen, GmbH, Hilden, Germany).
Labeled DNA was purified from unincorporated CyDye fluorescent label by using Qiaquick PCR Cleanup kit (Qiagen, Valencia, CA) and dried by vacuum.
Products were purified by using QIAquick Gel Extraction kit (Qiagen) and amplified by PCR.
Eluted DNA fragments were further purified by using Qiaquick PCR purification kits (Qiagen).
The 143-bp amplification product was detected by electrophoresis and purified by using QIAquick PCR Purification Kit (QIAGEN).
