Suretag labeling kit

The PathoChip screening procedure has been previously described [10 ,11 ,[16] (link), [17] (link), [18] (link)]. DNA and RNA were simultaneously extracted from cancer patients and control FFPE tissue samples using the AllPrep DNA/RNA FFPE Kit (Qiagen, Hilden, Germany), and absorbance was measured at 260/280 nm to assess quality. Patient sample RNA (100 ng) and DNA (50 ng) were used for whole genome and transcriptome amplification (WTA) using the TransPlex Complete Whole Transcriptome Amplification Kit (Sigma-Aldrich, St. Louis, MO). Human DNA and RNA were extracted from the human B cell line BJAB (obtained from ATCC) to serve as a reference for cross-hybridization of probes to the amplified patient genomes and to determine background normalization. Purified WTA product (PCR purification kit, Qiagen, Germantown, MD, USA) quality was determined using A260/280 measurements, and 1 μg was labeled with either Cy3 (amplified patient sample) or Cy5 (amplified human reference) (SureTag labeling kit, Agilent Technologies, Santa Clara, CA). All labeled specimens were purified, and a Cy3-labeled and Cy5-labeled reference were hybridized together on each PathoChIP array in constant rotation at 65 °C for 40 h, as previously described [10 ,11 ]. Array slides were washed and then scanned for visualization using an Agilent SureScan G4900DA array scanner.