NuGEN Agilent Solution

Interrogate small and degraded samples from a wide variety of sources including FFPE, LCM, fine needle aspirates, tissue biopsies, sorted cells, and more. In a single day, quickly and easily prepare targets from RNA samples as low as 500 picograms — up to 100-fold less than currently available IVT-based target preparation methods.

NuGEN has created an improved solution for labeling cDNA targets amplified using the proven, robust technology of the WT-Ovation Pico and WT-Ovation FFPE systems for interrogation on Agilent Dual-Mode Gene Expression DNA microarrays. Agilent microarray users can now access their valuable archives of well-annotated samples that were previously out of reach for inquiry.

The NuGEN Agilent Solution enables the use of WT-Ovation-generated cDNA for one-color or two-color analysis on the Agilent's Dual-Mode Gene Expression Arrays. The NuGEN WT-Ovation technology for RNA amplification is ideal for use with small and compromised RNA samples typically obtained from clinical specimens such as LCM, sorted cells, fine needle biopsies, and FFPE samples.

The workflow consists of the following steps:

  • Define Sample Type: Based on sample characteristics, choose one of NuGEN's validated whole-transcript amplification products such as the WT-Ovation FFPE System or the WT-Ovation Pico System.
  • Amplify RNA: Amplify RNA according to NuGEN protocols to generate amplified cDNA.
  • Label cDNA: Using the protocol outlined in the NuGEN Agilent Solution Application Note, label the amplified cDNA and proceed with hybridization to the Agilent Dual-Mode gene expression arrays.

The NuGEN Agilent Solution reproducibly amplifies and labels very small (down to 500 picograms) or degraded samples.

The reproducibility of the WT-Ovation Pico Amplification-generated targets on Agilent Dual-Mode Gene Expression arrays was determined by pairwise Pearson correlations among four independently amplified and labeled replicates of a 500 picogram UHR (Stratagene Universal Human Reference) total RNA sample. The average R2 of all pairwise signal comparisons was 0.99. An example of the linear array signal scatter plots for the 500 pg UHR samples is shown below.

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